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Xie M, Ye L, Chen K, Xu Q, Yang C, Chen X, Chan EWC, Li F, Chen S. Clinical use of tigecycline may contribute to the widespread dissemination of carbapenem-resistant hypervirulent Klebsiella pneumoniae strains. Emerg Microbes Infect 2024; 13:2306957. [PMID: 38240375 PMCID: PMC10829843 DOI: 10.1080/22221751.2024.2306957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 01/14/2024] [Indexed: 02/01/2024]
Abstract
The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) poses grave threats to human health. These strains increased dramatically in clinical settings in China in the past few years but not in other parts of the world. Four isogenic K. pneumoniae strains, including classical K. pneumoniae, carbapenem-resistant K. pneumoniae (CRKP), hypervirulent K. pneumoniae (hvKP) and CR-hvKP, were created and subjected to phenotypic characterization, competition assays, mouse sepsis model and rat colonization tests to investigate the mechanisms underlying the widespread nature of CR-hvKP in China. Acquisition of virulence plasmid led to reduced fitness and abolishment of colonization in the gastrointestinal tract, which may explain why hvKP is not clinically prevalent after its emergence for a long time. However, tigecycline treatment facilitated the colonization of hvKP and CR-hvKP and reduced the population of Lactobacillus spp. in animal gut microbiome. Feeding with Lactobacillus spp. could significantly reduce the colonization of hvKP and CR-hvKP in the animal gastrointestinal tract. Our data implied that the clinical use of tigecycline to treat carbapenem-resistant K. pneumoniae infections facilitated the high spread of CR-hvKP in clinical settings in China and demonstrated that Lactobacillus spp. was a potential candidate for anticolonization strategy against CR-hvKP.
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Affiliation(s)
- Miaomiao Xie
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kaichao Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Qi Xu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Chen Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Xiangnan Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Fuyong Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Food Science and Nutrition, Faculty of Science, The Hong Kong Polytechnic University, Kowloon, Hong Kong
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Sheng Y, Wang J, Gao Y, Peng Y, Li X, Huang W, Zhou H, Liu R, Zhang W. Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries. Comput Struct Biotechnol J 2024; 23:87-95. [PMID: 38116074 PMCID: PMC10730331 DOI: 10.1016/j.csbj.2023.11.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/21/2023] Open
Abstract
Despite extensive research on the gut microbiome of healthy individuals from a single country, there are still a limited number of population-level comparative studies. Moreover, the sequencing approach used in most related studies involves 16 S ribosomal RNA (rRNA) sequencing with a limited resolution, which cannot provide detailed functional profiles. In the present study, we applied a combined analysis approach to analyze whole metagenomic shotgun sequencing data from 2035 healthy adult samples from six countries across four continents. Analysis of core species revealed that 13 species were present in more than 90 % of all investigated individuals, the majority of which produced short-chain fatty acids (SCFA)-producing bacteria. Our analysis revealed consistently significant differences in gut microbial species and pathways between Western and non-Western countries, such as Escherichia coli and the relation of MetaCyc pathways to the TCA cycle. Specific changes in microbial species and pathways are potentially related to lifestyle and diet. Furthermore, we identified several noteworthy microbial species and pathways that exhibit distinct characteristics specific to China. Interestingly, we observed that China (CHN) was more similar to the United States (USA) and United Kingdom (GBR) in terms of the taxonomic and functional composition of the gut microbiome than India (IND) and Madagascar (MDG), which were more similar to the China (CHN) diet. The current study identified consistent microbial features associated with population and geography, which will inspire further clinical translations that consider paying attention to differences in microbiota backgrounds and confounding factors.
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Affiliation(s)
- Yanghao Sheng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jue Wang
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yongchao Gao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Yilei Peng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Xiong Li
- Center for Clinical Precision Pharmacy, School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
| | - Weihua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Honghao Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
- Institute of Clinical Pharmacology, Central South University, Changsha, China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Center for Clinical Precision Pharmacy, School of Clinical Pharmacy, Guangdong Pharmaceutical University, Guangzhou, China
- The First Affifiliated Hospital of Shantou University Medical College, Shantou, China
- Key Laboratory of Clinical Precision Pharmacy of Guangdong Higher Education, Institutes, The First Affiliated Hospital, Guangdong Pharmaceutical University, Guangzhou, China
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Fritz P, Fritz R, Bóday P, Bóday Á, Bató E, Kesserű P, Oláh C. Gut microbiome composition: link between sports performance and protein absorption? J Int Soc Sports Nutr 2024; 21:2297992. [PMID: 38151716 PMCID: PMC10763846 DOI: 10.1080/15502783.2023.2297992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 12/16/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Sufficient protein intake is essential for adequate physical condition and athletic performance. However, numerous factors can influence the absorption of consumed protein, including timing, type of protein intake, and gut microbiota. In the present study, elite male water polo players consumed a plant-based, vegan protein supplement with (n = 10) or without (n = 10) pre- and probiotics daily during the 31-day study period. METHODS We determined the anthropometric characteristics and body composition, dietary habits, gut microbiota composition, and blood parameters of the players at the beginning and at the end of the study. Body composition parameters were analyzed using the InBody 970 bioimpedance analyzer. Gut microbiome composition was determined from stool samples by metagenome sequencing. Paired and unpaired t-tests were used to determine differences between body composition and blood parameters within the groups and between the two groups at the two different sampling times. The Wilcoxon test was used to determine the change in bacterial composition during the study. Correlations between changes in body composition, blood parameters, and taxonomic groups were analyzed using a linear correlation calculation. RESULTS Skeletal muscle mass (p < 0.001), body cell mass (p = 0.002), arm circumference (p = 0.003), and protein mass (p < 0.001) increased, while body fat mass (p = 0.004) decreased significantly in the intervention group which consumed pre- and probiotics in addition to protein supplement. Activated acetate (reductive TCA cycle I) and propionate (pyruvate fermentation to propanoate I) pathways correlated positively with increased skeletal muscle mass (p < 0.01 and p < 0.05), and the relative abundance of butyrate-producing species showed a significant positive correlation with changes in body fat mass in the intervention group (p < 0.05). These correlations were not observed in the control group without the intake of pre- and probiotics. CONCLUSIONS The composition of the gut microbiota may influence protein absorption and therefore body composition and consequently physical condition and sports performance.
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Affiliation(s)
- Péter Fritz
- Károli Gáspár University of the Reformed Church in Hungary, Faculty of Economics, Health Sciences and Social Studies, Budapest, Hungary
| | - Réka Fritz
- University of Szeged, Doctoral School of Clinical Medicine, Szeged, Hungary
| | - Pál Bóday
- Multi-domain Statistics Department, Hungarian Central Statistical Office, Budapest, Hungary
| | - Ádám Bóday
- Cordi R&D nonprofit Inc, Budapest, Hungary
| | | | - Péter Kesserű
- Eötvös Loránd Research Network, Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Szeged, Hungary
- University of Pannonia Nagykanizsa - University Center for Circular Economy, Soós Ernő Research and Development Center, Nagykanizsa, Hungary
| | - Csilla Oláh
- University of Duisburg-Essen, Department of Urology, Essen, Germany
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du Preez LL, van der Walt E, Valverde A, Rothmann C, Neser FWC, Cason ED. A metagenomic survey of the fecal microbiome of the African savanna elephant (Loxodonta africana). Anim Genet 2024; 55:621-643. [PMID: 38923598 DOI: 10.1111/age.13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
The African savanna elephant (Loxodonta africana) is the largest terrestrial animal on Earth and is found primarily in Southern and Eastern Africa. It is a hindgut, colonic fermenter and subsists on a diet of raw plant materials found in its grazing area. In this study the bacterial, archaeal and fungal populations of seven African savanna elephant fecal metagenomes were first characterized using amplicon sequencing. On the genus level it was observed that the p-1088-a5 gut group in the bacteriome, Methanocorpusulum and Methanobrevibacter in the archaeome and Alternaria, Aurobasidium, Didymella and Preussia in the mycome, predominated. Subsequently, metagenomic shotgun sequencing was employed to identify possible functional pathways and carbohydrate-active enzymes (CAZymes). Carbohydrate catabolic pathways represented the main degradation pathways, and the fecal metagenome was enriched in the glycohydroside (GH) class of CAZymes. Additionally, the top GH families identified - GH43, GH2, GH13 and GH3 - are known to be associated with cellulytic, hemicellulytic and pectolytic activities. Finally, the CAZymes families identified in the African savanna elephant were compared with those found in the Asian elephant and it was demonstrated that there is a unique repository of CAZymes that could be leveraged in the biotechnological context such as the degradation of lignocellulose for the production of second-generation biofuels and energy.
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Affiliation(s)
- Louis Lategan du Preez
- Department of Animal Science, University of the Free State, Bloemfontein, Free State, South Africa
| | - Elzette van der Walt
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Free State, South Africa
| | - Angel Valverde
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Free State, South Africa
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas, Salamanca, Spain
| | - Christopher Rothmann
- Department of Animal Science, University of the Free State, Bloemfontein, Free State, South Africa
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Free State, South Africa
| | | | - Errol Duncan Cason
- Department of Animal Science, University of the Free State, Bloemfontein, Free State, South Africa
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Zachariasen T, Russel J, Petersen C, Vestergaard GA, Shah S, Atienza Lopez P, Passali M, Turvey SE, Sørensen SJ, Lund O, Stokholm J, Brejnrod A, Thorsen J. MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies. Nat Commun 2024; 15:5734. [PMID: 38977664 DOI: 10.1038/s41467-024-49958-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 06/21/2024] [Indexed: 07/10/2024] Open
Abstract
Metagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurate abundance estimation with functional profiling of assembled genomes. To define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes. Here, we present MAGinator, a freely available tool, tailored for profiling of shotgun metagenomics datasets. MAGinator provides de novo identification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes and genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences.
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Affiliation(s)
- Trine Zachariasen
- Department of Health and Technology, Section of Bioinformatics, Technical University of Denmark, Lyngby, Denmark.
| | - Jakob Russel
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Charisse Petersen
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada
| | - Gisle A Vestergaard
- Department of Health and Technology, Section of Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Shiraz Shah
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Pablo Atienza Lopez
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Moschoula Passali
- Danish Multiple Sclerosis Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet-Glostrup, Glostrup, Denmark
| | - Stuart E Turvey
- Department of Pediatrics, BC Children's Hospital, University of British Columbia, 950 West 28th Avenue, Vancouver, BC, Canada
| | - Søren J Sørensen
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ole Lund
- Department of Health and Technology, Section of Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Jakob Stokholm
- Department of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Asker Brejnrod
- Department of Health and Technology, Section of Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
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Shridhar SV, Beghini F, Alexander M, Singh A, Juárez RM, Brito IL, Christakis NA. Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages. Cell Rep 2024; 43:114442. [PMID: 38968070 DOI: 10.1016/j.celrep.2024.114442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/27/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024] Open
Abstract
Despite a growing interest in the gut microbiome of non-industrialized countries, data linking deeply sequenced microbiomes from such settings to diverse host phenotypes and situational factors remain uncommon. Using metagenomic data from a community-based cohort of 1,871 people from 19 isolated villages in the Mesoamerican highlands of western Honduras, we report associations between bacterial species and human phenotypes and factors. Among them, socioeconomic factors account for 51.44% of the total associations. Meta-analysis of species-level profiles across several datasets identified several species associated with body mass index, consistent with previous findings. Furthermore, the inclusion of strain-phylogenetic information modifies the overall relationship between the gut microbiome and the phenotypes, especially for some factors like household wealth (e.g., wealthier individuals harbor different strains of Eubacterium rectale). Our analysis suggests a role that gut microbiome surveillance can play in understanding broad features of individual and public health.
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Affiliation(s)
- Shivkumar Vishnempet Shridhar
- Yale Institute for Network Science, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Francesco Beghini
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Marcus Alexander
- Yale Institute for Network Science, Yale University, New Haven, CT, USA
| | - Adarsh Singh
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | | | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| | - Nicholas A Christakis
- Yale Institute for Network Science, Yale University, New Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA; Department of Statistics and Data Science, Yale University, New Haven, CT, USA; Department of Medicine, Yale School of Medicine, New Haven, CT, USA.
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Sardar P, Almeida A, Pedicord VA. Integrating functional metagenomics to decipher microbiome-immune interactions. Immunol Cell Biol 2024. [PMID: 38952337 DOI: 10.1111/imcb.12798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/04/2024] [Accepted: 06/13/2024] [Indexed: 07/03/2024]
Abstract
Microbial metabolites can be viewed as the cytokines of the microbiome, transmitting information about the microbial and metabolic environment of the gut to orchestrate and modulate local and systemic immune responses. Still, many immunology studies focus solely on the taxonomy and community structure of the gut microbiota rather than its functions. Early sequencing-based microbiota profiling approaches relied on PCR amplification of small regions of bacterial and fungal genomes to facilitate identification of the microbes present. However, recent microbiome analysis methods, particularly shotgun metagenomic sequencing, now enable culture-independent profiling of microbiome functions and metabolites in addition to taxonomic characterization. In this review, we showcase recent advances in functional metagenomics methods and applications and discuss the current limitations and potential avenues for future development. Importantly, we highlight a few examples of key areas of opportunity in immunology research where integrating functional metagenomic analyses of the microbiome can substantially enhance a mechanistic understanding of microbiome-immune interactions and their contributions to health and disease states.
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Affiliation(s)
- Puspendu Sardar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Alexandre Almeida
- Department of Veterinary Medicine, University of Cambridge School of Biological Sciences, Cambridge, UK
| | - Virginia A Pedicord
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge, UK
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Babikow E, Ghaltakhchyan N, Livingston T, Qu Y, Liu C, Hoxie A, Sulkowski T, Bocklage C, Marsh A, Phillips ST, Mitchell KB, Ribeiro ADA, Jackson TH, Roach J, Wu D, Divaris K, Jacox LA. Longitudinal Microbiome Changes in Supragingival Biofilm Transcriptomes Induced by Orthodontics. JDR Clin Trans Res 2024; 9:265-276. [PMID: 37876206 PMCID: PMC11184915 DOI: 10.1177/23800844231199393] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
INTRODUCTION Common oral diseases are known to be associated with dysbiotic shifts in the supragingival microbiome, yet most oral microbiome associations with clinical end points emanate from cross-sectional studies. Orthodontic treatment is an elective procedure that can be exploited to prospectively examine clinically relevant longitudinal changes in the composition and function of the supragingival microbiome. METHODS A longitudinal cohort study was conducted among 24 adolescent orthodontic patients who underwent saliva and plaque sampling and clinical examinations at time points: before fixed appliance bonding and at 1, 6, and 12 wk thereafter. Clinical indices included bleeding on probing (BOP), mean gingival index (GI), probing depths (PDs), and plaque index (PI). To study the biologically (i.e., transcriptionally) active microbial communities, RNA was extracted from plaque and saliva for RNA sequencing and microbiome bioinformatics analysis. Longitudinal changes in microbiome beta diversity were examined using PERMANOVA tests, and the relative abundance of microbial taxa was measured using Kruskal-Wallis tests, Wilcoxon rank-sum tests, and negative binomial and zero-inflated mixed models. RESULTS Clinical measures of oral health deteriorated over time-the proportion of sites with GI and PI ≥1 increased by over 70% between prebonding and 12 wk postbonding while the proportion of sites with PD ≥4 mm increased 2.5-fold. Streptococcus sanguinis, a health-associated species that antagonizes cariogenic pathogens, showed a lasting decrease in relative abundance during orthodontic treatment. Contrarily, caries- and periodontal disease-associated taxa, including Selenomonas sputigena, Leptotrichia wadei, and Lachnoanaerobaculum saburreum, increased in abundance after bonding. Relative abundances of Stomatobaculum longum and Mogibacterium diversum in prebonding saliva predicted elevated BOP 12 wk postbonding, whereas Neisseria subflava was associated with lower BOP. CONCLUSIONS This study offers insights into longitudinal community and species-specific changes in the supragingival microbiome transcriptome during fixed orthodontic treatment, advancing our understanding of microbial dysbioses and identifying targets of future health-promoting clinical investigations. KNOWLEDGE TRANSFER STATEMENT Bonding braces was associated with subsequent changes in the oral microbiome characterized by increases in disease-associated species, decreases in health-associated species, and worsened clinical measures of oral health.
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Affiliation(s)
- E. Babikow
- Orthodontics Group, Division of Craniofacial and Surgical Care, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - N. Ghaltakhchyan
- Orthodontics Group, Division of Craniofacial and Surgical Care, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - T. Livingston
- Orthodontics Group, Division of Craniofacial and Surgical Care, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
- Selden Orthodontics, Huntersville, NC, USA
| | - Y. Qu
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - C. Liu
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - A. Hoxie
- Orthodontics Group, Division of Craniofacial and Surgical Care, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - T. Sulkowski
- Orthodontics Group, Division of Craniofacial and Surgical Care, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
- University of Buffalo, School of Dental Medicine, Buffalo, NY, USA
| | - C. Bocklage
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - A. Marsh
- Microbiome Core Facility, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - S. T. Phillips
- GoHealth Clinical Research Unit, Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - K. B. Mitchell
- Orthodontics Group, Division of Craniofacial and Surgical Care, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - A. De A. Ribeiro
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - T. H. Jackson
- Orthodontics Group, Division of Craniofacial and Surgical Care, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
- Align Technology, Morrisville, NC, USA
| | - J. Roach
- Microbiome Core Facility, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - D. Wu
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - K. Divaris
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
| | - L. A. Jacox
- Orthodontics Group, Division of Craniofacial and Surgical Care, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina, Chapel Hill, NC, USA
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Khattak F, Galgano S, Pedersen NR, Hui Y, Matthiesen R, Houdijk J. Supplementation of lactobacillus-fermented rapeseed meal in broiler diet reduces Campylobacter jejuni cecal colonization and limits the l-tryptophan and l-histidine biosynthesis pathways. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:5474-5485. [PMID: 38391155 DOI: 10.1002/jsfa.13378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/04/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND Campylobacter jejuni (C. jejuni), a widely distributed global foodborne pathogen, primarily linked with contaminated chicken meat, poses a significant health risk. Reducing the abundance of this pathogen in poultry meat is challenging but essential. This study assessed the impact of Lactobacillus-fermented rapeseed meal (LFRM) on broilers exposed to C. jejuni-contaminated litter, evaluating growth performance, Campylobacter levels, and metagenomic profile. RESULTS By day 35, the litter contamination successfully colonized broilers with Campylobacter spp., particularly C. jejuni. In the grower phase, LFRM improved (P < 0.05) body weight and daily weight gain, resulting in a 9.2% better feed conversion ratio during the pre-challenge period (the period before artificial infection; days 13-20). The LFRM also reduced the C. jejuni concentration in the ceca (P < 0.05), without altering alpha and beta diversity. However, metagenomic data analysis revealed LFRM targeted a reduction in the abundance of C. jejuni biosynthetic pathways of l-tryptophan and l-histidine and gene families associated with transcription and virulence factors while also possibly leading to selected stress-induced resistance mechanisms. CONCLUSION The study demonstrated that LFRM inclusion improved growth and decreased cecal Campylobacter spp. concentration and the relative abundance of pivotal C. jejuni genes. Performance benefits likely resulted from LFRM metabolites. At the molecular level, LFRM may have reduced C. jejuni colonization, likely by decreasing the abundance of energy transduction and l-histidine and l-tryptophan biosynthesis genes otherwise required for bacterial survival and increased virulence. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Farina Khattak
- Monogastric Science Research Centre, SRUC, Edinburgh, UK
| | | | | | - Yan Hui
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark
| | | | - Jos Houdijk
- Monogastric Science Research Centre, SRUC, Edinburgh, UK
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10
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Yamaguchi M, Uchihashi T, Kawabata S. Hybrid sequence-based analysis reveals the distribution of bacterial species and genes in the oral microbiome at a high resolution. Biochem Biophys Rep 2024; 38:101717. [PMID: 38708423 PMCID: PMC11066573 DOI: 10.1016/j.bbrep.2024.101717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/07/2024] Open
Abstract
Bacteria in the oral microbiome are poorly identified owing to the lack of established culture methods for them. Thus, this study aimed to use culture-free analysis techniques, including bacterial single-cell genome sequencing, to identify bacterial species and investigate gene distribution in saliva. Saliva samples from the same individual were classified as inactivated or viable and then analyzed using 16S rRNA sequencing, metagenomic shotgun sequencing, and bacterial single-cell sequencing. The results of 16S rRNA sequencing revealed similar microbiota structures in both samples, with Streptococcus being the predominant genus. Metagenomic shotgun sequencing showed that approximately 80 % of the DNA in the samples was of non-bacterial origin, whereas single-cell sequencing showed an average contamination rate of 10.4 % per genome. Single-cell sequencing also yielded genome sequences for 43 out of 48 wells for the inactivated samples and 45 out of 48 wells for the viable samples. With respect to resistance genes, four out of 88 isolates carried cfxA, which encodes a β-lactamase, and four isolates carried erythromycin resistance genes. Tetracycline resistance genes were found in nine bacteria. Metagenomic shotgun sequencing provided complete sequences of cfxA, ermF, and ermX, whereas other resistance genes, such as tetQ and tetM, were detected as fragments. In addition, virulence factors from Streptococcus pneumoniae were the most common, with 13 genes detected. Our average nucleotide identity analysis also suggested five single-cell-isolated bacteria as potential novel species. These data would contribute to expanding the oral microbiome data resource.
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Affiliation(s)
- Masaya Yamaguchi
- Bioinformatics Research Unit, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
- Bioinformatics Center, Research Institute for Microbial Diseases, Osaka University, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Japan
| | - Toshihiro Uchihashi
- Department of Oral and Maxillofacial Surgery, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
| | - Shigetada Kawabata
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Osaka, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Japan
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11
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Ordinola-Zapata R, Costalonga M, Dietz M, Lima BP, Staley C. The root canal microbiome diversity and function. A whole-metagenome shotgun analysis. Int Endod J 2024; 57:872-884. [PMID: 36861850 DOI: 10.1111/iej.13911] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 03/03/2023]
Abstract
AIM To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing. METHODOLOGY Twenty-two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole-metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes. RESULTS Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol-activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase. CONCLUSIONS Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.
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Affiliation(s)
- Ronald Ordinola-Zapata
- Division of Endodontics, Department of Restorative Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Massimo Costalonga
- Division of Basic Sciences, Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Matthew Dietz
- Division of Basic & Translational Research, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Bruno P Lima
- Division of Basic Sciences, Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, Minnesota, USA
| | - Christopher Staley
- Division of Basic & Translational Research, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, USA
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12
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Kim H, Nzabarushimana E, Huttenhower C, Chan AT, Nguyen LH. Altered Microbial Transcription in Long-term Proton Pump Inhibitor Use: Findings From a United States Cohort Study. Gastroenterology 2024; 167:405-408.e3. [PMID: 38521094 PMCID: PMC11193639 DOI: 10.1053/j.gastro.2024.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 03/25/2024]
Affiliation(s)
- Hanseul Kim
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Etienne Nzabarushimana
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Broad Institute of MIT and Harvard University, Cambridge, Massachusetts; The Harvard Chan Microbiome in Public Health Center, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts; Department of Immunology and Infectious Diseases, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Long H Nguyen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
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13
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Maccaro JJ, Figueroa LL, McFrederick QS. From pollen to putrid: Comparative metagenomics reveals how microbiomes support dietary specialization in vulture bees. Mol Ecol 2024; 33:e17421. [PMID: 38828760 DOI: 10.1111/mec.17421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 05/12/2024] [Accepted: 05/20/2024] [Indexed: 06/05/2024]
Abstract
For most animals, the microbiome is key for nutrition and pathogen defence, and is often shaped by diet. Corbiculate bees, including honey bees, bumble bees, and stingless bees, share a core microbiome that has been shaped, at least in part, by the challenges associated with pollen digestion. However, three species of stingless bees deviate from the general rule of bees obtaining their protein exclusively from pollen (obligate pollinivores) and instead consume carrion as their sole protein source (obligate necrophages) or consume both pollen and carrion (facultative necrophages). These three life histories can provide missing insights into microbiome evolution associated with extreme dietary transitions. Here, we investigate, via shotgun metagenomics, the functionality of the microbiome across three bee diet types: obligate pollinivory, obligate necrophagy, and facultative necrophagy. We find distinct differences in microbiome composition and gene functional profiles between the diet types. Obligate necrophages and pollinivores have more specialized microbes, whereas facultative necrophages have a diversity of environmental microbes associated with several dietary niches. Our study suggests that necrophagous bee microbiomes may have evolved to overcome cellular stress and microbial competition associated with carrion. We hypothesize that the microbiome evolved social phenotypes, such as biofilms, that protect the bees from opportunistic pathogens present on carcasses, allowing them to overcome novel nutritional challenges. Whether specific microbes enabled diet shifts or diet shifts occurred first and microbial evolution followed requires further research to disentangle. Nonetheless, we find that necrophagous microbiomes, vertebrate and invertebrate alike, have functional commonalities regardless of their taxonomy.
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Affiliation(s)
- Jessica J Maccaro
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Laura L Figueroa
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Quinn S McFrederick
- Department of Entomology, University of California Riverside, Riverside, California, USA
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14
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Wang S, Liu Y, Tam WH, Ching JYL, Xu W, Yan S, Qin B, Lin L, Peng Y, Zhu J, Cheung CP, Ip KL, Wong YM, Cheong PK, Yeung YL, Kan WHB, Leung TF, Leung TY, Chang EB, Rubin DT, Claud EC, Wu WKK, Tun HM, Chan FKL, Ng SC, Zhang L. Maternal gestational diabetes mellitus associates with altered gut microbiome composition and head circumference abnormalities in male offspring. Cell Host Microbe 2024:S1931-3128(24)00223-3. [PMID: 38955186 DOI: 10.1016/j.chom.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 05/02/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024]
Abstract
The impact of gestational diabetes mellitus (GDM) on maternal or infant microbiome trajectory remains poorly understood. Utilizing large-scale longitudinal fecal samples from 264 mother-baby dyads, we present the gut microbiome trajectory of the mothers throughout pregnancy and infants during the first year of life. GDM mothers had a distinct microbiome diversity and composition during the gestation period. GDM leaves fingerprints on the infant's gut microbiome, which are confounded by delivery mode. Further, Clostridium species positively correlate with a larger head circumference at month 12 in male offspring but not females. The gut microbiome of GDM mothers with male fetuses displays depleted gut-brain modules, including acetate synthesis I and degradation and glutamate synthesis II. The gut microbiome of female infants of GDM mothers has higher histamine degradation and dopamine degradation. Together, our integrative analysis indicates that GDM affects maternal and infant gut composition, which is associated with sexually dimorphic infant head growth.
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Affiliation(s)
- Shilan Wang
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yingzhi Liu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Wing Hung Tam
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jessica Y L Ching
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wenye Xu
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shuai Yan
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Biyan Qin
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Ling Lin
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Ye Peng
- Microbiota I-Center (MagIC), Hong Kong SAR, China; JC School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jie Zhu
- Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Chun Pan Cheung
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ka Long Ip
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuen Man Wong
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pui Kuan Cheong
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuk Ling Yeung
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wing Him Betty Kan
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ting Fan Leung
- Department of Paediatrics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Eugene B Chang
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL 60637, USA
| | - David T Rubin
- Department of Medicine, Section of Gastroenterology, Hepatology, and Nutrition, University of Chicago, Chicago, IL 60637, USA
| | - Erika C Claud
- Departments of Pediatrics and Medicine, Pritzker School of Medicine/Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hein M Tun
- Microbiota I-Center (MagIC), Hong Kong SAR, China; JC School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Digestive Disease Institute of Digestive Disease, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Lin Zhang
- Microbiota I-Center (MagIC), Hong Kong SAR, China; Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China.
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15
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Pinto Y, Bhatt AS. Sequencing-based analysis of microbiomes. Nat Rev Genet 2024:10.1038/s41576-024-00746-6. [PMID: 38918544 DOI: 10.1038/s41576-024-00746-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2024] [Indexed: 06/27/2024]
Abstract
Microbiomes occupy a range of niches and, in addition to having diverse compositions, they have varied functional roles that have an impact on agriculture, environmental sciences, and human health and disease. The study of microbiomes has been facilitated by recent technological and analytical advances, such as cheaper and higher-throughput DNA and RNA sequencing, improved long-read sequencing and innovative computational analysis methods. These advances are providing a deeper understanding of microbiomes at the genomic, transcriptional and translational level, generating insights into their function and composition at resolutions beyond the species level.
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Affiliation(s)
- Yishay Pinto
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Divisions of Hematology and Blood & Marrow Transplantation, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine, Divisions of Hematology and Blood & Marrow Transplantation, Stanford University, Stanford, CA, USA.
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16
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Mei Z, Wang F, Bhosle A, Dong D, Mehta R, Ghazi A, Zhang Y, Liu Y, Rinott E, Ma S, Rimm EB, Daviglus M, Willett WC, Knight R, Hu FB, Qi Q, Chan AT, Burk RD, Stampfer MJ, Shai I, Kaplan RC, Huttenhower C, Wang DD. Strain-specific gut microbial signatures in type 2 diabetes identified in a cross-cohort analysis of 8,117 metagenomes. Nat Med 2024:10.1038/s41591-024-03067-7. [PMID: 38918632 DOI: 10.1038/s41591-024-03067-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 05/14/2024] [Indexed: 06/27/2024]
Abstract
The association of gut microbial features with type 2 diabetes (T2D) has been inconsistent due in part to the complexity of this disease and variation in study design. Even in cases in which individual microbial species have been associated with T2D, mechanisms have been unable to be attributed to these associations based on specific microbial strains. We conducted a comprehensive study of the T2D microbiome, analyzing 8,117 shotgun metagenomes from 10 cohorts of individuals with T2D, prediabetes, and normoglycemic status in the United States, Europe, Israel and China. Dysbiosis in 19 phylogenetically diverse species was associated with T2D (false discovery rate < 0.10), for example, enriched Clostridium bolteae and depleted Butyrivibrio crossotus. These microorganisms also contributed to community-level functional changes potentially underlying T2D pathogenesis, for example, perturbations in glucose metabolism. Our study identifies within-species phylogenetic diversity for strains of 27 species that explain inter-individual differences in T2D risk, such as Eubacterium rectale. In some cases, these were explained by strain-specific gene carriage, including loci involved in various mechanisms of horizontal gene transfer and novel biological processes underlying metabolic risk, for example, quorum sensing. In summary, our study provides robust cross-cohort microbial signatures in a strain-resolved manner and offers new mechanistic insights into T2D.
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Affiliation(s)
- Zhendong Mei
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Fenglei Wang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Amrisha Bhosle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Danyue Dong
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Raaj Mehta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Andrew Ghazi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yancong Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yuxi Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ehud Rinott
- Department of Medicine, Hebrew University and Hadassah Medical Center, Jerusalem, Israel
| | - Siyuan Ma
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric B Rimm
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martha Daviglus
- Institute for Minority Health Research, University of Illinois Chicago, Chicago, IL, USA
| | - Walter C Willett
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rob Knight
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Frank B Hu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qibin Qi
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andrew T Chan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert D Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Meir J Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Iris Shai
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Faculty of Health Sciences, The Health and Nutrition Innovative International Research Center, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Dong D Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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17
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Yang Y, Olah P, Radai Z, Maia G, Salava A, Salo V, Barker J, Lauerma A, Andersson B, Homey B, Fyhrquist N, Alenius H. Exploratory multi-omics analysis reveals host-microbe interactions associated with disease severity in psoriatic skin. EBioMedicine 2024; 105:105222. [PMID: 38924840 DOI: 10.1016/j.ebiom.2024.105222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/02/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Psoriasis (Pso) is a chronic inflammatory skin disease that poses both physical and psychological challenges. Dysbiosis of the skin microbiome has been implicated in Pso, yet a comprehensive multi-omics analysis of host-microbe interactions is still lacking. To bridge this gap, we conducted an exploratory study by adopting the integrated approach that combines whole metagenomic shotgun sequencing with skin transcriptomics. METHODS This was a cross-sectional study, adult patients with plaque-type Psoriasis (Pso) and healthy volunteers were included. Skin microbiota samples and biopsies were collected from both lesional and non-lesional skin areas on the lower back. Weighted Gene Correlation Network Analysis (WGCNA) was employed for co-expression network analysis, and cell deconvolution was conducted to estimate cell fractions. Taxonomic and functional features of the microbiome were identified using whole metagenomic shotgun sequencing. Association between host genes and microbes was analyzed using Spearman correlation. FINDINGS Host anti-viral responses and interferon-related networks were identified and correlated with the severity of psoriasis. The skin microbiome showed a greater prevalence of Corynebacterium simulans in the PASI severe-moderate groups, which correlated with interferon-induced host genes. Two distinct psoriatic clusters with varying disease severities were identified. Variations in the expression of cell apoptosis-associated antimicrobial peptides (AMPs) and microbial aerobic respiration I pathway may partly account for these differences in disease severity. INTERPRETATION Our multi-omics analysis revealed for the first time anti-viral responses and the presence of C. simulans associated with psoriasis severity. It also identified two psoriatic subtypes with distinct AMP and metabolic pathway expression. Our study provides new insights into understanding the host-microbe interaction in psoriasis and lays the groundwork for developing subtype-specific strategies for managing this chronic skin disease. FUNDING The research has received funding from the FP7 (MAARS-Grant 261366) and the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 821511 (BIOMAP). The JU receives support from the European Union's Horizon 2020 research and innovation programme and EFPIA. This publication reflects only the author's view and the JU is not responsible for any use that may be made of the information it contains. GAM was supported by a scholarship provided by CAPES-PRINT, financed by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES (Brazilian Government Agency). The authors thank all patients who participated in our study.
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Affiliation(s)
- Ying Yang
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Peter Olah
- Department of Dermatology, Medical Faculty and University Hospital Duesseldorf, Heinrich-Heine University Duesseldorf, Germany; Department of Dermatology, Venereology and Oncodermatology, Medical Faculty, University of Pécs, Hungary
| | - Zoltan Radai
- Department of Dermatology, Medical Faculty and University Hospital Duesseldorf, Heinrich-Heine University Duesseldorf, Germany; One Health Institute, Faculty of Health Sciences, University of Debrecen, Hungary
| | - Guilherme Maia
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Salava
- Department of Dermatology, Allergology and Venereology, University of Helsinki and Helsinki University Hospital, Inflammation Centre, Helsinki, Finland
| | - Ville Salo
- Department of Dermatology, Allergology and Venereology, University of Helsinki and Helsinki University Hospital, Inflammation Centre, Helsinki, Finland
| | - Jonathan Barker
- St John's Institute of Dermatology, Kings College London, London, UK
| | - Antti Lauerma
- Department of Dermatology, Allergology and Venereology, University of Helsinki and Helsinki University Hospital, Inflammation Centre, Helsinki, Finland
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Bernhard Homey
- Department of Dermatology, Medical Faculty and University Hospital Duesseldorf, Heinrich-Heine University Duesseldorf, Germany
| | - Nanna Fyhrquist
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Harri Alenius
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Human Microbiome Research Program (HUMI), Medical Faculty, University of Helsinki, Finland.
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18
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Espinoza JL, Phillips A, Prentice MB, Tan GS, Kamath PL, Lloyd KG, Dupont CL. Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing. Nucleic Acids Res 2024:gkae528. [PMID: 38909293 DOI: 10.1093/nar/gkae528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/21/2024] [Accepted: 06/10/2024] [Indexed: 06/24/2024] Open
Abstract
The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.
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Affiliation(s)
- Josh L Espinoza
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Allan Phillips
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Melanie B Prentice
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Gene S Tan
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Pauline L Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
- Maine Center for Genetics in the Environment, University of Maine, Orono, ME 04469, USA
| | - Karen G Lloyd
- Microbiology Department, University of Tennessee, Knoxville, TN 37917, USA
| | - Chris L Dupont
- Department of Environment and Sustainability, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Department of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
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19
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Yadav A, Devi P, Kumari P, Maurya R, Shamim U, Pandey R. Protocol to decode the role of transcriptionally active microbes in SARS-CoV-2-positive patients using an RNA-seq-based approach. STAR Protoc 2024; 5:103071. [PMID: 38768029 PMCID: PMC11111823 DOI: 10.1016/j.xpro.2024.103071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/13/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
The elucidation of the role of microorganisms in human infections has been hindered by difficulties using conventional culture-based techniques. Here, we present a protocol for the investigation of transcriptionally active microbes (TAMs) using an RNA sequencing (RNA-seq)-based approach. We describe the steps for RNA isolation, viral genome sequencing, RNA-seq library preparation, and metatranscriptomic and transcriptomic analysis. This protocol permits a comprehensive evaluation of TAMs' contributions to the differential severity of infectious diseases, with a particular focus on diseases such as COVID-19. For complete details on the use and execution of this protocol, please refer to Devi et al.1.
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Affiliation(s)
- Aanchal Yadav
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Priti Devi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Pallawi Kumari
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India; Indraprastha Institute of Information Technology (IIIT), New Delhi 110020, India
| | - Ranjeet Maurya
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Uzma Shamim
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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20
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Chen W, Li Y, Wang W, Gao S, Hu J, Xiang B, Wu D, Jiao N, Xu T, Zhi M, Zhu L, Zhu R. Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives. Cell Rep Med 2024:101624. [PMID: 38942021 DOI: 10.1016/j.xcrm.2024.101624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 04/09/2024] [Accepted: 06/07/2024] [Indexed: 06/30/2024]
Abstract
Prior studies indicate no correlation between the gut microbes of healthy first-degree relatives (HFDRs) of patients with Crohn's disease (CD) and the development of CD. Here, we utilize HFDRs as controls to examine the microbiota and metabolome in individuals with active (CD-A) and quiescent (CD-R) CD, thereby minimizing the influence of genetic and environmental factors. When compared to non-relative controls, the use of HFDR controls identifies fewer differential taxa. Faecalibacterium, Dorea, and Fusicatenibacter are decreased in CD-R, independent of inflammation, and correlated with fecal short-chain fatty acids (SCFAs). Validation with a large multi-center cohort confirms decreased Faecalibacterium and other SCFA-producing genera in CD-R. Classification models based on these genera distinguish CD from healthy individuals and demonstrate superior diagnostic power than models constructed with markers identified using unrelated controls. Furthermore, these markers exhibited limited discriminatory capabilities for other diseases. Finally, our results are validated across multiple cohorts, underscoring their robustness and potential for diagnostic and therapeutic applications.
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Affiliation(s)
- Wanning Chen
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China
| | - Yichen Li
- Medical College, Jiaying University, Meizhou 514031, P. R. China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, P.R. China; Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China
| | - Wenxia Wang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China
| | - Sheng Gao
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China
| | - Jun Hu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China
| | - Bingjie Xiang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China
| | - Dingfeng Wu
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310058, Zhejiang, P.R. China
| | - Na Jiao
- Department of Nephrology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310058, Zhejiang, P.R. China
| | - Tao Xu
- Medical College, Jiaying University, Meizhou 514031, P. R. China; Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, P.R. China
| | - Min Zhi
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China; Department of Gastroenterology, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China.
| | - Lixin Zhu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, P.R. China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou 510655, P.R. China.
| | - Ruixin Zhu
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, P.R. China.
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21
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Derosa L, Iebba V, Silva CAC, Piccinno G, Wu G, Lordello L, Routy B, Zhao N, Thelemaque C, Birebent R, Marmorino F, Fidelle M, Messaoudene M, Thomas AM, Zalcman G, Friard S, Mazieres J, Audigier-Valette C, Sibilot DM, Goldwasser F, Scherpereel A, Pegliasco H, Ghiringhelli F, Bouchard N, Sow C, Darik I, Zoppi S, Ly P, Reni A, Daillère R, Deutsch E, Lee KA, Bolte LA, Björk JR, Weersma RK, Barlesi F, Padilha L, Finzel A, Isaksen ML, Escudier B, Albiges L, Planchard D, André F, Cremolini C, Martinez S, Besse B, Zhao L, Segata N, Wojcik J, Kroemer G, Zitvogel L. Custom scoring based on ecological topology of gut microbiota associated with cancer immunotherapy outcome. Cell 2024; 187:3373-3389.e16. [PMID: 38906102 DOI: 10.1016/j.cell.2024.05.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/16/2024] [Accepted: 05/14/2024] [Indexed: 06/23/2024]
Abstract
The gut microbiota influences the clinical responses of cancer patients to immunecheckpoint inhibitors (ICIs). However, there is no consensus definition of detrimental dysbiosis. Based on metagenomics (MG) sequencing of 245 non-small cell lung cancer (NSCLC) patient feces, we constructed species-level co-abundance networks that were clustered into species-interacting groups (SIGs) correlating with overall survival. Thirty-seven and forty-five MG species (MGSs) were associated with resistance (SIG1) and response (SIG2) to ICIs, respectively. When combined with the quantification of Akkermansia species, this procedure allowed a person-based calculation of a topological score (TOPOSCORE) that was validated in an additional 254 NSCLC patients and in 216 genitourinary cancer patients. Finally, this TOPOSCORE was translated into a 21-bacterial probe set-based qPCR scoring that was validated in a prospective cohort of NSCLC patients as well as in colorectal and melanoma patients. This approach could represent a dynamic diagnosis tool for intestinal dysbiosis to guide personalized microbiota-centered interventions.
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Affiliation(s)
- Lisa Derosa
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France.
| | - Valerio Iebba
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Carolina Alves Costa Silva
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | | | - Guojun Wu
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA
| | - Leonardo Lordello
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Bertrand Routy
- Centre Hospitalier de l'Université de Montréal (CHUM), Hematology-Oncology Division, Department of Medicine, Montréal, QC, Canada; Centre de Recherche du CHUM (CRCHUM), Montréal, QC, Canada
| | - Naisi Zhao
- Department of Public Health and Community Medicine, School of Medicine, Tufts University, Boston, MA 02111, USA
| | - Cassandra Thelemaque
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Roxanne Birebent
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Federica Marmorino
- Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marine Fidelle
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | | | | | - Gerard Zalcman
- Université Paris Cité, Thoracic Oncology Department-CIC1425/CLIP2 Paris-Nord, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Sylvie Friard
- Pneumology Department, Foch Hospital, Suresnes, France
| | - Julien Mazieres
- Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | | | - Denis Moro- Sibilot
- Department of Thoracic Oncology, Centre Hospitalier Universitaire, Grenoble, France
| | - François Goldwasser
- INSERM U1016-CNRS UMR8104, Paris Cité University, Paris, France; Department of Medical Oncology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France; Immunomodulatory Therapies Multidisciplinary Study Group (CERTIM), Paris, France
| | - Arnaud Scherpereel
- Department of Pulmonary and Thoracic Oncology, University of Lille, University Hospital (CHU), Lille, France
| | | | - François Ghiringhelli
- Cancer Biology Transfer Platform, Centre Georges-François Leclerc, Dijon, France; Centre de Recherche INSERM LNC-UMR1231, Dijon, France; Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | | | - Cissé Sow
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Ines Darik
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Silvia Zoppi
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Pierre Ly
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Anna Reni
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Section of Oncology, Department of Medicine, University of Verona School of Medicine and Verona University Hospital Trust, Verona, Italy
| | | | - Eric Deutsch
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Radiation Oncology, Gustave Roussy, Villejuif, France; INSERM U1030, Radiothérapie Moléculaire et Innovation Thérapeutique, Villejuif, France
| | - Karla A Lee
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Laura A Bolte
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Johannes R Björk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Fabrice Barlesi
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Lucas Padilha
- Bio-Me AS, Oslo Science Park, Gaustadalléen 21, Oslo, Norway
| | - Ana Finzel
- Bio-Me AS, Oslo Science Park, Gaustadalléen 21, Oslo, Norway
| | | | - Bernard Escudier
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Laurence Albiges
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - David Planchard
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Fabrice André
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Chiara Cremolini
- Unit of Medical Oncology 2, University Hospital of Pisa, Pisa, Italy; Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Stéphanie Martinez
- Service des Maladies Respiratoires, Centre Hospitalier d'Aix-en-Provence, Aix-en-Provence, France
| | - Benjamin Besse
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Liping Zhao
- Center for Nutrition, Microbiome and Health, New Jersey Institute for Food, Nutrition and Health, Rutgers University, New Brunswick, NJ, USA; Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Rutgers-Jiaotong Joint Laboratory for Microbiome and Human Health, New Brunswick, NJ, USA; State Key Laboratory of Microbial Metabolism, Ministry of Education Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, European Institute of Oncology IRCCS, Milan, Italy
| | | | - Guido Kroemer
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Centre de Recherche des Cordeliers, Equipe labellisée-Ligue contre le cancer, Université de Paris Cité, Sorbonne Université, Institut Universitaire de France, Inserm U1138, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France; Institut du Cancer Paris CARPEM, Department of Biology, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, ClinicObiome, Villejuif, France; Université Paris-Saclay, Ile-de-France, France; Institut National de la Santé et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (BIOTHERIS) 1428, Villejuif, France.
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22
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Enav H, Paz I, Ley RE. Strain tracking in complex microbiomes using synteny analysis reveals per-species modes of evolution. Nat Biotechnol 2024:10.1038/s41587-024-02276-2. [PMID: 38898177 DOI: 10.1038/s41587-024-02276-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/10/2024] [Indexed: 06/21/2024]
Abstract
Microbial species diversify into strains through single-nucleotide mutations and structural changes, such as recombination, insertions and deletions. Most strain-comparison methods quantify differences in single-nucleotide polymorphisms (SNPs) and are insensitive to structural changes. However, recombination is an important driver of phenotypic diversification in many species, including human pathogens. We introduce SynTracker, a tool that compares microbial strains using genome synteny-the order of sequence blocks in homologous genomic regions-in pairs of metagenomic assemblies or genomes. Genome synteny is a rich source of genomic information untapped by current strain-comparison tools. SynTracker has low sensitivity to SNPs, has no database requirement and is robust to sequencing errors. It outperforms existing tools when tracking strains in metagenomic data and is particularly suited for phages, plasmids and other low-data contexts. Applied to single-species datasets and human gut metagenomes, SynTracker, combined with an SNP-based tool, detects strains enriched in either point mutations or structural changes, providing insights into microbial evolution in situ.
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Affiliation(s)
- Hagay Enav
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Inbal Paz
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany.
- Cluster of Excellence EXC 2124: Controlling Microbes to Fight Infections (CMFI), University of Tübingen, Tübingen, Germany.
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23
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Shi Z, Lan Y, Wang Y, Yan X, Ma X, Hassan FU, Rushdi HE, Xu Z, Wang W, Deng T. Multi-omics strategy reveals potential role of antimicrobial resistance and virulence factor genes responsible for Simmental diarrheic calves caused by Escherichia coli. mSystems 2024; 9:e0134823. [PMID: 38742910 DOI: 10.1128/msystems.01348-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/05/2024] [Indexed: 05/16/2024] Open
Abstract
Escherichia coli (E. coli) is reported to be an important pathogen associated with calf diarrhea. Antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) pose a considerable threat to both animal and human health. However, little is known about the characterization of ARGs and VFGs presented in the gut microbiota of diarrheic calves caused by E. coli. In this study, we used multi-omics strategy to analyze the ARG and VFG profiles of Simmental calves with diarrhea caused by E. coli K99. We found that gut bacterial composition and their microbiome metabolic functions varied greatly in diarrheic calves compared to healthy calves. In total, 175 ARGs were identified, and diarrheal calves showed a significantly higher diversity and abundance of ARGs than healthy calves. Simmental calves with diarrhea showed higher association of VFGs with pili function, curli assembly, and ferrienterobactin transport of E. coli. Co-occurrence patterns based on Pearson correlation analysis revealed that E. coli had a highly significant (P < 0.0001) correlation coefficient (>0.8) with 16 ARGs and 7 VFGs. Metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Phylotype analysis of E. coli genomes showed that the predominant phylogroup B1 in diarrheic Simmental calves was associated with 10 ARGs and 3 VFGs. These findings provide an overview of the diversity and abundance of the gut microbiota in diarrheic calves caused by E. coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the calves affected with diarrhea.IMPORTANCESimmental is a well-recognized beef cattle breed worldwide. They also suffer significant economic losses due to diarrhea. In this study, fecal metagenomic analysis was applied to characterize the antibiotic resistance gene (ARG) and virulence factor gene (VFG) profiles of diarrheic Simmental calves. We identified key ARGs and VFGs correlated with Escherichia coli isolated from Simmental calves. Additionally, metabolomics analysis showed that differentially expressed metabolites in Simmental calves with diarrhea displayed a high correlation with the aforementioned ARGs and VFGs. Our findings provide an insight into the diversity and abundance of the gut microbiota in diarrheic calves caused by Escherichia coli and pave the way for further studies on the mechanisms of antibiotic resistance and virulence in the diarrheal calves from cattle hosts.
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Affiliation(s)
- Zhihai Shi
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yali Lan
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yazhou Wang
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiangzhou Yan
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaoya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Hossam E Rushdi
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Zhaoxue Xu
- Institute of Animal Husbandry and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Wenjia Wang
- College of Veterinary Medicine, Henan University of Animal Husbandry and Economy, Zhengzhou, Henan, China
| | - Tingxian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
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24
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Meza-Perez S, Liu M, Silva-Sanchez A, Morrow CD, Eipers PG, Lefkowitz EJ, Ptacek T, Scharer CD, Rosenberg AF, Hill DD, Arend RC, Gray MJ, Randall TD. Proteobacteria impair anti-tumor immunity in the omentum by consuming arginine. Cell Host Microbe 2024:S1931-3128(24)00197-5. [PMID: 38942027 DOI: 10.1016/j.chom.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/19/2024] [Accepted: 06/04/2024] [Indexed: 06/30/2024]
Abstract
Gut microbiota influence anti-tumor immunity, often by producing immune-modulating metabolites. However, microbes consume a variety of metabolites that may also impact host immune responses. We show that tumors grow unchecked in the omenta of microbe-replete mice due to immunosuppressive Tregs. By contrast, omental tumors in germ-free, neomycin-treated mice or mice colonized with altered Schaedler's flora (ASF) are spontaneously eliminated by CD8+ T cells. These mice lack Proteobacteria capable of arginine catabolism, causing increases in serum arginine that activate the mammalian target of the rapamycin (mTOR) pathway in Tregs to reduce their suppressive capacity. Transfer of the Proteobacteria, Escherichia coli (E. coli), but not a mutant unable to catabolize arginine, to ASF mice reduces arginine levels, restores Treg suppression, and prevents tumor clearance. Supplementary arginine similarly decreases Treg suppressive capacity, increases CD8+ T cell effectiveness, and reduces tumor burden. Thus, microbial consumption of arginine alters anti-tumor immunity, offering potential therapeutic strategies for tumors in visceral adipose tissue.
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Affiliation(s)
- Selene Meza-Perez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Mingyong Liu
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aaron Silva-Sanchez
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Peter G Eipers
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Elliot J Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Travis Ptacek
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Alexander F Rosenberg
- Department of Biomedical Informatics and Data Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dave D Hill
- Department of Biomedical Informatics and Data Science, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rebecca C Arend
- Department of Obstetrics and Gynecology, Division of Gynecological Oncology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael J Gray
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Troy D Randall
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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25
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Zhuo LB, Yang Y, Xiao C, Li F, Lin L, Xi Y, Fu Y, Zheng JS, Chen YM. Gut microbiota-bile acid axis mediated the beneficial associations between dietary lignans and hyperuricemia: a prospective study. Food Funct 2024; 15:6438-6449. [PMID: 38775706 DOI: 10.1039/d4fo00961d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Background: The escalating prevalence of hyperuricemia is emerging as a significant public health concern. The association between dietary lignans and hyperuricemia is yet to be fully elucidated. Our study aims to evaluate the relationships between dietary lignan intake and hyperuricemia among middle-aged and elderly Chinese individuals, with an additional focus on investigating the underlying mechanisms. Methods: Dietary lignan intake was measured using a validated Food Frequency Questionnaire in 3801 participants at the baseline. Among them, 2552 participants were included in the longitudinal study with a median follow-up of 10.5 years. The gut microbiota was analyzed by shotgun metagenome sequencing in 1789 participants, and the targeted fecal metabolome was determined in 987 participants using UPLC-MS/MS at the midpoint of follow-up. Results: The multivariable-adjusted HRs (95% CIs) for hyperuricemia incidence in the highest quartile (vs. the lowest quartile) of dietary intake of total lignans, matairesinol, pinoresinol, and secoisolariciresinol were 0.93 (0.78-1.10), 0.77 (0.66-0.90), 0.83 (0.70-0.97), and 0.85 (0.73-1.00), respectively. The gut microbial and fecal metabolic compositions were significantly different across the dietary lignan groups and the hyperuricemia groups. The beneficial associations between dietary lignans and hyperuricemia might be mediated by several gut microbes (e.g., Fusobacterium mortiferum and Blautia sp. CAG-257) and the downstream bile acid products (e.g., NorCA, glycochenodeoxycholic acid, and glycoursodeoxycholic acid). Conclusion: We found that dietary lignans were inversely associated with hyperuricemia incidence, and the gut microbiota-bile acid axis might mediate this association. Our findings provide new perspectives on precise therapeutic targets and underlying mechanisms for conditions associated with elevated uric acid.
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Affiliation(s)
- Lai-Bao Zhuo
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
| | - Yingdi Yang
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
| | - Congmei Xiao
- Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, School of Medicine and School of Life Sciences, Westlake University, Hangzhou 310030, China.
- Shenzhen Bao'an Center for Chronic Diseases Control, Shenzhen, China
| | - Fanqin Li
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
| | - Lishan Lin
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
| | - Yue Xi
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
| | - Yuanqing Fu
- Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, School of Medicine and School of Life Sciences, Westlake University, Hangzhou 310030, China.
- Shenzhen Bao'an Center for Chronic Diseases Control, Shenzhen, China
| | - Ju-Sheng Zheng
- Zhejiang Key Laboratory of Multi-Omics in Infection and Immunity, School of Medicine and School of Life Sciences, Westlake University, Hangzhou 310030, China.
| | - Yu-Ming Chen
- Department of Epidemiology, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
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26
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Wang H, Zhang Y, Zhou Q, Yu L, Fu J, Lin D, Huang L, Lai X, Wu L, Zhang J, Zi J, Liao X, Huang S, Xie Y, He Y, Yang L. Microbial metagenomic shifts in children with acute lymphoblastic leukaemia during induction therapy and predictive biomarkers for infection. Ann Clin Microbiol Antimicrob 2024; 23:52. [PMID: 38879505 PMCID: PMC11180392 DOI: 10.1186/s12941-024-00717-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/10/2024] [Indexed: 06/19/2024] Open
Abstract
BACKGROUND Emerging evidence has indicated a link between the gut microbiota and acute lymphoblastic leukaemia (ALL). However, the acute changes in gut microbiota during chemotherapy and the predictive value of baseline gut microbiota in infectious complication remain largely unknown. METHODS Faecal samples (n = 126) from children with ALL (n = 49) undergoing induction chemotherapy were collected at three timepoints, i.e., initiation of chemotherapy (baseline, T0), 7 days (T1) and 33 days (T2) after initiation of chemotherapy. Gut microbiome profile was performed via metagenomic shotgun sequencing. The bioBakery3 pipeline (Kneaddata, Metaphlan 3 and HUMAnN) was performed to assign taxonomy and functional annotations. Gut microbiome at T0 were used to predict infection during chemotherapy. RESULTS The microbial diversities and composition changed significantly during chemotherapy, with Escherichia coli, Klebsiella pneumoniae and Bifidobacterium longum being the most prominent species. The microbial metabolic pathways were also significantly altered during chemotherapy, including the pathway of pyruvate fermentation to acetate and lactate, and assimilatory sulfate reduction pathway. The receiver operating characteristic (ROC) models based on Bifidobacterium longum at T0 could predict infectious complications during the first month of chemotherapy with the area under the curve (AUC) of 0.720. CONCLUSIONS Our study provides new insights into the acute changes in microbial and functional characteristics in children with ALL during chemotherapy. The baseline gut microbiota could be potential biomarkers for infections during chemotherapy. TRIAL REGISTRATION The study was approved by the Ethics Committee of Zhujiang Hospital, Southern Medical University (2021-KY-171-01) and registered on http://www.chictr.org.cn (ChiCTR2200065406, Registration Date: November 4, 2022).
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Affiliation(s)
- Huidi Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Yajie Zhang
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Qianyi Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Lihua Yu
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Jingxiang Fu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Danna Lin
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Lulu Huang
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Xiaorong Lai
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Li Wu
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Jingxin Zhang
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Juan Zi
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Xu Liao
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Siying Huang
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China
| | - Yugu Xie
- Department of Laboratory Medicine, Clinical Biobank Centre, Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, China
| | - Yan He
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China.
| | - Lihua Yang
- Department of Paediatric Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510280, Guangdong, China.
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27
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Dubois L, Valles-Colomer M, Ponsero A, Helve O, Andersson S, Kolho KL, Asnicar F, Korpela K, Salonen A, Segata N, de Vos WM. Paternal and induced gut microbiota seeding complement mother-to-infant transmission. Cell Host Microbe 2024; 32:1011-1024.e4. [PMID: 38870892 DOI: 10.1016/j.chom.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 04/03/2024] [Accepted: 05/07/2024] [Indexed: 06/15/2024]
Abstract
Microbial colonization of the neonatal gut involves maternal seeding, which is partially disrupted in cesarean-born infants and after intrapartum antibiotic prophylaxis. However, other physically close individuals could complement such seeding. To assess the role of both parents and of induced seeding, we analyzed two longitudinal metagenomic datasets (health and early life microbiota [HELMi]: N = 74 infants, 398 samples, and SECFLOR: N = 7 infants, 35 samples) with cesarean-born infants who received maternal fecal microbiota transplantation (FMT). We found that the father constitutes a stable source of strains for the infant independently of the delivery mode, with the cumulative contribution becoming comparable to that of the mother after 1 year. Maternal FMT increased mother-infant strain sharing in cesarean-born infants, raising the average bacterial empirical growth rate while reducing pathogen colonization. Overall, our results indicate that maternal seeding is partly complemented by that of the father and support the potential of induced seeding to restore potential deviations in this process.
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Affiliation(s)
- Léonard Dubois
- Department CIBIO, University of Trento, 38123 Trento, Italy
| | - Mireia Valles-Colomer
- Department CIBIO, University of Trento, 38123 Trento, Italy; MELIS Department, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Alise Ponsero
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Otto Helve
- Children's Hospital, Pediatric Research Center, University of Helsinki, and Helsinki University Hospital, 00014 Helsinki, Finland; Department of Health Security, Finnish Institute for Health and Welfare, 0014 Helsinki, Finland
| | - Sture Andersson
- Children's Hospital, Pediatric Research Center, University of Helsinki, and Helsinki University Hospital, 00014 Helsinki, Finland
| | - Kaija-Leena Kolho
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | | | - Katri Korpela
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Anne Salonen
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland
| | - Nicola Segata
- Department CIBIO, University of Trento, 38123 Trento, Italy; Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy.
| | - Willem M de Vos
- Human Microbiota Research Program, Faculty of Medicine, University of Helsinki, 0014 Helsinki, Finland; Laboratory of Microbiology, University of Wageningen, 6703 WE Wageningen, the Netherlands.
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28
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Simpson JB, Walker ME, Sekela JJ, Ivey SM, Jariwala PB, Storch CM, Kowalewski ME, Graboski AL, Lietzan AD, Walton WG, Davis KA, Cloer EW, Borlandelli V, Hsiao YC, Roberts LR, Perlman DH, Liang X, Overkleeft HS, Bhatt AP, Lu K, Redinbo MR. Gut microbial β-glucuronidases influence endobiotic homeostasis and are modulated by diverse therapeutics. Cell Host Microbe 2024; 32:925-944.e10. [PMID: 38754417 PMCID: PMC11176022 DOI: 10.1016/j.chom.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/18/2024] [Accepted: 04/24/2024] [Indexed: 05/18/2024]
Abstract
Hormones and neurotransmitters are essential to homeostasis, and their disruptions are connected to diseases ranging from cancer to anxiety. The differential reactivation of endobiotic glucuronides by gut microbial β-glucuronidase (GUS) enzymes may influence interindividual differences in the onset and treatment of disease. Using multi-omic, in vitro, and in vivo approaches, we show that germ-free mice have reduced levels of active endobiotics and that distinct gut microbial Loop 1 and FMN GUS enzymes drive hormone and neurotransmitter reactivation. We demonstrate that a range of FDA-approved drugs prevent this reactivation by intercepting the catalytic cycle of the enzymes in a conserved fashion. Finally, we find that inhibiting GUS in conventional mice reduces free serotonin and increases its inactive glucuronide in the serum and intestines. Our results illuminate the indispensability of gut microbial enzymes in sustaining endobiotic homeostasis and indicate that therapeutic disruptions of this metabolism promote interindividual response variabilities.
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Affiliation(s)
- Joshua B Simpson
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Morgan E Walker
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Joshua J Sekela
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Samantha M Ivey
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Parth B Jariwala
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Cameron M Storch
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Mark E Kowalewski
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Amanda L Graboski
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Adam D Lietzan
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - William G Walton
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Kacey A Davis
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Erica W Cloer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Valentina Borlandelli
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Yun-Chung Hsiao
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lee R Roberts
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - David H Perlman
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Xue Liang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA 02141, USA
| | - Hermen S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Aadra P Bhatt
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Division of Gastroenterology and Hepatology, Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Matthew R Redinbo
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA; Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA.
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29
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Selma-Royo M, Dubois L, Manara S, Armanini F, Cabrera-Rubio R, Valles-Colomer M, González S, Parra-Llorca A, Escuriet R, Bode L, Martínez-Costa C, Segata N, Collado MC. Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year. Cell Host Microbe 2024; 32:996-1010.e4. [PMID: 38870906 PMCID: PMC11183301 DOI: 10.1016/j.chom.2024.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 04/24/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024]
Abstract
The composition and maturation of the early-life microbiota are modulated by a number of perinatal factors, whose interplay in relation to microbial vertical transmission remains inadequately elucidated. Using recent strain-tracking methodologies, we analyzed mother-to-infant microbiota transmission in two different birth environments: hospital-born (vaginal/cesarean) and home-born (vaginal) infants and their mothers. While delivery mode primarily explains initial compositional differences, place of birth impacts transmission timing-being early in homebirths and delayed in cesarean deliveries. Transmission patterns vary greatly across species and birth groups, yet certain species, like Bifidobacterium longum, are consistently vertically transmitted regardless of delivery setting. Strain-level analysis of B. longum highlights relevant and consistent subspecies replacement patterns mainly explained by breastfeeding practices, which drive changes in human milk oligosaccharide (HMO) degrading capabilities. Our findings highlight how delivery setting, breastfeeding duration, and other lifestyle preferences collectively shape vertical transmission, impacting infant gut colonization during early life.
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Affiliation(s)
- Marta Selma-Royo
- Institute of Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain; Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Léonard Dubois
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Serena Manara
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Federica Armanini
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Raúl Cabrera-Rubio
- Institute of Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Mireia Valles-Colomer
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy; MELIS Department, Universitat Pompeu Fabra, Barcelona, Spain
| | - Sonia González
- Department of Functional Biology, University of Oviedo, Oviedo, Spain; Diet Microbiota and Health Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Anna Parra-Llorca
- Health Research Institute La Fe, Neonatal Research Group, Division of Neonatology, Valencia, Spain
| | - Ramon Escuriet
- Gerencia de Procesos Integrales de Salud. Area Asistencial, Servicio Catalan de la Salud, Generalitat de Catalunya, Centre for Research in Health and Economics, Universidad Pompeu Fabra, Barcelona, Spain
| | - Lars Bode
- Department of Pediatrics, Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (LRF MOMI CORE), Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA, USA
| | - Cecilia Martínez-Costa
- Department of Pediatrics, Hospital Clínico Universitario, University of Valencia, Spain; Nutrition Research Group of INCLIVA, Valencia, Spain
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy.
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain.
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30
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Liao XL, Chen ZF, Liu QY, Zhou JM, Cai WX, Wang Y, Cai Z. Tissue Accumulation and Biotransformation of 6PPD-Quinone in Adult Zebrafish and Its Effects on the Intestinal Microbial Community. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:10275-10286. [PMID: 38825773 DOI: 10.1021/acs.est.4c01409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The pronounced lethality of N-(1,3-dimethylbutyl)-N'-phenyl-p-phenylenediamine quinone (6PPD-quinone or 6PPDQ) toward specific salmonids, while sparing other fish species, has received considerable attention. However, the underlying cause of this species-specific toxicity remains unresolved. This study explored 6PPDQ toxicokinetics and intestinal microbiota composition in adult zebrafish during a 14-day exposure to environmentally realistic concentrations, followed by a 7-day recovery phase. Predominant accumulation occurred in the brain, intestine, and eyes, with the lowest levels in the liver. Six metabolites were found to undergo hydroxylation, with two additionally undergoing O-sulfonation. Semiquantitative analyses revealed that the predominant metabolite featured a hydroxy group situated on the phenyl ring adjacent to the quinone. This was further validated by assessing enzyme activity and determining in silico binding interactions. Notably, the binding affinity between 6PPDQ and zebrafish phase I and II enzymes exceeded that with the corresponding coho salmon enzymes by 1.04-1.53 times, suggesting a higher potential for 6PPDQ detoxification in tolerant species. Whole-genome sequencing revealed significant increases in the genera Nocardioides and Rhodococcus after exposure to 6PPDQ. Functional annotation and pathway enrichment analyses predicted that these two genera would be responsible for the biodegradation and metabolism of xenobiotics. These findings offer crucial data for comprehending 6PPDQ-induced species-specific toxicity.
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Affiliation(s)
- Xiao-Liang Liao
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Zhi-Feng Chen
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Qian-Yi Liu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Jia-Ming Zhou
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Wen-Xi Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yujie Wang
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Zongwei Cai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, China
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Flores-Vargas G, Bergsveinson J, Korber DR. Environmentally Relevant Antibiotic Concentrations Exert Stronger Selection Pressure on River Biofilm Resistomes than AMR-Reservoir Effluents. Antibiotics (Basel) 2024; 13:539. [PMID: 38927205 PMCID: PMC11200958 DOI: 10.3390/antibiotics13060539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Freshwater environments are primary receiving systems of wastewater and effluents, which carry low concentrations of antibiotics and antimicrobial-resistant (AMR) bacteria and genes. Aquatic microbial communities are thus exposed to environmentally relevant concentrations of antibiotics (ERCA) that presumably influence the acquisition and spread of environmental AMR. Here, we analyzed ERCA exposure with and without the additional presence of municipal wastewater treatment plant effluent (W) and swine manure run-off (M) on aquatic biofilm resistomes. Microscopic analyses revealed decreased taxonomic diversity and biofilm structural integrity, while metagenomic analysis revealed an increased abundance of resistance, virulence, and mobile element-related genes at the highest ERCA exposure levels, with less notable impacts observed when solely exposed to W or M effluents. Microbial function predictions indicated increased gene abundance associated with energy and cell membrane metabolism and heavy metal resistance under ERCA conditions. In silico predictions of increased resistance mechanisms did not correlate with observed phenotypic resistance patterns when whole communities were exposed to antimicrobial susceptibility testing. This reveals important insight into the complexity of whole-community coordination of physical and genetic responses to selective pressures. Lastly, the environmental AMR risk assessment of metagenomic data revealed a higher risk score for biofilms grown at sub-MIC antibiotic conditions.
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Affiliation(s)
- Gabriela Flores-Vargas
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
| | - Jordyn Bergsveinson
- Environment and Climate Change Canada, 11 Innovation Blvd., Saskatoon, SK S7N 3H5, Canada;
| | - Darren R. Korber
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
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32
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Grogan M, Hoyd R, Benedict J, Janse S, Williams N, Naughton M, Burd CE, Paskett ED, Rosko A, Spakowicz DJ, Presley CJ. The FITNESS study: longitudinal geriatric assessment, treatment toxicity, and biospecimen collection to assess functional disability among older adults with lung cancer. FRONTIERS IN AGING 2024; 5:1268232. [PMID: 38911592 PMCID: PMC11190321 DOI: 10.3389/fragi.2024.1268232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 05/06/2024] [Indexed: 06/25/2024]
Abstract
Introduction Older adults with chronic disease prioritize functional independence. We aimed to describe the feasibility of capturing functional disability and treatment toxicity among older adults with lung cancer using a longitudinal comprehensive geriatric assessment (CGA) and molecular biomarkers of aging. Methods This prospective study included adults ≥60 years with any newly diagnosed non-small-cell lung cancer. Participants were recruited from central Ohio (2018-2020). Study assessments included the Cancer and Aging Research Group CGA (CARG-CGA), short physical performance battery (SPPB), and the blessed orientation-memory concentration (BOMC) test at baseline, 3, 6, and 12 months. Activities of daily living (ADLs) and instrumental ADLs (IADLs), quality of life (QoL, PROMIS 10), and treatment toxicity were captured monthly. Stool and blood were collected to characterize the gut microbiome and age-related blood biomarkers. Results This study enrolled 50 participants with an average age of 71.7 years. Ninety-two percent of participants were Caucasian, 58% were male, and all were non-Hispanic. Most had advanced stage (stage III/IV: 90%; stage I/II: 10%), with adenocarcinoma the predominant histologic subtype (68% vs. 24% squamous). First-line treatments included chemotherapy (44%), immune checkpoint inhibitors (ICIs, 22%), chemotherapy and ICIs (30%), or tyrosine kinase inhibitors (4%). The median baseline CARG toxicity score was 8 (range 2-12). Among patients with treatment-related toxicity (n = 49), 39 (79.6%) cases were mild (grade 1-2), and 10 (20.4%) were moderate to severe (≥ grade 3). Treatment toxicity was greater among those with a CARG score ≥8 (28.0% vs. 13.6%). Higher IADL independence, QoL, and SPPB scores at baseline were positively associated with Candidatus Gastranaerophilales bacterium, Lactobacillus rogosae, and Enterobacteria phage P4. Romboutsia ilealis, Streptococcus, and Lachnoclostridium sp An138 and T cell lag3 and cd8a were associated with worse IADLs, QoL, and SPPB scores at baseline. Discussion A longitudinal CGA and biomarker collection is feasible among older adults undergoing lung cancer treatment. Gut microbe and T cell gene expression changes correlated with subjective and objective functional status assessments. Future research will test causality in these associations to improve outcomes through novel supportive care interventions to prevent functional disability.
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Affiliation(s)
- Madison Grogan
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Rebecca Hoyd
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Jason Benedict
- Center for Biostatistics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Sarah Janse
- Center for Biostatistics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Nyelia Williams
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Michelle Naughton
- Division of Cancer Prevention and Control, Department of Medicine, College of Medicine, and The Ohio State University Comprehensive Cancer Center, The Ohio State University Columbus, OH, United States
| | - Christin E. Burd
- Pelotonia Institute for Immuno-Oncology, The Ohio State University James Comprehensive Cancer Center–James Cancer Hospital and Solove Research Institute, Columbus, OH, United States
- Departments of Molecular Genetics, Cancer Biology, and Genetics, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Electra D. Paskett
- Division of Cancer Prevention and Control, Department of Medicine, College of Medicine, and The Ohio State University Comprehensive Cancer Center, The Ohio State University Columbus, OH, United States
| | - Ashley Rosko
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Daniel J. Spakowicz
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
- Division of Cancer Prevention and Control, Department of Medicine, College of Medicine, and The Ohio State University Comprehensive Cancer Center, The Ohio State University Columbus, OH, United States
- Pelotonia Institute for Immuno-Oncology, The Ohio State University James Comprehensive Cancer Center–James Cancer Hospital and Solove Research Institute, Columbus, OH, United States
| | - Carolyn J. Presley
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
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Trepka KR, Kidder WA, Kyaw TS, Olson CA, Upadhyay V, Noecker C, Stanfield D, Steiding P, Spanogiannopoulos P, Dumlao D, Turnbaugh JA, Stachler MD, Van Blarigan EL, Venook AP, Atreya CE, Turnbaugh PJ. Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597471. [PMID: 38895199 PMCID: PMC11185696 DOI: 10.1101/2024.06.04.597471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Dose-limiting toxicities remain a major barrier to drug development and therapy, revealing the limited predictive power of human genetics. Herein, we demonstrate the utility of a more comprehensive approach to studying drug toxicity through longitudinal study of the human gut microbiome during colorectal cancer (CRC) treatment (NCT04054908) coupled to cell culture and mouse experiments. 16S rRNA gene and metagenomic sequencing revealed significant shifts in gut microbial community structure during treatment with oral fluoropyrimidines, which was validated in an independent cohort. Gene abundance was also markedly changed by oral fluoropyrimidines, including an enrichment for the preTA operon, which is sufficient for the inactivation of active metabolite 5-fluorouracil (5-FU). Higher levels of preTA led to increased 5-FU depletion by the gut microbiota grown ex vivo. Germ-free and antibiotic-treated mice had increased fluoropyrimidine toxicity, which was rescued by colonization with the mouse gut microbiota, preTA+ E. coli, or CRC patient stool with high preTA levels. preTA abundance was negatively associated with patient toxicities. Together, these data support a causal, clinically relevant interaction between a human gut bacterial operon and the dose-limiting side effects of cancer treatment. Our approach is generalizable to other drugs, including cancer immunotherapies, and provides valuable insights into host-microbiome interactions in the context of disease.
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Affiliation(s)
- Kai R. Trepka
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Wesley A. Kidder
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Than S. Kyaw
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Christine A. Olson
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Vaibhav Upadhyay
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Cecilia Noecker
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Dalila Stanfield
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Paige Steiding
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Peter Spanogiannopoulos
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Darren Dumlao
- Department of Gastroenterology, University of California San Francisco; San Francisco, USA
| | - Jessie A. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
| | - Matthew D. Stachler
- Department of Pathology, University of California San Francisco; San Francisco, USA
| | - Erin L. Van Blarigan
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco; San Francisco, USA
- Department of Urology, University of California San Francisco; San Francisco, USA
| | - Alan P. Venook
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Chloe E. Atreya
- Department of Medicine, Division of Hematology and Oncology, University of California San Francisco; San Francisco, USA
- UCSF Helen Diller Family Comprehensive Cancer Center; San Francisco, USA
| | - Peter J. Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco; San Francisco, USA
- Chan Zuckerberg Biohub-San Francisco; San Francisco, USA
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34
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McCurry MD, D'Agostino GD, Walsh JT, Bisanz JE, Zalosnik I, Dong X, Morris DJ, Korzenik JR, Edlow AG, Balskus EP, Turnbaugh PJ, Huh JR, Devlin AS. Gut bacteria convert glucocorticoids into progestins in the presence of hydrogen gas. Cell 2024; 187:2952-2968.e13. [PMID: 38795705 PMCID: PMC11179439 DOI: 10.1016/j.cell.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 02/03/2024] [Accepted: 05/02/2024] [Indexed: 05/28/2024]
Abstract
Recent studies suggest that human-associated bacteria interact with host-produced steroids, but the mechanisms and physiological impact of such interactions remain unclear. Here, we show that the human gut bacteria Gordonibacter pamelaeae and Eggerthella lenta convert abundant biliary corticoids into progestins through 21-dehydroxylation, thereby transforming a class of immuno- and metabo-regulatory steroids into a class of sex hormones and neurosteroids. Using comparative genomics, homologous expression, and heterologous expression, we identify a bacterial gene cluster that performs 21-dehydroxylation. We also uncover an unexpected role for hydrogen gas production by gut commensals in promoting 21-dehydroxylation, suggesting that hydrogen modulates secondary metabolism in the gut. Levels of certain bacterial progestins, including allopregnanolone, better known as brexanolone, an FDA-approved drug for postpartum depression, are substantially increased in feces from pregnant humans. Thus, bacterial conversion of corticoids into progestins may affect host physiology, particularly in the context of pregnancy and women's health.
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Affiliation(s)
- Megan D McCurry
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Gabriel D D'Agostino
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jasmine T Walsh
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jordan E Bisanz
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, State College, PA 16802, USA
| | - Ines Zalosnik
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Xueyang Dong
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - David J Morris
- Emeritus Professor of Pathology and Laboratory Medicine, Brown University Alpert School of Medicine, Providence, RI 02903, USA
| | - Joshua R Korzenik
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham & Women's Hospital, Boston, MA 02115, USA
| | - Andrea G Edlow
- Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Emily P Balskus
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA
| | - Jun R Huh
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - A Sloan Devlin
- Department of Biological Chemistry & Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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35
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Spörri L, Uldry AC, Kreuzer M, Herzog EL, Zinkernagel MS, Unterlauft JD, Zysset-Burri DC. Exploring the Ocular Surface Microbiome and Tear Proteome in Glaucoma. Int J Mol Sci 2024; 25:6257. [PMID: 38892444 PMCID: PMC11172891 DOI: 10.3390/ijms25116257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 05/10/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Although glaucoma is a leading cause of irreversible blindness worldwide, its pathogenesis is incompletely understood, and intraocular pressure (IOP) is the only modifiable risk factor to target the disease. Several associations between the gut microbiome and glaucoma, including the IOP, have been suggested. There is growing evidence that interactions between microbes on the ocular surface, termed the ocular surface microbiome (OSM), and tear proteins, collectively called the tear proteome, may also play a role in ocular diseases such as glaucoma. This study aimed to find characteristic features of the OSM and tear proteins in patients with glaucoma. The whole-metagenome shotgun sequencing of 32 conjunctival swabs identified Actinobacteria, Firmicutes, and Proteobacteria as the dominant phyla in the cohort. The species Corynebacterium mastitidis was only found in healthy controls, and their conjunctival microbiomes may be enriched in genes of the phospholipase pathway compared to glaucoma patients. Despite these minor differences in the OSM, patients showed an enrichment of many tear proteins associated with the immune system compared to controls. In contrast to the OSM, this emphasizes the role of the proteome, with a potential involvement of immunological processes in glaucoma. These findings may contribute to the design of new therapeutic approaches targeting glaucoma and other associated diseases.
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Affiliation(s)
- Livia Spörri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
| | | | - Marco Kreuzer
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, 3012 Bern, Switzerland;
| | - Elio L. Herzog
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Martin S. Zinkernagel
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
| | - Jan D. Unterlauft
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
| | - Denise C. Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland; (E.L.H.); (M.S.Z.); (J.D.U.); (D.C.Z.-B.)
- Department for BioMedical Research, University of Bern, 3008 Bern, Switzerland;
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36
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Wang B, Luan Y. Evaluation of normalization methods for predicting quantitative phenotypes in metagenomic data analysis. Front Genet 2024; 15:1369628. [PMID: 38903761 PMCID: PMC11188486 DOI: 10.3389/fgene.2024.1369628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/13/2024] [Indexed: 06/22/2024] Open
Abstract
Genotype-to-phenotype mapping is an essential problem in the current genomic era. While qualitative case-control predictions have received significant attention, less emphasis has been placed on predicting quantitative phenotypes. This emerging field holds great promise in revealing intricate connections between microbial communities and host health. However, the presence of heterogeneity in microbiome datasets poses a substantial challenge to the accuracy of predictions and undermines the reproducibility of models. To tackle this challenge, we investigated 22 normalization methods that aimed at removing heterogeneity across multiple datasets, conducted a comprehensive review of them, and evaluated their effectiveness in predicting quantitative phenotypes in three simulation scenarios and 31 real datasets. The results indicate that none of these methods demonstrate significant superiority in predicting quantitative phenotypes or attain a noteworthy reduction in Root Mean Squared Error (RMSE) of the predictions. Given the frequent occurrence of batch effects and the satisfactory performance of batch correction methods in predicting datasets affected by these effects, we strongly recommend utilizing batch correction methods as the initial step in predicting quantitative phenotypes. In summary, the performance of normalization methods in predicting metagenomic data remains a dynamic and ongoing research area. Our study contributes to this field by undertaking a comprehensive evaluation of diverse methods and offering valuable insights into their effectiveness in predicting quantitative phenotypes.
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Affiliation(s)
- Beibei Wang
- Frontier Science Center for Nonlinear Expectations, Ministry of Education, Qingdao, China
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China
- School of Mathematics, Shandong University, Jinan, China
| | - Yihui Luan
- Frontier Science Center for Nonlinear Expectations, Ministry of Education, Qingdao, China
- Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China
- School of Mathematics, Shandong University, Jinan, China
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37
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Liu Z, Zhang Q, Zhang H, Yi Z, Ma H, Wang X, Wang J, Liu Y, Zheng Y, Fang W, Huang P, Liu X. Colorectal cancer microbiome programs DNA methylation of host cells by affecting methyl donor metabolism. Genome Med 2024; 16:77. [PMID: 38840170 PMCID: PMC11151592 DOI: 10.1186/s13073-024-01344-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 05/09/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) arises from complex interactions between host and environment, which include the gut and tissue microbiome. It is hypothesized that epigenetic regulation by gut microbiota is a fundamental interface by which commensal microbes dynamically influence intestinal biology. The aim of this study is to explore the interplay between gut and tissue microbiota and host DNA methylation in CRC. METHODS Metagenomic sequencing of fecal samples was performed on matched CRC patients (n = 18) and healthy controls (n = 18). Additionally, tissue microbiome was profiled with 16S rRNA gene sequencing on tumor (n = 24) and tumor-adjacent normal (n = 24) tissues of CRC patients, while host DNA methylation was assessed through whole-genome bisulfite sequencing (WGBS) in a subset of 13 individuals. RESULTS Our analysis revealed substantial alterations in the DNA methylome of CRC tissues compared to adjacent normal tissues. An extensive meta-analysis, incorporating publicly available and in-house data, identified significant shifts in microbial-derived methyl donor-related pathways between tumor and adjacent normal tissues. Of note, we observed a pronounced enrichment of microbial-associated CpGs within the promoter regions of genes in adjacent normal tissues, a phenomenon notably absent in tumor tissues. Furthermore, we established consistent and recurring associations between methylation patterns of tumor-related genes and specific bacterial taxa. CONCLUSIONS This study emphasizes the pivotal role of the gut microbiota and pathogenic bacteria in dynamically shaping DNA methylation patterns, impacting physiological homeostasis, and contributing to CRC tumorigenesis. These findings provide valuable insights into the intricate host-environment interactions in CRC development and offer potential avenues for therapeutic interventions in this disease.
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Affiliation(s)
- Zhi Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Qingqing Zhang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Hong Zhang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhongyuan Yi
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Huihui Ma
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Xiaoyi Wang
- Core Facility Center, The First Affiliated Hospital of Nanjing Medical University, No. 300 Guangzhou Road, Nanjing, 210029, China
| | - Jingjing Wang
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215008, China
| | - Yang Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China
| | - Yi Zheng
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Weijia Fang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Ping Huang
- Department of Surgery, The Third Affiliated Hospital, Nanjing Medical University, Nanjing, 211166, China.
| | - Xingyin Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing, 211166, China.
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, 215008, China.
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38
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Kitsios GD, Sayed K, Fitch A, Yang H, Britton N, Shah F, Bain W, Evankovich JW, Qin S, Wang X, Li K, Patel A, Zhang Y, Radder J, Dela Cruz C, Okin DA, Huang CY, Van Tyne D, Benos PV, Methé B, Lai P, Morris A, McVerry BJ. Longitudinal multicompartment characterization of host-microbiota interactions in patients with acute respiratory failure. Nat Commun 2024; 15:4708. [PMID: 38830853 PMCID: PMC11148165 DOI: 10.1038/s41467-024-48819-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/13/2024] [Indexed: 06/05/2024] Open
Abstract
Critical illness can significantly alter the composition and function of the human microbiome, but few studies have examined these changes over time. Here, we conduct a comprehensive analysis of the oral, lung, and gut microbiota in 479 mechanically ventilated patients (223 females, 256 males) with acute respiratory failure. We use advanced DNA sequencing technologies, including Illumina amplicon sequencing (utilizing 16S and ITS rRNA genes for bacteria and fungi, respectively, in all sample types) and Nanopore metagenomics for lung microbiota. Our results reveal a progressive dysbiosis in all three body compartments, characterized by a reduction in microbial diversity, a decrease in beneficial anaerobes, and an increase in pathogens. We find that clinical factors, such as chronic obstructive pulmonary disease, immunosuppression, and antibiotic exposure, are associated with specific patterns of dysbiosis. Interestingly, unsupervised clustering of lung microbiota diversity and composition by 16S independently predicted survival and performed better than traditional clinical and host-response predictors. These observations are validated in two separate cohorts of COVID-19 patients, highlighting the potential of lung microbiota as valuable prognostic biomarkers in critical care. Understanding these microbiome changes during critical illness points to new opportunities for microbiota-targeted precision medicine interventions.
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Affiliation(s)
- Georgios D Kitsios
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Khaled Sayed
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
- Department of Electrical and Computer Engineering & Computer Science, University of New Haven, West Haven, CT, USA
| | - Adam Fitch
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Haopu Yang
- School of Medicine, Tsinghua University, Beijing, China
| | - Noel Britton
- Division of Pulmonary Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Faraaz Shah
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran's Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - William Bain
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Veteran's Affairs Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - John W Evankovich
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shulin Qin
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaohong Wang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kelvin Li
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Asha Patel
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Josiah Radder
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Charles Dela Cruz
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Daniel A Okin
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ching-Ying Huang
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Barbara Methé
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peggy Lai
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Alison Morris
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bryan J McVerry
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Center for Medicine and the Microbiome, University of Pittsburgh, Pittsburgh, PA, USA
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Prins FM, Collij V, Groot HE, Björk JR, Swarte JC, Andreu-Sánchez S, Jansen BH, Fu J, Harmsen HJM, Zhernakova A, Lipsic E, van der Harst P, Weersma RK, Gacesa R. The gut microbiome across the cardiovascular risk spectrum. Eur J Prev Cardiol 2024; 31:935-944. [PMID: 38060843 DOI: 10.1093/eurjpc/zwad377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 06/04/2024]
Abstract
AIMS Despite treatment advancements, cardiovascular disease remains a leading cause of death worldwide. Identifying new targets is crucial for enhancing preventive and therapeutic strategies. The gut microbiome has been associated with coronary artery disease (CAD), however our understanding of specific changes during CAD development remains limited. We aimed to investigate microbiome changes in participants without clinically manifest CAD with different cardiovascular risk levels and in patients with ST-elevation myocardial infarction (STEMI). METHODS AND RESULTS In this cross-sectional study, we characterized the gut microbiome using metagenomics of 411 faecal samples from individuals with low (n = 130), intermediate (n = 130), and high (n = 125) cardiovascular risk based on the Framingham score, and STEMI patients (n = 26). We analysed diversity, and differential abundance of species and functional pathways while accounting for confounders including medication and technical covariates. Collinsella stercoris, Flavonifractor plautii, and Ruthenibacterium lactatiformans showed increased abundances with cardiovascular risk, while Streptococcus thermophilus was negatively associated. Differential abundance analysis revealed eight species and 49 predicted metabolic pathways that were differently abundant among the groups. In the gut microbiome of STEMI patients, there was a depletion of pathways linked to vitamin, lipid, and amino acid biosynthesis. CONCLUSION We identified four microbial species showing a gradual trend in abundance from low-risk individuals to those with STEMI, and observed differential abundant species and pathways in STEMI patients compared to those without clinically manifest CAD. Further investigation is warranted to gain deeper understanding of their precise role in CAD progression and potential implications, with the ultimate goal of identifying novel therapeutic targets.
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Affiliation(s)
- Femke M Prins
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, The Netherlands
| | - Valerie Collij
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Hilde E Groot
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, The Netherlands
| | - Johannes R Björk
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - J Casper Swarte
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Sergio Andreu-Sánchez
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Bernadien H Jansen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, The Netherlands
| | - Hermie J M Harmsen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection prevention, Groningen, The Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Erik Lipsic
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen, The Netherlands
| | - Pim van der Harst
- Department of Cardiology, Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rinse K Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Ranko Gacesa
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
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40
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Young MG, Straub TJ, Worby CJ, Metsky HC, Gnirke A, Bronson RA, van Dijk LR, Desjardins CA, Matranga C, Qu J, Villicana JB, Azimzadeh P, Kau A, Dodson KW, Schreiber HL, Manson AL, Hultgren SJ, Earl AM. Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582780. [PMID: 38463963 PMCID: PMC10925322 DOI: 10.1101/2024.02.29.582780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Low-abundance members of microbial communities are difficult to study in their native habitats. This includes Escherichia coli, a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenic Escherichia coli (UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverse E. coli in gastrointestinal communities, we developed E. coli PanSelect which uses a set of probes designed to specifically recognize and capture E. coli's broad pangenome from sequencing libraries. We demonstrated the ability of E. coli PanSelect to enrich, by orders of magnitude, sequencing data from diverse E. coli using a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes between E. coli residing in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gut E. coli are responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of native in vivo biology of E. coli in other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.
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Affiliation(s)
- Mark G Young
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Timothy J Straub
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Colin J Worby
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Hayden C Metsky
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Andreas Gnirke
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Ryan A Bronson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Lucas R van Dijk
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
| | | | - Christian Matranga
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - James Qu
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Jesús Bazan Villicana
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Philippe Azimzadeh
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrew Kau
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen W Dodson
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Henry L Schreiber
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Abigail L Manson
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
- Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, USA
| | - Ashlee M Earl
- Infectious Disease & Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
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Guimond AJ, Ke S, Tworoger SS, Huang T, Chan AT, Kubzansky LD, Liu YY. Fulfilled Mind, Healthy Gut? Relationships of Eudaimonic Psychological Well-Being With the Gut Microbiome in Postmenopausal Women. Psychosom Med 2024; 86:398-409. [PMID: 38345311 PMCID: PMC11142870 DOI: 10.1097/psy.0000000000001278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
OBJECTIVE Eudaimonic facets of psychological well-being (PWB), like purpose in life and sense of mastery, are associated with healthy aging. Variation in the gut microbiome may be one pathway by which mental health influences age-related health outcomes. However, associations between eudaimonic PWB and the gut microbiome are understudied. We examined whether purpose in life and sense of mastery, separately, were associated with features of the gut microbiome in older women. METHODS Participants were from the Mind-Body Study ( N = 206, mean age = 61 years), a substudy of the Nurses' Health Study II cohort. In 2013, participants completed the Life Engagement Test and the Pearlin Mastery Scale. Three months later, up to two pairs of stool samples were collected, 6 months apart. Covariates included sociodemographics, depression, health status, and health behaviors. Analyses examined associations of PWB with gut microbiome taxonomic diversity, overall community structure, and specific species/pathways. To account for multiple testing, statistical significance was established using Benjamini-Hochberg adjusted p values (i.e., q values ≤0.25). RESULTS We found no evidence of an association between PWB and gut microbiome alpha diversity. In multivariate analysis, higher purpose levels were significantly associated with lower abundance of species previously linked with poorer health outcomes, notably Blautia hydrogenotrophica and Eubacterium ventriosum ( q values ≤0.25). No significant associations were found between PWB and metabolic pathways. CONCLUSIONS These findings offer early evidence suggesting that eudaimonic PWB is linked with variation in the gut microbiome, and this might be one pathway by which PWB promotes healthy aging.
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Affiliation(s)
- Anne-Josee Guimond
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Lee Kum Sheung Center for Health and Happiness, Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Shanlin Ke
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Shelley S. Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Tianyi Huang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew T. Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Laura D. Kubzansky
- Department of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Lee Kum Sheung Center for Health and Happiness, Harvard T. H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
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42
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Hu P, Henry J, Tiesman JP, Parlov M, Bacon R, Charbonneau D, Venkataraman A, Locker KCS, Krigbaum H, Schwartz J. Scalp microbiome composition changes and pathway evaluations due to effective treatment with Piroctone Olamine shampoo. Int J Cosmet Sci 2024; 46:333-347. [PMID: 38196163 DOI: 10.1111/ics.12933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/30/2023] [Accepted: 11/14/2023] [Indexed: 01/11/2024]
Abstract
OBJECTIVE To characterize the scalp microbial composition, function, and connection to dandruff severity using a metagenomics approach and to understand the impact of a Piroctone Olamine containing anti-dandruff shampoo on the scalp microbiome. METHODS Shotgun metagenomics was used to characterize the composition of the scalp microbiomes from 94 subjects with and without clinically defined dandruff. Furthermore, the microbiome of the scalps of 100 dandruff sufferers before and after 3 weeks of treatment with either control or anti-dandruff shampoo containing 0.5% Piroctone Olamine (PO) was characterized and compared to identify microorganisms associated with the dandruff condition and the associated pathways and processes that may contribute to PO's effect on scalp microbiome. RESULTS A higher relative abundance of Malassezia restricta and Staphylococcus capitis and a lower abundance of Cutibacterium acnes were associated with the dandruff scalps relative to the no-dandruff scalps. A 3-week PO shampoo treatment reduced the relative abundance of Malassezia species and Staphylococcus capitis and increased the relative abundance of Cutibacterium acnes. This change to the scalp microbiome composition is consistent with a return to a healthy no-dandruff microbiome and improved clinical signs and symptoms as measured by adherent scalp flaking score (ASFS) compared with the control shampoo. Functional genomics analysis showed that the PO shampoo treatment reduced oxidative stress-associated genes and decreased the abundance of protease, urease, and lipase genes. These changes correlated positively to improvements in dandruff severity. PO treatment favourably shifted scalp microbiomes in dandruff subjects toward the no-dandruff state. CONCLUSION Our results suggest that part of the aetiology of dandruff can be attributed to dysbiosis of the scalp microbiome. PO treatment can restore a healthier microbiome, reducing oxidative stress and promoting better scalp health.
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Affiliation(s)
- Ping Hu
- The Procter & Gamble Company, Mason, Ohio, USA
| | - Jim Henry
- The Procter & Gamble Company, Mason, Ohio, USA
| | | | | | - Rob Bacon
- The Procter & Gamble Company, Mason, Ohio, USA
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Ye T, He S, Li J, Luo J, Yang S, Wang P, Li C. Metagenomic and transcriptomic analysis revealing the impact of oxytetracycline and ciprofloxacin on gut microbiota and gene expression in the Chinese giant salamander (Andrias davidianus). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 271:106925. [PMID: 38718521 DOI: 10.1016/j.aquatox.2024.106925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/30/2024] [Accepted: 04/11/2024] [Indexed: 05/21/2024]
Abstract
Excessive antibiotic use has led to the spread of antibiotic resistance genes (ARGs), impacting gut microbiota and host health. However, the effects of antibiotics on amphibian populations remain unclear. We investigated the impact of oxytetracycline (OTC) and ciprofloxacin (CIP) on Chinese giant salamanders (Andrias davidianus), focusing on gut microbiota, ARGs, and gene expression by performing metagenome and transcriptome sequencing. A. davidianus were given OTC (20 or 40 mg/kg) or CIP (50 or 100 mg/kg) orally for 7 days. The results revealed that oral administration of OTC and CIP led to distinct changes in microbial composition and functional potential, with CIP treatment having a greater impact than OTC. Antibiotic treatment also influenced the abundance of ARGs, with an increase in fluoroquinolone and multi-drug resistance genes observed post-treatment. The construction of metagenome-assembled genomes (MAGs) accurately validated that CIP intervention enriched fish-associated potential pathogens Aeromonas hydrophila carrying an increased number of ARGs. Additionally, mobile genetic elements (MGEs), such as phages and plasmids, were implicated in the dissemination of ARGs. Transcriptomic analysis of the gut revealed significant alterations in gene expression, particularly in immune-related pathways, with differential effects observed between OTC and CIP treatments. Integration of metagenomic and transcriptomic data highlighted potential correlations between gut gene expression and microbial composition, suggesting complex interactions between the host gut and its gut microbiota in response to antibiotic exposure. These findings underscore the importance of understanding the impact of antibiotic intervention on the gut microbiome and host health in amphibians, particularly in the context of antibiotic resistance and immune function.
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Affiliation(s)
- Ting Ye
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, Guizhou, 550005, PR China
| | - Shumao He
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, Guizhou, 550005, PR China
| | - Jiahui Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, Guizhou, 550005, PR China
| | - Jianlin Luo
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, Guizhou, 550005, PR China
| | - Sixue Yang
- Zhiran Biotechnology Co. Ltd, Tianjin, 301000, PR China
| | - Peng Wang
- Zhiran Biotechnology Co. Ltd, Tianjin, 301000, PR China.
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Department of Biology and Engineering of Environment, Guiyang University, Guiyang, Guizhou, 550005, PR China.
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Wang T, Shi Z, Ren H, Xu M, Lu J, Yang F, Ye C, Wu K, Chen M, Xu X, Liu D, Kong L, Zheng R, Zheng J, Li M, Xu Y, Zhao Z, Chen Y, Yang H, Wang J, Ning G, Li J, Zhong H, Bi Y, Wang W. Divergent age-associated and metabolism-associated gut microbiome signatures modulate cardiovascular disease risk. Nat Med 2024; 30:1722-1731. [PMID: 38844795 DOI: 10.1038/s41591-024-03038-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 04/30/2024] [Indexed: 06/13/2024]
Abstract
Insight into associations between the gut microbiome with metabolism and aging is crucial for tailoring interventions to promote healthy longevity. In a discovery cohort of 10,207 individuals aged 40-93 years, we used 21 metabolic parameters to classify individuals into five clusters, termed metabolic multimorbidity clusters (MCs), that represent different metabolic subphenotypes. Compared to the cluster classified as metabolically healthy (MC1), clusters classified as 'obesity-related mixed' (MC4) and 'hyperglycemia' (MC5) exhibited an increased 11.1-year cardiovascular disease (CVD) risk by 75% (multivariable-adjusted hazard ratio (HR): 1.75, 95% confidence interval (CI): 1.43-2.14) and by 117% (2.17, 1.72-2.74), respectively. These associations were replicated in a second cohort of 9,061 individuals with a 10.0-year follow-up. Based on analysis of 4,491 shotgun fecal metagenomes from the discovery cohort, we found that gut microbial composition was associated with both MCs and age. Next, using 55 age-specific microbial species to capture biological age, we developed a gut microbial age (MA) metric, which was validated in four external cohorts comprising 4,425 metagenomic samples. Among individuals aged 60 years or older, the increased CVD risk associated with MC4 or MC5, as compared to MC1, MC2 or MC3, was exacerbated in individuals with high MA but diminished in individuals with low MA, independent of age, sex and other lifestyle and dietary factors. This pattern, in which younger MA appears to counteract the CVD risk attributable to metabolic dysfunction, implies a modulating role of MA in cardiovascular health for metabolically unhealthy older people.
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Affiliation(s)
- Tiange Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhun Shi
- BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Huahui Ren
- BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
| | - Min Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jieli Lu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Chaojie Ye
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kui Wu
- BGI Research, Shenzhen, China
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, BGI Research, Shenzhen, China
| | - Mingling Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xun Xu
- BGI Research, Shenzhen, China
| | - Dong Liu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lijie Kong
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruizhi Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mian Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhiyun Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuhong Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Huanzi Zhong
- BGI Research, Shenzhen, China.
- Institute of Intelligent Medical Research (IIMR), BGI Genomics, Shenzhen, China.
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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45
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Jang CS, Kim H, Kim D, Han B. MicroPredict: predicting species-level taxonomic abundance of whole-shotgun metagenomic data using only 16S amplicon sequencing data. Genes Genomics 2024; 46:701-712. [PMID: 38700829 PMCID: PMC11102407 DOI: 10.1007/s13258-024-01514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/26/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND The importance of the human microbiome in the analysis of various diseases is emerging. The two main methods used to profile the human microbiome are 16S rRNA gene sequencing (16S sequencing) and whole-genome shotgun sequencing (WGS). Owing to the full coverage of the genome in sequencing, WGS has multiple advantages over 16S sequencing, including higher taxonomic profiling resolution at the species-level and functional profiling analysis. However, 16S sequencing remains widely used because of its relatively low cost. Although WGS is the standard method for obtaining accurate species-level data, we found that 16S sequencing data contained rich information to predict high-resolution species-level abundances with reasonable accuracy. OBJECTIVE In this study, we proposed MicroPredict, a method for accurately predicting WGS-comparable species-level abundance data using 16S taxonomic profile data. METHODS We employed a mixed model using two key strategies: (1) modeling both sample- and species-specific information for predicting WGS abundances, and (2) accounting for the possible correlations among different species. RESULTS We found that MicroPredict outperformed the other machine learning methods. CONCLUSION We expect that our approach will help researchers accurately approximate the species-level abundances of microbiome profiles in datasets for which only cost-effective 16S sequencing has been applied.
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Affiliation(s)
- Chloe Soohyun Jang
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Hakin Kim
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, South Korea
| | - Donghyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea.
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, South Korea.
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46
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Sequino G, Cobo-Diaz JF, Valentino V, Tassou C, Volpe S, Torrieri E, Nychas GJ, Álvarez Ordóñez A, Ercolini D, De Filippis F. Microbiome mapping in beef processing reveals safety-relevant variations in microbial diversity and genomic features. Food Res Int 2024; 186:114318. [PMID: 38729711 DOI: 10.1016/j.foodres.2024.114318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/05/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024]
Abstract
The microbiome of surfaces along the beef processing chain represents a critical nexus where microbial ecosystems play a pivotal role in meat quality and safety of end products. This study offers a comprehensive analysis of the microbiome along beef processing using whole metagenomics with a particular focus on antimicrobial resistance and virulence-associated genes distribution. Our findings highlighted that microbial communities change dynamically in the different steps along beef processing chain, influenced by the specific conditions of each micro-environment. Brochothrix thermosphacta, Carnobacterium maltaromaticum, Pseudomonas fragi, Psychrobacter cryohalolentis and Psychrobacter immobilis were identified as the key species that characterize beef processing environments. Carcass samples and slaughterhouse surfaces exhibited a high abundance of antibiotic resistance genes (ARGs), mainly belonging to aminoglycosides, β-lactams, amphenicols, sulfonamides and tetracyclines antibiotic classes, also localized on mobile elements, suggesting the possibility to be transmitted to human pathogens. We also evaluated how the initial microbial contamination of raw beef changes in response to storage conditions, showing different species prevailing according to the type of packaging employed. We identified several genes leading to the production of spoilage-associated compounds, and highlighted the different genomic potential selected by the storage conditions. Our results suggested that surfaces in beef processing environments represent a hotspot for beef contamination and evidenced that mapping the resident microbiome in these environments may help in reducing meat microbial contamination, increasing shelf-life, and finally contributing to food waste restraint.
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Affiliation(s)
- Giuseppina Sequino
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | - José F Cobo-Diaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Vincenzo Valentino
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | - Chrysoula Tassou
- Hellenic Agricultural Organization - DIMITRA, Institute of Technology of Agricultural Products, Sofokli Venizelou 1, 14123 Lycovrissi, Attica, Greece
| | - Stefania Volpe
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | - Elena Torrieri
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy
| | | | - Avelino Álvarez Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy; Task Force on Microbiome Studies, University of Naples Federico II, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, University of Naples Federico II, via Università 100, 80055 Portici, (NA), Italy; Task Force on Microbiome Studies, University of Naples Federico II, Italy.
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47
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Wolter M, Grant ET, Boudaud M, Pudlo NA, Pereira GV, Eaton KA, Martens EC, Desai MS. Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility. Mol Syst Biol 2024; 20:596-625. [PMID: 38745106 PMCID: PMC11148096 DOI: 10.1038/s44320-024-00036-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/06/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
The erosion of the colonic mucus layer by a dietary fiber-deprived gut microbiota results in heightened susceptibility to an attaching and effacing pathogen, Citrobacter rodentium. Nevertheless, the questions of whether and how specific mucolytic bacteria aid in the increased pathogen susceptibility remain unexplored. Here, we leverage a functionally characterized, 14-member synthetic human microbiota in gnotobiotic mice to deduce which bacteria and functions are responsible for the pathogen susceptibility. Using strain dropouts of mucolytic bacteria from the community, we show that Akkermansia muciniphila renders the host more vulnerable to the mucosal pathogen during fiber deprivation. However, the presence of A. muciniphila reduces pathogen load on a fiber-sufficient diet, highlighting the context-dependent beneficial effects of this mucin specialist. The enhanced pathogen susceptibility is not owing to altered host immune or pathogen responses, but is driven by a combination of increased mucus penetrability and altered activities of A. muciniphila and other community members. Our study provides novel insights into the mechanisms of how discrete functional responses of the same mucolytic bacterium either resist or enhance enteric pathogen susceptibility.
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Affiliation(s)
- Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Gabriel V Pereira
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kathryn A Eaton
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark.
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48
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You L, Yang C, Jin H, Kwok LY, Lv R, Ma T, Zhao Z, Zhang H, Sun Z. Shotgun metagenomic analysis of microbiota dynamics during long-term backslopping fermentation of traditional fermented milk in a controlled laboratory environment. J Dairy Sci 2024:S0022-0302(24)00826-9. [PMID: 38825103 DOI: 10.3168/jds.2023-23710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 04/08/2024] [Indexed: 06/04/2024]
Abstract
Traditional fermented milks are produced through an inoculation process that involves the deliberate introduction of microorganisms that have been adapted and perpetuated across successive generations. However, the changes in the microbiota of traditional fermented milk during long-term inoculation fermentation in a laboratory environment remain unclear. In this study, we collected 5 samples of traditional fermented milk samples from 5 different counties in Tibet (3 kurut products) and Xinjiang (2 tarag products) of China, which served as starter cultures for a 9-mo continuous inoculation fermentation experiment. We analyzed the inter- and intra-population variations in the microbial communities of the collected samples, representing their macrodiversity and microdiversity, using shotgun metagenomic sequencing. Across all samples, we obtained a total of 186 high-quality metagenomic-assembled genomes, including 7 genera and 13 species with a relative abundance of more than 1%. The majority of these genomes were annotated as Lactobacillus helveticus (60.46%), Enterococcus durans (9.52%), and Limosilactobacillus fermentum (6.23%). We observed significant differences in species composition and abundance among the 5 initial inoculants. During the long-term inoculation fermentation, we found an overall increasing trend in species diversity, composition, and abundances of carbohydrate metabolism module-encoding genes in the fermented milk bacterial metagenome, while the fermented milk virome exhibited a relatively narrow range of variation. Lactobacillus helveticus, a dominant species in traditional fermented milk, displayed high stability during the long-term inoculation fermentation. Our study provides valuable insights for the industrial production of traditional fermented milk.
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Affiliation(s)
- Lijun You
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Chengcong Yang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Hao Jin
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Lai-Yu Kwok
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Ruirui Lv
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Teng Ma
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhixin Zhao
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Heping Zhang
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhihong Sun
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China. Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
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49
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Mohr AE, Sweazea KL, Bowes DA, Jasbi P, Whisner CM, Sears DD, Krajmalnik-Brown R, Jin Y, Gu H, Klein-Seetharaman J, Arciero KM, Gumpricht E, Arciero PJ. Gut microbiome remodeling and metabolomic profile improves in response to protein pacing with intermittent fasting versus continuous caloric restriction. Nat Commun 2024; 15:4155. [PMID: 38806467 PMCID: PMC11133430 DOI: 10.1038/s41467-024-48355-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
The gut microbiome (GM) modulates body weight/composition and gastrointestinal functioning; therefore, approaches targeting resident gut microbes have attracted considerable interest. Intermittent fasting (IF) and protein pacing (P) regimens are effective in facilitating weight loss (WL) and enhancing body composition. However, the interrelationships between IF- and P-induced WL and the GM are unknown. The current randomized controlled study describes distinct fecal microbial and plasma metabolomic signatures between combined IF-P (n = 21) versus a heart-healthy, calorie-restricted (CR, n = 20) diet matched for overall energy intake in free-living human participants (women = 27; men = 14) with overweight/obesity for 8 weeks. Gut symptomatology improves and abundance of Christensenellaceae microbes and circulating cytokines and amino acid metabolites favoring fat oxidation increase with IF-P (p < 0.05), whereas metabolites associated with a longevity-related metabolic pathway increase with CR (p < 0.05). Differences indicate GM and metabolomic factors play a role in WL maintenance and body composition. This novel work provides insight into the GM and metabolomic profile of participants following an IF-P or CR diet and highlights important differences in microbial assembly associated with WL and body composition responsiveness. These data may inform future GM-focused precision nutrition recommendations using larger sample sizes of longer duration. Trial registration, March 6, 2020 (ClinicalTrials.gov as NCT04327141), based on a previous randomized intervention trial.
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Affiliation(s)
- Alex E Mohr
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Institute Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
| | - Karen L Sweazea
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Institute Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
- Center for Evolution and Medicine, College of Liberal Arts and Sciences, Arizona State University, Tempe, AZ, USA
| | - Devin A Bowes
- Biodesign Institute Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
| | - Paniz Jasbi
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Systems Precision Engineering and Advanced Research (SPEAR), Theriome Inc., Phoenix, AZ, USA
| | - Corrie M Whisner
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Biodesign Institute Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
| | - Dorothy D Sears
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Institute Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
| | - Yan Jin
- Center of Translational Science, Florida International University, Port St. Lucie, FL, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center of Translational Science, Florida International University, Port St. Lucie, FL, USA
| | - Judith Klein-Seetharaman
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Karen M Arciero
- Human Nutrition and Metabolism Laboratory, Department of Health and Human Physiological Sciences, Skidmore College, Saratoga Springs, NY, USA
| | | | - Paul J Arciero
- Human Nutrition and Metabolism Laboratory, Department of Health and Human Physiological Sciences, Skidmore College, Saratoga Springs, NY, USA.
- School of Health and Rehabilitation Sciences, Department of Sports Medicine and Nutrition, University of Pittsburgh, Pittsburgh, PA, USA.
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50
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Vasco KA, Hansen ZA, Schilmiller AL, Bowcutt B, Carbonell SL, Ruegg PL, Quinn RA, Zhang L, Manning SD. Untargeted metabolomics and metagenomics reveal signatures for intramammary ceftiofur treatment and lactation stage in the cattle hindgut. Front Mol Biosci 2024; 11:1364637. [PMID: 38836107 PMCID: PMC11148447 DOI: 10.3389/fmolb.2024.1364637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/29/2024] [Indexed: 06/06/2024] Open
Abstract
The gut microbiota in cattle is essential for protein, energy, and vitamin production and hence, microbiota perturbations can affect cattle performance. This study evaluated the effect of intramammary (IMM) ceftiofur treatment and lactation stage on the functional gut microbiome and metabolome. Forty dairy cows were enrolled at dry-off. Half received IMM ceftiofur and a non-antibiotic teat sealant containing bismuth subnitrate (cases), while the other half received the teat sealant (controls). Fecal samples were collected before treatment at dry off, during the dry period (weeks 1 and 5) and the first week after calving (week 9). Shotgun metagenomic sequencing was applied to predict microbial metabolic pathways whereas untargeted metabolomics was used identify polar and nonpolar metabolites. Compared to controls, long-term changes were observed in the cows given ceftiofur, including a lower abundance of microbial pathways linked to energy production, amino acid biosynthesis, and other vital molecules. The metabolome of treated cows had elevated levels of stachyose, phosphatidylethanolamine diacylglycerol (PE-DAG), and inosine a week after the IMM ceftiofur application, indicating alterations in microbial fermentation, lipid metabolism, energy, and cellular signaling. Differences were also observed by sampling, with cows in late lactation having more diverse metabolic pathways and a unique metabolome containing higher levels of histamine and histamine-producing bacteria. These data illustrate how IMM ceftiofur treatment can alter the functionality of the hindgut metabolome and microbiome. Understanding how antibiotics and lactation stages, which are each characterized by unique diets and physiology, impact the function of resident microbes is critical to define normal gut function in dairy cattle.
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Affiliation(s)
- Karla A Vasco
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
| | - Zoe A Hansen
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
| | - Anthony L Schilmiller
- Research Technology Support Facility, Mass Spectrometry and Metabolomics Core, Michigan State University, East Lansing, MI, United States
| | - Bailey Bowcutt
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
| | - Samantha L Carbonell
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
| | - Pamela L Ruegg
- Department of Large Animal and Clinical Sciences, Michigan State University, East Lansing, MI, United States
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Lixin Zhang
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, United States
| | - Shannon D Manning
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI, United States
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