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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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Ng DZW, Low A, Tan AJH, Ong JH, Kwa WT, Lee JWJ, Chan ECY. Ex vivo metabolism kinetics of primary to secondary bile acids via a physiologically relevant human faecal microbiota model. Chem Biol Interact 2024; 399:111140. [PMID: 38992765 DOI: 10.1016/j.cbi.2024.111140] [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: 05/09/2024] [Revised: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 07/13/2024]
Abstract
Bile acids (BA) are synthesized in the human liver and undergo metabolism by host gut bacteria. In diseased states, gut microbial dysbiosis may lead to high primary unconjugated BA concentrations and significant perturbations to secondary BA. Hence, it is important to understand the microbial-mediated formation kinetics of secondary bile acids using physiologically relevant ex vivo human faecal microbiota models. Here, we optimized an ex vivo human faecal microbiota model to recapitulate the metabolic kinetics of primary unconjugated BA and applied it to investigate the formation kinetics of novel secondary BA metabolites and their sequential pathways. We demonstrated (1) first-order depletion of primary BA, cholic acid (CA) and chenodeoxycholic acid (CDCA), under non-saturable conditions and (2) saturable Michaelis-Menten kinetics for secondary BA metabolite formation with increasing substrate concentration. Notably, relatively lower Michaelis constants (Km) were associated with the formation of deoxycholic acid (DCA, 14.3 μM) and lithocholic acid (LCA, 140 μM) versus 3-oxo CA (>1000 μM), 7-keto DCA (443 μM) and 7-keto LCA (>1000 μM), thereby recapitulating clinically observed saturation of 7α-dehydroxylation relative to oxidation of primary BA. Congruently, metagenomics revealed higher relative abundance of functional genes related to the oxidation pathway as compared to the 7α-dehydroxylation pathway. In addition, we demonstrated gut microbial-mediated hyocholic acid (HCA) and hyodeoxycholic acid (HDCA) formation from CDCA. In conclusion, we optimized a physiologically relevant ex vivo human faecal microbiota model to investigate gut microbial-mediated metabolism of primary BA and present a novel gut microbial-catalysed two-step pathway from CDCA to HCA and, subsequently, HDCA.
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Affiliation(s)
- Daniel Zhi Wei Ng
- Department of Pharmacy and Pharmaceutical Sciences, National University of Singapore, 18 Science Drive 4, 117543, Singapore
| | - Adrian Low
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6 Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore
| | - Amanda Jia Hui Tan
- Department of Pharmacy and Pharmaceutical Sciences, National University of Singapore, 18 Science Drive 4, 117543, Singapore
| | - Jia Hui Ong
- Department of Pharmacy and Pharmaceutical Sciences, National University of Singapore, 18 Science Drive 4, 117543, Singapore
| | - Wit Thun Kwa
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6 Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore
| | - Jonathan Wei Jie Lee
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, MD6 Centre for Translational Medicine, 14 Medical Drive, Singapore, 117599, Singapore; Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, E7, 15 Kent Ridge Crescent, Singapore, 119276, Singapore; Division of Gastroenterology & Hepatology, Department of Medicine, National University Hospital, Singapore.
| | - Eric Chun Yong Chan
- Department of Pharmacy and Pharmaceutical Sciences, National University of Singapore, 18 Science Drive 4, 117543, Singapore.
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5
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Anthony WE, Allison SD, Broderick CM, Chavez Rodriguez L, Clum A, Cross H, Eloe-Fadrosh E, Evans S, Fairbanks D, Gallery R, Gontijo JB, Jones J, McDermott J, Pett-Ridge J, Record S, Rodrigues JLM, Rodriguez-Reillo W, Shek KL, Takacs-Vesbach T, Blanchard JL. From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology. ENVIRONMENTAL MICROBIOME 2024; 19:56. [PMID: 39095861 DOI: 10.1186/s40793-024-00599-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024]
Abstract
Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.
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Affiliation(s)
| | - Steven D Allison
- University of California Irvine, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Caitlin M Broderick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | | | - Alicia Clum
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Hugh Cross
- National Ecological Observatory Network - Battelle, Boulder, CO, USA
| | | | - Sarah Evans
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Dawson Fairbanks
- University of California Riverside, Riverside, CA, USA
- The University of Arizona, Tucson, AZ, USA
| | | | | | - Jennifer Jones
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, USA
| | - Jason McDermott
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Jennifer Pett-Ridge
- Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California Merced, Merced, CA, 95343, USA
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De Filippis F, Valentino V, Yap M, Cabrera-Rubio R, Barcenilla C, Carlino N, Cobo-Díaz JF, Quijada NM, Calvete-Torre I, Ruas-Madiedo P, Sabater C, Sequino G, Pasolli E, Wagner M, Margolles A, Segata N, Álvarez-Ordóñez A, Cotter PD, Ercolini D. Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities. NPJ Biofilms Microbiomes 2024; 10:67. [PMID: 39095404 DOI: 10.1038/s41522-024-00541-5] [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: 03/19/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
The resident microbiome in food industries may impact on food quality and safety. In particular, microbes residing on surfaces in dairy industries may actively participate in cheese fermentation and ripening and contribute to the typical flavor and texture. In this work, we carried out an extensive microbiome mapping in 73 cheese-making industries producing different types of cheeses (fresh, medium and long ripened) and located in 4 European countries. We sequenced and analyzed metagenomes from cheese samples, raw materials and environmental swabs collected from both food contact and non-food contact surfaces, as well as operators' hands and aprons. Dairy plants were shown to harbor a very complex microbiome, characterized by high prevalence of genes potentially involved in flavor development, probiotic activities, and resistance to gastro-intestinal transit, suggesting that these microbes may potentially be transferred to the human gut microbiome. More than 6100 high-quality Metagenome Assembled Genomes (MAGs) were reconstructed, including MAGs from several Lactic Acid Bacteria species and putative new species. Although microbial pathogens were not prevalent, we found several MAGs harboring genes related to antibiotic resistance, highlighting that dairy industry surfaces represent a potential hotspot for antimicrobial resistance (AR) spreading along the food chain. Finally, we identified facility-specific strains that can represent clear microbial signatures of different cheesemaking facilities, suggesting an interesting potential of microbiome tracking for the traceability of cheese origin.
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Affiliation(s)
- Francesca De Filippis
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, NA, Italy
| | - Vincenzo Valentino
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
| | - Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Raul Cabrera-Rubio
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Paterna, Spain
| | - Coral Barcenilla
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | | | - José F Cobo-Díaz
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Narciso Martín Quijada
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Department of Microbiology and Genetics, Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Inés Calvete-Torre
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Carlos Sabater
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Giuseppina Sequino
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
| | - Edoardo Pasolli
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, NA, Italy
| | - Martin Wagner
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
- Department for Farm Animals and Veterinary Public Health, Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias - Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Villaviciosa, Spain
- Microhealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Danilo Ercolini
- Dept. of Agricultural Sciences, University of Naples Federico II, Portici, NA, Italy.
- Task Force on Microbiome Studies, University of Naples Federico II, Napoli, NA, Italy.
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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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8
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Feng Y, Zheng H, Yin C, Liang D, Zhang S, Chen J, Mai F, Lan Z, Zhu M, Mai Z, Shen S, Jayawardana T, Wu R, Tang W, Zhang R, He X, Zheng S, Hu Q, Han Y, Yang Y, Gong S, Wang Z, El-Omar EM, Luo W, Chen X, Chen G, Li P, Chen X. β-resorcylic acid released by Limosilactobacillusreuteri protects against cisplatin-induced ovarian toxicity and infertility. Cell Rep Med 2024:101678. [PMID: 39096912 DOI: 10.1016/j.xcrm.2024.101678] [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: 05/08/2024] [Revised: 06/07/2024] [Accepted: 07/11/2024] [Indexed: 08/05/2024]
Abstract
Chemotherapy-induced premature ovarian insufficiency (CIPOI) triggers gonadotoxicity in women undergoing cancer treatment, leading to loss of ovarian reserves and subfertility, with no effective therapies available. In our study, fecal microbiota transplantation in a cisplatin-induced POI mouse model reveals that a dysbiotic gut microbiome negatively impacts ovarian health in CIPOI. Multi-omics analyses show a significant decrease in Limosilactobacillus reuteri and its catabolite, β-resorcylic acid , in the CIPOI group in comparison to healthy controls. Supplementation with L. reuteri or β-RA mitigates cisplatin-induced hormonal disruptions, morphological damages, and reductions in follicular reserve. Most importantly, β-RA pre-treatment effectively preserves oocyte function, embryonic development, and fetus health, thereby protecting against chemotherapy-induced subfertility. Our results provide evidence that β-RA suppresses the nuclear accumulation of sex-determining region Y-box 7, which in turn reduces Bcl-2-associated X activation and inhibits granulosa cell apoptosis. These findings highlight the therapeutic potential of targeting the gut-ovary axis for fertility preservation in CIPOI.
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Affiliation(s)
- Yinglin Feng
- Central Laboratory of the Medical Research Center, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China; Department of Obstetrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong Province, China
| | - Huimin Zheng
- Central Laboratory of the Medical Research Center, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China
| | - Chunhua Yin
- Department of Gynecology and Obstetrics, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Dong Liang
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Siyou Zhang
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Jingrui Chen
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Feihong Mai
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Zixin Lan
- The Second Clinical Medical College, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Menglin Zhu
- The Second Clinical Medical College, Southern Medical University, Guangzhou, Guangdong Province, China
| | - Zhensheng Mai
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Sj Shen
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW, Australia
| | - Thisun Jayawardana
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW, Australia
| | - Rong Wu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Wenli Tang
- Central Laboratory of the Medical Research Center, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China
| | - Renfang Zhang
- Department of Gynecology and Obstetrics, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Xiaoyun He
- Department of Gynecology and Obstetrics, First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, China
| | - Shanshan Zheng
- Health Medical Center, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Qian Hu
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Yubin Han
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Yuanhao Yang
- Mater Research Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia; Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Shenhai Gong
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China
| | - Zhang Wang
- Institute of Ecological Science, School of Life Science, South China Normal University, Guangzhou, Guangdong Province, China
| | - Emad M El-Omar
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW, Australia
| | - Wei Luo
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Xueqin Chen
- Central Laboratory of the Medical Research Center, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China.
| | - Guoqiang Chen
- Institute of Translational Medicine, The First People's Hospital of Foshan, Foshan, Guangdong Province, China.
| | - Pan Li
- UNSW Microbiome Research Centre, St George and Sutherland Clinical Campuses, UNSW Sydney, Sydney, NSW, Australia.
| | - Xia Chen
- Central Laboratory of the Medical Research Center, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang Province, China.
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9
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Pu Y, Sun Z, Zhang H, Huang Q, Wang Z, Mei Z, Wang P, Kong M, Yang W, Lin C, Zhou X, Lin S, Huang Q, Huang L, Sun L, Yuan C, Xu Q, Tang H, Wang X, Zheng Y. Gut microbial features and circulating metabolomic signatures of frailty in older adults. NATURE AGING 2024:10.1038/s43587-024-00678-0. [PMID: 39054372 DOI: 10.1038/s43587-024-00678-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/03/2024] [Indexed: 07/27/2024]
Abstract
Frailty, a multidimensional indicator of suboptimal aging, reflects cumulative declines across multiple physiological systems. Although age-related changes have been reported in gut microbiota, their role in healthy aging remains unclear. In this study, we calculated frailty index (FI) from 33 health-related items to reflect the overall health status of 1,821 older adults (62-96 years, 55% female) and conducted multi-omics analysis using gut metagenomic sequencing data and plasma metabolomic data. We identified 18 microbial species and 17 metabolites shifted along with frailty severity, with stronger links observed in females. The associations of nine species, including various Clostridium species and Faecalibacterium prausnitzii, with FI were reproducible in two external populations. Plasma glycerol levels, white blood cell count and kidney function partially mediated these associations. A composite microbial score derived from FI significantly predicted 2-year mortality (adjusted hazard ratio across extreme quartiles, 2.86; 95% confidence interval, 1.38-5.93), highlighting the potential of microbiota-based strategies for risk stratification in older adults.
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Affiliation(s)
- Yanni Pu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhonghan Sun
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hui Zhang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingxia Huang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zhengdong Wang
- Department of Gastroenterology, Rugao People's Hospital, Rugao, China
| | - Zhendong Mei
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Peilu Wang
- Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Institute of Nutrition, Fudan University, Shanghai, China
| | - Mengmeng Kong
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wenjun Yang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chenhao Lin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaofeng Zhou
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shuchun Lin
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiumin Huang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lili Huang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Liang Sun
- Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Institute of Nutrition, Fudan University, Shanghai, China
| | - Changzheng Yuan
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Qian Xu
- Institute of Gut Microbiota Research and Engineering Development, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huiru Tang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Xiaofeng Wang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Institute of Nutrition, Fudan University, Shanghai, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China.
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10
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Kim Y, Kim G, Kim S, Cho B, Kim SY, Do EJ, Bae DJ, Kim S, Kweon MN, Song JS, Park SH, Hwang SW, Kim MN, Kim Y, Min K, Kim SH, Adams MD, Lee C, Park H, Park SR. Fecal microbiota transplantation improves anti-PD-1 inhibitor efficacy in unresectable or metastatic solid cancers refractory to anti-PD-1 inhibitor. Cell Host Microbe 2024:S1931-3128(24)00228-2. [PMID: 39059396 DOI: 10.1016/j.chom.2024.06.010] [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: 10/17/2023] [Revised: 04/30/2024] [Accepted: 06/10/2024] [Indexed: 07/28/2024]
Abstract
The gut microbiome significantly influences immune responses and the efficacy of immune checkpoint inhibitors. We conducted a clinical trial (NCT04264975) combining an anti-programmed death-1 (PD-1) inhibitor with fecal microbiota transplantation (FMT) from anti-PD-1 responder in 13 patients with anti-PD-1-refractory advanced solid cancers. FMT induced sustained microbiota changes and clinical benefits in 6 of 13 patients, with 1 partial response and 5 stable diseases, achieving an objective response rate of 7.7% and a disease control rate of 46.2%. The clinical response correlates with increased cytotoxic T cells and immune cytokines in blood and tumors. We isolated Prevotella merdae Immunoactis from a responder to FMT, which stimulates T cell activity and suppresses tumor growth in mice by enhancing cytotoxic T cell infiltration. Additionally, we found Lactobacillus salivarius and Bacteroides plebeius may inhibit anti-tumor immunity. Our findings suggest that FMT with beneficial microbiota can overcome resistance to anti-PD-1 inhibitors in advanced solid cancers, especially gastrointestinal cancers.
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Affiliation(s)
- Yunjae Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Gihyeon Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea; Genome and Company, Suwon-si 16229, Gyeonggi-do, Republic of Korea
| | - Sujeong Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Beomki Cho
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sang-Yeob Kim
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Republic of Korea
| | - Eun-Ju Do
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Republic of Korea
| | - Dong-Jun Bae
- PrismCDX Co., Ltd., Hwaseong-si 18469, Gyeonggi-do, Republic of Korea
| | - Seungil Kim
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Mi-Na Kweon
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Joon Seon Song
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sung Wook Hwang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Mi-Na Kim
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Yeongmin Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Kyungchan Min
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sung-Han Kim
- Department of Infectious Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Mark D Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Hansoo Park
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea; Genome and Company, Suwon-si 16229, Gyeonggi-do, Republic of Korea.
| | - Sook Ryun Park
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea.
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11
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Johnson KE, Hernandez-Alvarado N, Blackstad M, Heisel T, Allert M, Fields DA, Isganaitis E, Jacobs KM, Knights D, Lock EF, Rudolph MC, Gale CA, Schleiss MR, Albert FW, Demerath EW, Blekhman R. Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth. Nat Commun 2024; 15:6216. [PMID: 39043677 PMCID: PMC11266569 DOI: 10.1038/s41467-024-50282-4] [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: 07/31/2023] [Accepted: 07/03/2024] [Indexed: 07/25/2024] Open
Abstract
Human cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full-term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3-dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreased Bifidobacterium in the infant gut. Our data indicate two opposing CMV-associated effects on infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full-term infant development.
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Affiliation(s)
- Kelsey E Johnson
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA.
| | | | - Mark Blackstad
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Timothy Heisel
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mattea Allert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - David A Fields
- Department of Pediatrics, Section of Diabetes and Endocrinology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | | | - Katherine M Jacobs
- Department of Obstetrics, Gynecology and Women's Health, Division of Maternal-Fetal Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Dan Knights
- BioTechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Eric F Lock
- Division of Biostatistics and Health Data Science, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Michael C Rudolph
- Harold Hamm Diabetes Center, Department of Biochemistry and Physiology, Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | - Cheryl A Gale
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Mark R Schleiss
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Frank W Albert
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, University of Minnesota School of Public Health, Minneapolis, MN, USA
| | - Ran Blekhman
- Section of Genetic Medicine, Division of Biological Sciences, University of Chicago, Chicago, IL, USA
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12
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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 PMCID: PMC11290354 DOI: 10.1016/j.celrep.2024.114442] [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: 01/09/2024] [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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13
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Hussan H, Ali MR, Lyo V, Webb A, Pietrzak M, Zhu J, Choueiry F, Li H, Cummings BP, Marco ML, Medici V, Clinton SK. Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study. Obes Surg 2024:10.1007/s11695-024-07420-0. [PMID: 39042309 DOI: 10.1007/s11695-024-07420-0] [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: 01/09/2024] [Revised: 07/04/2024] [Accepted: 07/17/2024] [Indexed: 07/24/2024]
Abstract
INTRODUCTION Excess body fat elevates colorectal cancer risk. While bariatric surgery (BRS) induces significant weight loss, its effects on the fecal stream and colon biology are poorly understood. Specifically, limited data exist on the impact of bariatric surgery (BRS) on fecal secondary bile acids (BA), including lithocholic acid (LCA), a putative promotor of colorectal carcinogenesis. METHODS This cross-sectional case-control study included 44 patients with obesity; 15 pre-BRS (controls) vs. 29 at a median of 24.1 months post-BRS. We examined the fecal concentrations of 11 BA by liquid chromatography and gene abundance of BA-metabolizing bacterial enzymes through fecal metagenomic sequencing. Differences were quantified using non-parametric tests for BA levels and linear discriminant analysis (LDA) effect size (LEfSe) for genes encoding BA-metabolizing enzymes. RESULTS Total fecal secondary BA concentrations trended towards lower levels post- vs. pre-BRS controls (p = 0.07). Individually, fecal LCA concentrations were significantly lower post- vs. pre-BRS (8477.0 vs. 11,914.0 uM/mg, p < 0.008). Consistent with this finding, fecal bacterial genes encoding BA-metabolizing enzymes, specifically 3-betahydroxycholanate-3-dehydrogenase (EC 1.1.1.391) and 3-alpha-hydroxycholanate dehydrogenase (EC 1.1.1.52), were also lower post- vs. pre-BRS controls (LDA of - 3.32 and - 2.64, respectively, adjusted p < 0.0001). Post-BRS fecal BA concentrations showed significant inverse correlations with weight loss, a healthy diet quality, and increased physical activity. CONCLUSIONS Concentrations of LCA, a secondary BA, and bacterial genes needed for BA metabolism are lower post-BRS. These changes can impact health and modulate the colorectal cancer cascade. Further research is warranted to examine how surgical alterations and the associated dietary changes impact bile acid metabolism.
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Affiliation(s)
- Hisham Hussan
- Division of Gastroenterology, Department of Internal Medicine, University of California, Davis, Sacramento, CA, 95616, USA.
- The UC Davis Comprehensive Cancer Center, Sacramento, CA, 95616, USA.
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, UC Davis Medical Center, 4150 V Street, Suite 3500, Sacramento, CA, 95817, USA.
| | - Mohamed R Ali
- Division of Foregut, Metabolic, and General Surgery, Department of Surgery, University of California Davis, Sacramento, CA, 95616, USA
- Center for Alimentary and Metabolic Sciences, Department of Surgery, University of California, Davis, Sacramento, CA, 95616, USA
| | - Victoria Lyo
- Division of Foregut, Metabolic, and General Surgery, Department of Surgery, University of California Davis, Sacramento, CA, 95616, USA
- Center for Alimentary and Metabolic Sciences, Department of Surgery, University of California, Davis, Sacramento, CA, 95616, USA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Jiangjiang Zhu
- The Department of Human Sciences, The Ohio State University, Columbus, OH, 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Fouad Choueiry
- The Department of Human Sciences, The Ohio State University, Columbus, OH, 43210, USA
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
| | - Hong Li
- The UC Davis Comprehensive Cancer Center, Sacramento, CA, 95616, USA
- Division of Biostatistics, Public Health Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Bethany P Cummings
- Center for Alimentary and Metabolic Sciences, Department of Surgery, University of California, Davis, Sacramento, CA, 95616, USA
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis, Davis, CA, 95616, USA
| | - Maria L Marco
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Valentina Medici
- Division of Gastroenterology, Department of Internal Medicine, University of California, Davis, Sacramento, CA, 95616, USA
| | - Steven K Clinton
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA
- Division of Medical Oncology, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA
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14
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Bellinzona G, Nardi T, Castelli M, Batisti Biffignandi G, Adjou K, Betson M, Blanchard Y, Bujila I, Chalmers R, Davidson R, D'Avino N, Enbom T, Gomes J, Karadjian G, Klotz C, Östlund E, Plutzer J, Rimhanen-Finne R, Robinson G, Sannella AR, Sroka J, Stensvold CR, Troell K, Vatta P, Zalewska B, Bandi C, Sassera D, Cacciò SM. Comparative genomics of Cryptosporidium parvum reveals the emergence of an outbreak-associated population in Europe and its spread to the United States. Genome Res 2024; 34:877-887. [PMID: 38977307 PMCID: PMC11293552 DOI: 10.1101/gr.278830.123] [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: 12/11/2023] [Accepted: 06/05/2024] [Indexed: 07/10/2024]
Abstract
The zoonotic parasite Cryptosporidium parvum is a global cause of gastrointestinal disease in humans and ruminants. Sequence analysis of the highly polymorphic gp60 gene enabled the classification of C. parvum isolates into multiple groups (e.g., IIa, IIc, Id) and a large number of subtypes. In Europe, subtype IIaA15G2R1 is largely predominant and has been associated with many water- and food-borne outbreaks. In this study, we generated new whole-genome sequence (WGS) data from 123 human- and ruminant-derived isolates collected in 13 European countries and included other available WGS data from Europe, Egypt, China, and the United States (n = 72) in the largest comparative genomics study to date. We applied rigorous filters to exclude mixed infections and analyzed a data set from 141 isolates from the zoonotic groups IIa (n = 119) and IId (n = 22). Based on 28,047 high-quality, biallelic genomic SNPs, we identified three distinct and strongly supported populations: Isolates from China (IId) and Egypt (IIa and IId) formed population 1; a minority of European isolates (IIa and IId) formed population 2; and the majority of European (IIa, including all IIaA15G2R1 isolates) and all isolates from the United States (IIa) clustered in population 3. Based on analyses of the population structure, population genetics, and recombination, we show that population 3 has recently emerged and expanded throughout Europe to then, possibly from the United Kingdom, reach the United States, where it also expanded. The reason(s) for the successful spread of population 3 remain elusive, although genes under selective pressure uniquely in this population were identified.
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Affiliation(s)
- Greta Bellinzona
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Tiago Nardi
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy
| | | | - Karim Adjou
- UMR BIPAR, Anses, Laboratoire de Santé Animale, INRAE, École Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France
| | - Martha Betson
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, United Kingdom
| | - Yannick Blanchard
- Viral Genetics and Biosecurity Unit (GVB), French Agency for Food, Environmental and Occupational Health Safety (ANSES), 22440 Ploufragan, France
| | - Ioana Bujila
- Department of Microbiology, Public Health Agency of Sweden, SE-171 82 Solna, Sweden
| | - Rachel Chalmers
- Cryptosporidium Reference Unit, Public Health Wales, Swansea SA2 8QA, United Kingdom
- Swansea Medical School, Swansea University, Swansea SA2 8PP, United Kingdom
| | | | - Nicoletta D'Avino
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, 06126 Perugia, Italy
| | - Tuulia Enbom
- Animal Health Diagnostic Unit, Finnish Food Authority, FI-70210 Kuopio, Finland
| | - Jacinto Gomes
- National Institute for Agricultural and Veterinary Research, 1300 Lisbon, Portugal
| | - Gregory Karadjian
- UMR BIPAR, Anses, Laboratoire de Santé Animale, INRAE, École Nationale Vétérinaire d'Alfort, 94700 Maisons-Alfort, France
| | - Christian Klotz
- Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Emma Östlund
- Swedish Veterinary Agency, SE-751 89 Uppsala, Sweden
| | - Judith Plutzer
- National Institute for Public Education, Budapest, 1007, Hungary
| | | | - Guy Robinson
- Cryptosporidium Reference Unit, Public Health Wales, Swansea SA2 8QA, United Kingdom
- Swansea Medical School, Swansea University, Swansea SA2 8PP, United Kingdom
| | - Anna Rosa Sannella
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Jacek Sroka
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, 24-100 Pulawy, Poland
| | | | - Karin Troell
- Swedish Veterinary Agency, SE-751 89 Uppsala, Sweden
| | - Paolo Vatta
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Barbora Zalewska
- Veterinary Research Institute, Department of Food and Feed Safety, 621 00 Brno, Czech Republic
| | - Claudio Bandi
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy;
- IRCCS Fondazione Policlinico San Matteo, 27100 Pavia, Italy
| | - Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy;
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15
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Stothart MR, McLoughlin PD, Medill SA, Greuel RJ, Wilson AJ, Poissant J. Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses. Nat Commun 2024; 15:6012. [PMID: 39039075 PMCID: PMC11263349 DOI: 10.1038/s41467-024-49963-x] [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: 11/03/2023] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.
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Affiliation(s)
- Mason R Stothart
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
- Department of Biology, University of Oxford, Oxford, United Kingdom.
| | - Philip D McLoughlin
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sarah A Medill
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ruth J Greuel
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
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16
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Bauer BA, Schmidt CM, Ruddy KJ, Olson JE, Meydan C, Schmidt JC, Smith SY, Couch FJ, Earls JC, Price ND, Dudley JT, Mason CE, Zhang B, Phipps SM, Schmidt MA. A Multiomics, Molecular Atlas of Breast Cancer Survivors. Metabolites 2024; 14:396. [PMID: 39057719 PMCID: PMC11279123 DOI: 10.3390/metabo14070396] [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: 06/02/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Breast cancer imposes a significant burden globally. While the survival rate is steadily improving, much remains to be elucidated. This observational, single time point, multiomic study utilizing genomics, proteomics, targeted and untargeted metabolomics, and metagenomics in a breast cancer survivor (BCS) and age-matched healthy control cohort (N = 100) provides deep molecular phenotyping of breast cancer survivors. In this study, the BCS cohort had significantly higher polygenic risk scores for breast cancer than the control group. Carnitine and hexanoyl carnitine were significantly different. Several bile acid and fatty acid metabolites were significantly dissimilar, most notably the Omega-3 Index (O3I) (significantly lower in BCS). Proteomic and metagenomic analyses identified group and pathway differences, which warrant further investigation. The database built from this study contributes a wealth of data on breast cancer survivorship where there has been a paucity, affording the ability to identify patterns and novel insights that can drive new hypotheses and inform future research. Expansion of this database in the treatment-naïve, newly diagnosed, controlling for treatment confounders, and through the disease progression, can be leveraged to profile and contextualize breast cancer and breast cancer survivorship, potentially leading to the development of new strategies to combat this disease and improve the quality of life for its victims.
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Affiliation(s)
| | - Caleb M. Schmidt
- Sovaris Aerospace, Boulder, CO 80302, USA
- Advanced Pattern Analysis and Human Performance Group, Boulder, CO 80302, USA
| | | | | | - Cem Meydan
- Thorne Research, Inc., Summerville, SC 29483, USA
| | - Julian C. Schmidt
- Sovaris Aerospace, Boulder, CO 80302, USA
- Advanced Pattern Analysis and Human Performance Group, Boulder, CO 80302, USA
| | | | | | | | - Nathan D. Price
- Thorne Research, Inc., Summerville, SC 29483, USA
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | | | | | - Bodi Zhang
- Thorne Research, Inc., Summerville, SC 29483, USA
| | | | - Michael A. Schmidt
- Sovaris Aerospace, Boulder, CO 80302, USA
- Advanced Pattern Analysis and Human Performance Group, Boulder, CO 80302, USA
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17
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Trinh P, Teichman S, Roberts MC, Rabinowitz PM, Willis AD. A cross-sectional comparison of gut metagenomes between dairy workers and community controls. BMC Genomics 2024; 25:708. [PMID: 39033279 DOI: 10.1186/s12864-024-10562-1] [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: 08/22/2023] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases. RESULTS Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). CONCLUSIONS This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.
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Affiliation(s)
- Pauline Trinh
- Department of Biostatistics, University of Washington, Seattle, USA
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Sarah Teichman
- Department of Statistics, University of Washington, Seattle, USA
| | - Marilyn C Roberts
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Peter M Rabinowitz
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Amy D Willis
- Department of Biostatistics, University of Washington, Seattle, USA.
- Department of Statistics, University of Washington, Seattle, USA.
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18
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Nanetti E, Scicchitano D, Palladino G, Interino N, Corlatti L, Pedrotti L, Zanetti F, Pagani E, Esposito E, Brambilla A, Grignolio S, Marotti I, Turroni S, Fiori J, Rampelli S, Candela M. The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion. iScience 2024; 27:110194. [PMID: 38989465 PMCID: PMC11233967 DOI: 10.1016/j.isci.2024.110194] [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: 02/01/2024] [Revised: 04/24/2024] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.
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Affiliation(s)
- Enrico Nanetti
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Daniel Scicchitano
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
| | - Giorgia Palladino
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
| | - Nicolò Interino
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Luca Corlatti
- Stelvio National Park, 23032 Bormio, Italy
- University of Freiburg, 79098 Freiburg, Germany
| | | | - Federica Zanetti
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Elena Pagani
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Erika Esposito
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Alice Brambilla
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich (CH), Switzerland
- Centro Studi Fauna Alpina, Parco Nazionale Gran Paradiso, Loc. Degioz 11, 11010 Valsavarenche, Aosta, Italy
| | - Stefano Grignolio
- University of Ferrara, Department of Life Science and Biotechnology, via Borsari 46, I-44121 Ferrara, Italy
| | - Ilaria Marotti
- Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Jessica Fiori
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology (FaBiT), Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
- Fano Marine Center, The Inter-Institute Center for Research on Marine Biodiversity, Resources and Biotechnologies, 61032 Fano, Italy
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19
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Dong Z, Han K, Xie Q, Lin C, Shen X, Hao Y, Li J, Xu H, He L, Yu T, Kuang W. Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder. J Affect Disord 2024; 363:507-519. [PMID: 39033825 DOI: 10.1016/j.jad.2024.07.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/20/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
INTRODUCTION The relationship between depression and gut microbiota remains unclear, but an important role of gut microbiota has been verified. The relationship between gut microbiota and antibiotic resistance genes (ARGs) may be a potential new explanatory pathway. METHODS We collected samples from 63 depressed patients and 30 healthy controls for metagenomic sequencing. The two groups' microbiota characteristics, functional characteristics, and ARG differences were analyzed. RESULTS We obtained 30 differential KEGG orthologs (KOs) and their producers in 5 genera and 7 species by HUMAnN3. We found 6 KOs from Weissella_cibaria and Lactobacillus_plantaru are potentially coring functional mechanism of gut microbiota. Different metabolites including sphingolipids, pyrans, prenol lipids, and isoflavonoids also showed significance between MDD and HC. We detected 48 significantly different ARGs: 5 ARGs up-regulated and 43 ARGs down-regulated in MDD compared to HC. Based on Cox model results, Three ARGs significantly affected drug efficacy (ARG29, ARG105, and ARG111). Eggerthella, Weissella, and Lactobacillus were correlated with different core ARGs, which indicated different mechanisms in affecting MDD. LIMITATIONS The present study needs to be replicated in different ethnic groups. At the same time, a larger Chinese cohort study and detailed experimental verification are also the key to further discussion. CONCLUSION Our findings suggest that ARGs play a role in the interplay between major depressive disorder and gut microbiota. The role of ARGs should be taken into account when understanding the relationship between depression and gut microbiota.
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Affiliation(s)
- Zaiquan Dong
- Mental Health Center, West China Hospital, Sichuan University, Chengdu 610041, PR China; Department of Psychiatry, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Ke Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, PR China; Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, PR China
| | - Qinglian Xie
- Department of outpatient, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Chunting Lin
- Huaxi MR Research Center (HMRRC), Department of Radiology, West China Hospital of Sichuan University, Chengdu 610041, PR China
| | - Xiaoling Shen
- Mental Health Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Yanni Hao
- Mental Health Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Jin Li
- Mental Health Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Haizhen Xu
- Mental Health Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, PR China; Shanghai Key Laboratory of Psychotic Disorders, Brain Science and Technology Research Center, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, PR China
| | - Tao Yu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai 200030, PR China; Shanghai Center for Women and Children's Health, 339 Luding Road, Shanghai 200062, PR China
| | - Weihong Kuang
- Mental Health Center, West China Hospital, Sichuan University, Chengdu 610041, PR China; Department of Psychiatry, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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20
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Ratsika A, Codagnone MG, Bastiaanssen TFS, Hoffmann Sarda FA, Lynch CMK, Ventura-Silva AP, Rosell-Cardona C, Caputi V, Stanton C, Fülling C, Cryan JF. Maternal high-fat diet-induced microbiota changes are associated with alterations in embryonic brain metabolites and adolescent behaviour. Brain Behav Immun 2024:S0889-1591(24)00489-6. [PMID: 39032541 DOI: 10.1016/j.bbi.2024.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 07/09/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
The developing central nervous system is highly sensitive to nutrient changes during the perinatal period, emphasising the potential impact of alterations of maternal diet on offspring brain development and behaviour. A growing body of research implicates the gut microbiota in neurodevelopment and behaviour. Maternal overweight and obesity during the perinatal period has been linked to changes in neurodevelopment, plasticity and affective disorders in the offspring, with implications for microbial signals from the maternal gut. Here we investigate the impact of maternal high-fat diet (mHFD)-induced changes in microbial signals on offspring brain development, and neuroimmune signals, and the enduring effects on behaviour into adolescence. We first demonstrate that maternal caecal microbiota composition at term pregnancy (embryonic day 18: E18) differs significantly in response to maternal diet. Moreover, mHFD resulted in the upregulation of microbial genes in the maternal intestinal tissue linked to alterations in quinolinic acid synthesis and elevated kynurenine levels in the maternal plasma, both neuronal plasticity mediators related to glutamate metabolism. Metabolomics of mHFD embryonic brains at E18 also detected molecules linked to glutamate-glutamine cycle, including glutamic acid, glutathione disulphide and kynurenine. During adolescence, the mHFD offspring exhibited increased locomotor activity and anxiety-like behaviour in a sex-dependent manner, along with upregulation of glutamate-related genes compared to controls. Overall, our results demonstrate that maternal exposure to high-fat diet results in microbiota changes, behavioural imprinting, altered brain metabolism and glutamate signalling during critical developmental windows during the perinatal period.
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Affiliation(s)
- Anna Ratsika
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Martin G Codagnone
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Thomaz F S Bastiaanssen
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Fabiana A Hoffmann Sarda
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Caoimhe M K Lynch
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland
| | - Ana Paula Ventura-Silva
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland
| | - Cristina Rosell-Cardona
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland
| | - Valentina Caputi
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland
| | | | - Christine Fülling
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland
| | - John F Cryan
- APC Microbiome Ireland, Biosciences Institute, University College Cork, Cork T12YT20, Ireland; Department of Anatomy and Neuroscience, University College Cork, Cork T12YT20, Ireland.
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Debray R, Dickson CC, Webb SE, Archie EA, Tung J. When is microbial strain sharing evidence for transmission? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604082. [PMID: 39071345 PMCID: PMC11275843 DOI: 10.1101/2024.07.18.604082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
In humans and other social animals, social partners have more similar microbiomes than expected by chance, suggesting that social contact transfers microorganisms. However, social microbiome transmission can be difficult to identify if social partners also have other traits in common or live in a shared environment. Strain-resolved metagenomics has been proposed as a solution for tracking microbial transmission. Using a fecal microbiota transplant dataset, we show that strain sharing can recapitulate true transmission networks under ideal settings when donor-recipient pairs are unambiguous. However, gut metagenomes from a wild baboon population, where social networks predict compositional similarity, show that strain sharing is also driven by demographic and environmental factors that can override signals of social interactions. We conclude that strain-level analyses provide useful information about microbiome similarity, but other facets of study design, especially longitudinal sampling and careful consideration of host characteristics, are essential for conclusions about the underlying mechanisms.
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Affiliation(s)
- Reena Debray
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, Germany
| | - Carly C Dickson
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Shasta E Webb
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jenny Tung
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Saxony, Germany
- Department of Biology, Duke University, Durham, North Carolina, USA
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
- Duke Population Research Institute, Duke University, Durham, North Carolina, USA
- Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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22
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Lee M, Kaul A, Ward JM, Zhu Q, Richards M, Wang Z, González A, Parks CG, Beane Freeman LE, Umbach DM, Motsinger-Reif AA, Knight R, London SJ. House dust metagenome and pulmonary function in a US farming population. MICROBIOME 2024; 12:129. [PMID: 39026261 PMCID: PMC11256371 DOI: 10.1186/s40168-024-01823-y] [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: 09/26/2023] [Accepted: 04/25/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Chronic exposure to microorganisms inside homes can impact respiratory health. Few studies have used advanced sequencing methods to examine adult respiratory outcomes, especially continuous measures. We aimed to identify metagenomic profiles in house dust related to the quantitative traits of pulmonary function and airway inflammation in adults. Microbial communities, 1264 species (389 genera), in vacuumed bedroom dust from 779 homes in a US cohort were characterized by whole metagenome shotgun sequencing. We examined two overall microbial diversity measures: richness (the number of individual microbial species) and Shannon index (reflecting both richness and relative abundance). To identify specific differentially abundant genera, we applied the Lasso estimator with high-dimensional inference methods, a novel framework for analyzing microbiome data in relation to continuous traits after accounting for all taxa examined together. RESULTS Pulmonary function measures (forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio) were not associated with overall dust microbial diversity. However, many individual microbial genera were differentially abundant (p-value < 0.05 controlling for all other microbial taxa examined) in relation to FEV1, FVC, or FEV1/FVC. Similarly, fractional exhaled nitric oxide (FeNO), a marker of airway inflammation, was unrelated to overall microbial diversity but associated with differential abundance for many individual genera. Several genera, including Limosilactobacillus, were associated with a pulmonary function measure and FeNO, while others, including Moraxella to FEV1/FVC and Stenotrophomonas to FeNO, were associated with a single trait. CONCLUSIONS Using state-of-the-art metagenomic sequencing, we identified specific microorganisms in indoor dust related to pulmonary function and airway inflammation. Some were previously associated with respiratory conditions; others were novel, suggesting specific environmental microbial components contribute to various respiratory outcomes. The methods used are applicable to studying microbiome in relation to other continuous outcomes. Video Abstract.
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Affiliation(s)
- Mikyeong Lee
- Immunity Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), Durham, NC, 27709, USA.
| | - Abhishek Kaul
- Department of Mathematics and Statistics, Washington State University, Pullman, WA, USA
| | - James M Ward
- Integrative Bioinformatics Support Group, NIEHS, Durham, NC, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | | | - Ziyue Wang
- Biostatistics and Computational Biology Branch, NIEHS, Durham, NC, USA
| | - Antonio González
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Christine G Parks
- Immunity Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), Durham, NC, 27709, USA
| | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - David M Umbach
- Biostatistics and Computational Biology Branch, NIEHS, Durham, NC, USA
| | | | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Stephanie J London
- Immunity Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), Durham, NC, 27709, USA
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23
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Dhariwal A, Rajar P, Salvadori G, Åmdal HA, Berild D, Saugstad OD, Fugelseth D, Greisen G, Dahle U, Haaland K, Petersen FC. Prolonged hospitalization signature and early antibiotic effects on the nasopharyngeal resistome in preterm infants. Nat Commun 2024; 15:6024. [PMID: 39019886 PMCID: PMC11255206 DOI: 10.1038/s41467-024-50433-7] [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: 09/13/2023] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
Respiratory pathogens, commonly colonizing nasopharynx, are among the leading causes of death due to antimicrobial resistance. Yet, antibiotic resistance determinants within nasopharyngeal microbial communities remain poorly understood. In this prospective cohort study, we investigate the nasopharynx resistome development in preterm infants, assess early antibiotic impact on its trajectory, and explore its association with clinical covariates using shotgun metagenomics. Our findings reveal widespread nasopharyngeal carriage of antibiotic resistance genes (ARGs) with resistomes undergoing transient changes, including increased ARG diversity, abundance, and composition alterations due to early antibiotic exposure. ARGs associated with the critical nosocomial pathogen Serratia marcescens persist up to 8-10 months of age, representing a long-lasting hospitalization signature. The nasopharyngeal resistome strongly correlates with microbiome composition, with inter-individual differences and postnatal age explaining most of the variation. Our report on the collateral effects of antibiotics and prolonged hospitalization underscores the urgency of further studies focused on this relatively unexplored reservoir of pathogens and ARGs.
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Affiliation(s)
- Achal Dhariwal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Polona Rajar
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
- Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Gabriela Salvadori
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Heidi Aarø Åmdal
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Dag Berild
- Department of Infectious Diseases, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | | | - Drude Fugelseth
- Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gorm Greisen
- Department of Neonatology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Ulf Dahle
- Centre for Antimicrobial Resistance, Norwegian Institute of Public Health, Oslo, Norway
| | - Kirsti Haaland
- Department of Neonatal Intensive Care, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
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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; 5:101624. [PMID: 38942021 PMCID: PMC11293350 DOI: 10.1016/j.xcrm.2024.101624] [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: 11/04/2023] [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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25
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Steimle A, Neumann M, Grant ET, Willieme S, De Sciscio A, Parrish A, Ollert M, Miyauchi E, Soga T, Fukuda S, Ohno H, Desai MS. Gut microbial factors predict disease severity in a mouse model of multiple sclerosis. Nat Microbiol 2024:10.1038/s41564-024-01761-3. [PMID: 39009690 DOI: 10.1038/s41564-024-01761-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Gut bacteria are linked to neurodegenerative diseases but the risk factors beyond microbiota composition are limited. Here we used a pre-clinical model of multiple sclerosis (MS), experimental autoimmune encephalomyelitis (EAE), to identify microbial risk factors. Mice with different genotypes and complex microbiotas or six combinations of a synthetic human microbiota were analysed, resulting in varying probabilities of severe neuroinflammation. However, the presence or relative abundances of suspected microbial risk factors failed to predict disease severity. Akkermansia muciniphila, often associated with MS, exhibited variable associations with EAE severity depending on the background microbiota. Significant inter-individual disease course variations were observed among mice harbouring the same microbiota. Evaluation of microbial functional characteristics and host immune responses demonstrated that the immunoglobulin A coating index of certain bacteria before disease onset is a robust individualized predictor of disease development. Our study highlights the need to consider microbial community networks and host-specific bidirectional interactions when aiming to predict severity of neuroinflammation.
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Affiliation(s)
- Alex Steimle
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Mareike Neumann
- 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
| | - Stéphanie Willieme
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Alessandro De Sciscio
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Amy Parrish
- 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
| | - Markus Ollert
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama City, Kanagawa, Japan
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis, University of Southern Denmark, Odense, Denmark.
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26
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Odriozola I, Rasmussen JA, Gilbert MTP, Limborg MT, Alberdi A. A practical introduction to holo-omics. CELL REPORTS METHODS 2024; 4:100820. [PMID: 38986611 PMCID: PMC11294832 DOI: 10.1016/j.crmeth.2024.100820] [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: 12/14/2023] [Revised: 04/17/2024] [Accepted: 06/20/2024] [Indexed: 07/12/2024]
Abstract
Holo-omics refers to the joint study of non-targeted molecular data layers from host-microbiota systems or holobionts, which is increasingly employed to disentangle the complex interactions between the elements that compose them. We navigate through the generation, analysis, and integration of omics data, focusing on the commonalities and main differences to generate and analyze the various types of omics, with a special focus on optimizing data generation and integration. We advocate for careful generation and distillation of data, followed by independent exploration and analyses of the single omic layers to obtain a better understanding of the study system, before the integration of multiple omic layers in a final model is attempted. We highlight critical decision points to achieve this aim and flag the main challenges to address complex biological questions regarding the integrative study of host-microbiota relationships.
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Affiliation(s)
- Iñaki Odriozola
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jacob A Rasmussen
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Morten T Limborg
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
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27
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Ewere EE, White S, Mauleon R, Benkendorff K. Soil microbial communities and degradation of pesticides in greenhouse effluent through a woodchip bioreactor. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 359:124561. [PMID: 39019308 DOI: 10.1016/j.envpol.2024.124561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 07/05/2024] [Accepted: 07/14/2024] [Indexed: 07/19/2024]
Abstract
Pesticides, including insecticides and fungicides, are major contaminants in the effluent from intensive agricultural systems, such as greenhouses. Because of their constant use and persistence, some pesticides can accumulate in soil and/or run off into adjacent waterways. Microbial communities in soil can degrade some pesticides, and bioreactors with enhanced microbial communities have the potential to facilitate decontamination before the effluent is released into the environment. In this study, we sampled the soil along a gradient from immediately below greenhouses, into, through and below a bioreactor. Multi-analyte pesticide screening was undertaken along with shotgun metagenomic sequencing, to assess microbial community taxonomic profiles and metabolic pathway responses for functional analysis. Two insecticides (imidacloprid and fipronil) and nine fungicides were identified in the soil samples, with a general decrease in most pesticides with increasing distance from the greenhouses. Diversity indexes of taxonomic profiles show changes in the microbial community along the gradient. In particular, microbial communities were significantly different in the bioreactor, with lower Shannon diversity compared to immediately below the greenhouses, in the channels leading into the bioreactor and further downstream. Metabolic pathway analysis revealed significant changes in a wide range of core housekeeping genes such as protein/amino acid synthesis and lipid/fatty acid biosynthesis among the sampling sites. The result demonstrates that the composition and potential functional pathways of the microbial community shifted towards an increased tendency for phytol and contaminant degradation in the bioreactor, facilitated by high organic matter content. This highlights the potential to use enhanced microbial communities within bioreactors to reduce contamination by some pesticides in sediment receiving run-off from greenhouses.
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Affiliation(s)
- Endurance E Ewere
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, 2450, Australia
| | - Shane White
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, 2450, Australia
| | - Ramil Mauleon
- Faculty of Science and Engineering, Southern Cross University, East Lismore, NSW, 2480, Australia
| | - Kirsten Benkendorff
- National Marine Science Centre, Southern Cross University, Coffs Harbour, NSW, 2450, Australia.
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28
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Özçam M, Lin DL, Gupta CL, Li A, Wheatley LM, Baloh CH, Sanda S, Jones SM, Lynch SV. Enhanced Gut Microbiome Capacity for Amino Acid Metabolism is associated with Peanut Oral Immunotherapy Failure. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24309840. [PMID: 39072014 PMCID: PMC11275660 DOI: 10.1101/2024.07.15.24309840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Peanut Oral Immunotherapy (POIT) holds promise for remission of peanut allergy, though treatment is protracted and successful in only a subset of patients. Because the gut microbiome is linked to food allergy, we sought to identify fecal microbial predictors of POIT efficacy and to develop mechanistic insights into treatment response. Longitudinal functional analysis of the fecal microbiome of children (n=79) undergoing POIT in a first double-blind, placebo-controlled clinical trial, identified five microbial-derived bile acids enriched in fecal samples prior to POIT initiation that predicted treatment efficacy (AUC 0.71). Failure to induce disease remission was associated with a distinct fecal microbiome with enhanced capacity for bile acid deconjugation, amino acid metabolism, and increased peanut peptide degradation in vitro . Thus, microbiome mechanisms of POIT failure appear to include depletion of immunomodulatory secondary bile and amino acids and the antigenic peanut peptides necessary to promote peanut allergy desensitization and remission.
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29
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Sun Y, Gan Z, Wang X, Liu J, Zhong W, Zhang Z, Zuo J, Zhong H, Huang X, Yan Z, Cao Q. Integrative metagenomic, transcriptomic, and proteomic analysis reveal the microbiota-host interplay in early-stage lung adenocarcinoma among non-smokers. J Transl Med 2024; 22:652. [PMID: 38997719 PMCID: PMC11245786 DOI: 10.1186/s12967-024-05485-0] [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: 12/15/2023] [Accepted: 07/03/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND The incidence of early-stage lung adenocarcinoma (ES-LUAD) is steadily increasing among non-smokers. Previous research has identified dysbiosis in the gut microbiota of patients with lung cancer. However, the local microbial profile of non-smokers with ES-LUAD remains largely unknown. In this study, we systematically characterized the local microbial community and its associated features to enable early intervention. METHODS A prospective collection of ES-LUAD samples (46 cases) and their corresponding normal tissues adjacent to the tumor (41 cases), along with normal lung tissue samples adjacent to pulmonary bullae in patients with spontaneous pneumothorax (42 cases), were subjected to ultra-deep metagenomic sequencing, host transcriptomic sequencing, and proteomic sequencing. The obtained omics data were subjected to both individual and integrated analysis using Spearman correlation coefficients. RESULTS We concurrently detected the presence of bacteria, fungi, and viruses in the lung tissues. The microbial profile of ES-LUAD exhibited similarities to NAT but demonstrated significant differences from the healthy controls (HCs), characterized by an overall reduction in species diversity. Patients with ES-LUAD exhibited local microbial dysbiosis, suggesting the potential pathogenicity of certain microbial species. Through multi-omics correlations, intricate local crosstalk between the host and local microbial communities was observed. Additionally, we identified a significant positive correlation (rho > 0.6) between Methyloversatilis discipulorum and GOLM1 at both the transcriptional and protein levels using multi-omics data. This correlated axis may be associated with prognosis. Finally, a diagnostic model composed of six bacterial markers successfully achieved precise differentiation between patients with ES-LUAD and HCs. CONCLUSIONS Our study depicts the microbial spectrum in patients with ES-LUAD and provides evidence of alterations in lung microbiota and their interplay with the host, enhancing comprehension of the pathogenic mechanisms that underlie ES-LUAD. The specific model incorporating lung microbiota can serve as a potential diagnostic tool for distinguishing between ES-LUAD and HCs.
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Affiliation(s)
- Yaohui Sun
- Department of Thoracic Surgery and Lung Transplantation, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Zhiming Gan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Xiaojin Wang
- Department of Thoracic Surgery and Lung Transplantation, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Jian Liu
- Department of Thoracic Surgery and Lung Transplantation, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Wei Zhong
- Department of Thoracic Surgery and Lung Transplantation, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Zhiyan Zhang
- Department of Thoracic Surgery and Lung Transplantation, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Jiebin Zuo
- Cardiovascular Disease Center, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Hang Zhong
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Xiuting Huang
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China
| | - Zhixiang Yan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.
| | - Qingdong Cao
- Department of Thoracic Surgery and Lung Transplantation, The Fifth Affiliated Hospital of Sun Yat-Sen University, Zhuhai, 519000, Guangdong, China.
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30
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Fishbein SRS, DeVeaux AL, Khanna S, Ferreiro AL, Liao J, Agee W, Ning J, Mahmud B, Wallace MJ, Hink T, Reske KA, Guruge J, Leekha S, Dubberke ER, Dantas G. Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603094. [PMID: 39026847 PMCID: PMC11257545 DOI: 10.1101/2024.07.11.603094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Gastrointestinal colonization by Clostridioides difficile is common in healthcare settings and ranges in clinical presentation from asymptomatic carriage to lethal C. difficile infection (CDI). We used a systems biology approach to investigate why patients colonized with C. difficile have a range of outcomes. Microbiota-humanization of germ-free mice with fecal samples from toxigenic C. difficile carriers revealed a spectrum of virulence among clade 1 lineages and identified commensal Blautia associated with markers of non-pathogenic colonization. Using gnotobiotic mice engrafted with defined human microbiota, we observed strain-specific CDI severity across clade 1 strains. Yet, mice engrafted with a higher diversity community were protected from severe disease across all strains without suppression of C. difficile colonization. These results indicate that when colonization resistance has been breached without overt infection, commensals can attenuate a diversity of virulent strains without inhibiting pathogen colonization, providing insight into determinants of stable C. difficile carriage.
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31
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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; 32:1177-1191.e7. [PMID: 38942027 PMCID: PMC11245731 DOI: 10.1016/j.chom.2024.06.003] [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: 11/16/2023] [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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32
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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; 32:1192-1206.e5. [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] [MESH Headings] [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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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 PMCID: PMC11231285 DOI: 10.1038/s41467-024-49958-8] [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: 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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Hwang J, Lee JH, Kim YJ, Hwang I, Kim YY, Kim HS, Park DY. Highly accurate measurement of the relative abundance of oral pathogenic bacteria using colony-forming unit-based qPCR. J Periodontal Implant Sci 2024; 54:54.e17. [PMID: 39058349 DOI: 10.5051/jpis.2304520226] [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: 12/05/2023] [Revised: 04/09/2024] [Accepted: 05/08/2024] [Indexed: 07/28/2024] Open
Abstract
PURPOSE Quantitative polymerase chain reaction (qPCR) has recently been employed to measure the number of bacterial cells by quantifying their DNA fragments. However, this method can yield inaccurate bacterial cell counts because the number of DNA fragments varies among different bacterial species. To resolve this issue, we developed a novel optimized qPCR method to quantify bacterial colony-forming units (CFUs), thereby ensuring a highly accurate count of bacterial cells. METHODS To establish a new qPCR method for quantifying 6 oral bacteria namely, Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, Fusobacterium nucleatum, and Streptococcus mutans, the most appropriate primer-probe sets were selected based on sensitivity and specificity. To optimize the qPCR for predicting bacterial CFUs, standard curves were produced by plotting bacterial CFU against Ct values. To validate the accuracy of the predicted CFU values, a spiking study was conducted to calculate the recovery rates of the predicted CFUs to the true CFUs. To evaluate the reliability of the predicted CFU values, the consistency between the optimized qPCR method and shotgun metagenome sequencing (SMS) was assessed by comparing the relative abundance of the bacterial composition. RESULTS For each bacterium, the selected primer-probe set amplified serial-diluted standard templates indicative of bacterial CFUs. The resultant Ct values and the corresponding bacterial CFU values were used to construct a standard curve, the linearity of which was determined by a coefficient of determination (r²) >0.99. The accuracy of the predicted CFU values was validated by recovery rates ranging from 95.1% to 106.8%. The reliability of the predicted CFUs was reflected by the consistency between the optimized qPCR and SMS, as demonstrated by a Spearman rank correlation coefficient (ρ) value of 1 for all 6 bacteria. CONCLUSIONS The CFU-based qPCR quantification method provides highly accurate and reliable quantitation of oral pathogenic bacteria.
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Affiliation(s)
- Jiyoung Hwang
- R&D Center, DOCSMEDI OralBiome Co. Ltd., Goyang, Korea
| | - Jeong-Hoo Lee
- R&D Center, DOCSMEDI OralBiome Co. Ltd., Goyang, Korea
| | - Yeon-Jin Kim
- R&D Center, DOCSMEDI OralBiome Co. Ltd., Goyang, Korea
| | - Inseong Hwang
- Apple Tree Institute of Biomedical Science, Apple Tree Medical Foundation, Goyang, Korea
| | - Young-Youn Kim
- Apple Tree Dental Hospital, Apple Tree Medical Foundation, Goyang, Korea
| | - Hye-Sung Kim
- Apple Tree Dental Hospital, Apple Tree Medical Foundation, Goyang, Korea
| | - Do-Young Park
- R&D Center, DOCSMEDI OralBiome Co. Ltd., Goyang, Korea.
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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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Piperni E, Nguyen LH, Manghi P, Kim H, Pasolli E, Andreu-Sánchez S, Arrè A, Bermingham KM, Blanco-Míguez A, Manara S, Valles-Colomer M, Bakker E, Busonero F, Davies R, Fiorillo E, Giordano F, Hadjigeorgiou G, Leeming ER, Lobina M, Masala M, Maschio A, McIver LJ, Pala M, Pitzalis M, Wolf J, Fu J, Zhernakova A, Cacciò SM, Cucca F, Berry SE, Ercolini D, Chan AT, Huttenhower C, Spector TD, Segata N, Asnicar F. Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries. Cell 2024:S0092-8674(24)00692-5. [PMID: 38981480 DOI: 10.1016/j.cell.2024.06.018] [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: 05/12/2023] [Revised: 02/23/2024] [Accepted: 06/11/2024] [Indexed: 07/11/2024]
Abstract
Diet impacts human health, influencing body adiposity and the risk of developing cardiometabolic diseases. The gut microbiome is a key player in the diet-health axis, but while its bacterial fraction is widely studied, the role of micro-eukaryotes, including Blastocystis, is underexplored. We performed a global-scale analysis on 56,989 metagenomes and showed that human Blastocystis exhibits distinct prevalence patterns linked to geography, lifestyle, and dietary habits. Blastocystis presence defined a specific bacterial signature and was positively associated with more favorable cardiometabolic profiles and negatively with obesity (p < 1e-16) and disorders linked to altered gut ecology (p < 1e-8). In a diet intervention study involving 1,124 individuals, improvements in dietary quality were linked to weight loss and increases in Blastocystis prevalence (p = 0.003) and abundance (p < 1e-7). Our findings suggest a potentially beneficial role for Blastocystis, which may help explain personalized host responses to diet and downstream disease etiopathogenesis.
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Affiliation(s)
- Elisa Piperni
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy
| | - Long H Nguyen
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Paolo Manghi
- Department CIBIO, University of Trento, Trento, Italy
| | - Hanseul Kim
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Edoardo Pasolli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alberto Arrè
- Department CIBIO, University of Trento, Trento, Italy; Zoe Ltd, London, UK
| | - Kate M Bermingham
- Zoe Ltd, London, UK; Department of Nutritional Sciences, King's College London, London, UK
| | | | - Serena Manara
- Department CIBIO, University of Trento, Trento, Italy
| | | | | | - Fabio Busonero
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | | | - Emily R Leeming
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Monia Lobina
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Andrea Maschio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Mauro Pala
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - Maristella Pitzalis
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | | | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Simone M Cacciò
- Department of Infectious Diseases, Istituto Superiore Di Sanità, Rome, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy; Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK
| | - Danilo Ercolini
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Harvard Chan Microbiome in Public Health Center, Boston, MA, USA
| | - Curtis Huttenhower
- Harvard T.H. Chan School of Public Health, Boston, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tim D Spector
- Department of Twins Research and Genetic Epidemiology, King's College London, London, UK
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy; IEO, Istituto Europeo di Oncologia IRCSS, Milan, Italy; Department of Twins Research and Genetic Epidemiology, King's College London, London, UK.
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Alfaifi AA, Holm JB, Wang TW, Lim J, Meiller TF, Rock P, Sultan AS, Jabra-Rizk MA. Oral Microbiota Alterations in Subjects with SARS-CoV-2 Displaying Prevalence of the Opportunistic Fungal Pathogen Candida albicans. Microorganisms 2024; 12:1356. [PMID: 39065125 PMCID: PMC11278750 DOI: 10.3390/microorganisms12071356] [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: 05/15/2024] [Revised: 06/19/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
The oral cavity remains an underappreciated site for SARS-CoV-2 infection despite the myriad of oral conditions in COVID-19 patients. Recently, SARS-CoV-2 was shown to replicate in the salivary gland cells causing tissue inflammation. Given the established association between inflammation and microbiome disruption, we comparatively profiled oral microbial differences at a metagenomic level in a cohort of hospitalized COVID-19 patients and matched healthy controls. Specifically, we aimed to evaluate colonization by the opportunistic fungal pathogen Candida albicans, the etiologic agent of oral candidiasis. Comprehensive shotgun metagenomic analysis indicated that, overall, COVID-19 patients exhibited significantly reduced bacterial and viral diversity/richness; we identified 12 differentially abundant bacterial species to be negatively associated with COVID-19, and the functional pathways of certain bacteria to be highly associated with COVID-19 status. Strikingly, C. albicans was recovered from approximately half of the COVID-19 subjects but not from any of the healthy controls. The prevalence of Candida is likely linked to immune hypo-dysregulation caused by COVID-19 favoring Candida proliferation, warranting investigations into the interplay between Candida and SARS-CoV2 and potential therapeutic approaches directed toward oral candidiasis. Collectively, our findings prompt a reassessment of oral opportunistic infection risks during COVID-19 disease and their potential long-term impacts on oral health.
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Affiliation(s)
- Areej A. Alfaifi
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland Baltimore, Baltimore, MD 21201, USA; (A.A.A.); (T.W.W.); (T.F.M.); (A.S.S.)
- Department of Restorative and Prosthetic Dental Sciences, College of Dentistry, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11426, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), Riyadh 11481, Saudi Arabia
| | - Johanna B. Holm
- Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (J.B.H.); (J.L.)
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Tristan W. Wang
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland Baltimore, Baltimore, MD 21201, USA; (A.A.A.); (T.W.W.); (T.F.M.); (A.S.S.)
| | - Jonathan Lim
- Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (J.B.H.); (J.L.)
| | - Timothy F. Meiller
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland Baltimore, Baltimore, MD 21201, USA; (A.A.A.); (T.W.W.); (T.F.M.); (A.S.S.)
- Greenebaum Cancer Center, University of Maryland, Baltimore, MD 21201, USA
| | - Peter Rock
- Department of Anesthesia, School of Medicine, University of Maryland, Baltimore, MD 21201, USA;
| | - Ahmed S. Sultan
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland Baltimore, Baltimore, MD 21201, USA; (A.A.A.); (T.W.W.); (T.F.M.); (A.S.S.)
- Greenebaum Cancer Center, University of Maryland, Baltimore, MD 21201, USA
| | - Mary Ann Jabra-Rizk
- Department of Oncology and Diagnostic Sciences, School of Dentistry, University of Maryland Baltimore, Baltimore, MD 21201, USA; (A.A.A.); (T.W.W.); (T.F.M.); (A.S.S.)
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
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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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Klauer RR, Hansen DA, Wu D, Monteiro LMO, Solomon KV, Blenner MA. Biological Upcycling of Plastics Waste. Annu Rev Chem Biomol Eng 2024; 15:315-342. [PMID: 38621232 DOI: 10.1146/annurev-chembioeng-100522-115850] [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] [Indexed: 04/17/2024]
Abstract
Plastic wastes accumulate in the environment, impacting wildlife and human health and representing a significant pool of inexpensive waste carbon that could form feedstock for the sustainable production of commodity chemicals, monomers, and specialty chemicals. Current mechanical recycling technologies are not economically attractive due to the lower-quality plastics that are produced in each iteration. Thus, the development of a plastics economy requires a solution that can deconstruct plastics and generate value from the deconstruction products. Biological systems can provide such value by allowing for the processing of mixed plastics waste streams via enzymatic specificity and using engineered metabolic pathways to produce upcycling targets. We focus on the use of biological systems for waste plastics deconstruction and upcycling. We highlight documented and predicted mechanisms through which plastics are biologically deconstructed and assimilated and provide examples of upcycled products from biological systems. Additionally, we detail current challenges in the field, including the discovery and development of microorganisms and enzymes for deconstructing non-polyethylene terephthalate plastics, the selection of appropriate target molecules to incentivize development of a plastic bioeconomy, and the selection of microbial chassis for the valorization of deconstruction products.
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Affiliation(s)
- Ross R Klauer
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - D Alex Hansen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - Derek Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | | | - Kevin V Solomon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
| | - Mark A Blenner
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware, USA; ,
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Zhang P, Shi H, Guo R, Li L, Guo X, Yang H, Chang D, Cheng Y, Zhao G, Li S, Zhong Q, Zhang H, Zhao P, Fu C, Song Y, Yang L, Wang Y, Zhang Y, Jiang J, Wang T, Zhao J, Li Y, Wang B, Chen F, Zhao H, Wang Y, Wang J, Ma S. Metagenomic analysis reveals altered gut virome and diagnostic potential in pancreatic cancer. J Med Virol 2024; 96:e29809. [PMID: 39016466 DOI: 10.1002/jmv.29809] [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: 01/24/2024] [Revised: 06/15/2024] [Accepted: 07/08/2024] [Indexed: 07/18/2024]
Abstract
Pancreatic cancer (PC) is a highly aggressive malignancy with a poor prognosis, making early diagnosis crucial for improving patient outcomes. While the gut microbiome, including bacteria and viruses, is believed to be essential in cancer pathogenicity, the potential contribution of the gut virome to PC remains largely unexplored. In this study, we conducted a comparative analysis of the gut viral compositional and functional profiles between PC patients and healthy controls, based on fecal metagenomes from two publicly available data sets comprising a total of 101 patients and 82 healthy controls. Our results revealed a decreasing trend in the gut virome diversity of PC patients with disease severity. We identified significant alterations in the overall viral structure of PC patients, with a meta-analysis revealing 219 viral operational taxonomic units (vOTUs) showing significant differences in relative abundance between patients and healthy controls. Among these, 65 vOTUs were enriched in PC patients, and 154 were reduced. Host prediction revealed that PC-enriched vOTUs preferentially infected bacterial members of Veillonellaceae, Enterobacteriaceae, Fusobacteriaceae, and Streptococcaceae, while PC-reduced vOTUs were more likely to infect Ruminococcaceae, Lachnospiraceae, Clostridiaceae, Oscillospiraceae, and Peptostreptococcaceae. Furthermore, we constructed random forest models based on the PC-associated vOTUs, achieving an optimal average area under the curve (AUC) of up to 0.879 for distinguishing patients from controls. Through additional 10 public cohorts, we demonstrated the reproducibility and high specificity of these viral signatures. Our study suggests that the gut virome may play a role in PC development and could serve as a promising target for PC diagnosis and therapeutic intervention. Future studies should further explore the underlying mechanisms of gut virus-bacteria interactions and validate the diagnostic models in larger and more diverse populations.
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Affiliation(s)
- Pan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Haitao Shi
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan, Hubei, China
| | - Lu Li
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Xiaoyan Guo
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Hui Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Danyan Chang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yan Cheng
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Gang Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan, Hubei, China
| | - Qingling Zhong
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Huan Zhang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ping Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Cui Fu
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yahua Song
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Longbao Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yan Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan, Hubei, China
| | - Jiong Jiang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ting Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Juhui Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yong Li
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Biyuan Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Fenrong Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Hongli Zhao
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Yonghua Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Jinhai Wang
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
| | - Shiyang Ma
- Department of Gastroenterology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Shaanxi Key Laboratory of Gastrointestinal Motility Disorders, Xi'an, Shaanxi, China
- Shaanxi Provincial Clinical Research Center for Gastrointestinal Diseases, Xi'an, Shaanxi, China
- Digestive Disease Quality Control Center of Shaanxi Province, Xi'an, Shaanxi, China
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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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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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43
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Lu Y, Zhang L, Liu X, Lan Y, Wu L, Wang J, Wu K, Yang C, Lv R, Yi D, Zhuo G, Li Y, Shen F, Hou R, Yue B, Fan Z. Red pandas with different diets and environments exhibit different gut microbial functional composition and capacity. Integr Zool 2024; 19:662-682. [PMID: 38420673 DOI: 10.1111/1749-4877.12813] [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] [Indexed: 03/02/2024]
Abstract
The red panda (Ailurus fulgens) is a distinctive mammal known for its reliance on a diet primarily consisting of bamboo. The gut microbiota and overall health of animals are strongly influenced by diets and environments. Therefore, conducting research to explore the taxonomical and functional variances within the gut microbiota of red pandas exposed to various dietary and environmental conditions could shed light on the dynamic complexities of their microbial communities. In this study, normal fecal samples were obtained from red pandas residing in captive and semi-free environments under different dietary regimes and used for metabolomic, 16S rRNA, and metagenomic sequencing analysis, with the pandas classified into four distinct cohorts according to diet and environment. In addition, metagenomic sequencing was conducted on mucus fecal samples to elucidate potential etiological agents of disease. Results revealed an increased risk of gastrointestinal diseases in red pandas consuming bamboo shoots due to the heightened presence of pathogenic bacteria, although an increased presence of microbiota-derived tryptophan metabolites appeared to facilitate intestinal balance. The red pandas fed bamboo leaves also exhibited a decrease in gut microbial diversity, which may be attributed to the antibacterial flavonoids and lower protein levels in leaves. Notably, red pandas residing in semi-free environments demonstrated an enriched gut microbial diversity. Moreover, the occurrence of mucus secretion may be due to an increased presence of species associated with diarrhea and a reduced level of microbiota-derived tryptophan metabolites. In summary, our findings substantiate the influential role of diet and environment in modulating the gut microbiota of red pandas, offering potential implications for improved captive breeding practices.
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Affiliation(s)
- Yunwei Lu
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Liang Zhang
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Xu Liu
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yue Lan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Lixia Wu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Jiao Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Kongju Wu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Chaojie Yang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
| | - Ruiqing Lv
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Dejiao Yi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Guifu Zhuo
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Yan Li
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Fujun Shen
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
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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: 4] [Impact Index Per Article: 4.0] [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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Lee CS, Lin CR, Chua HH, Wu JF, Chang KC, Ni YH, Chang MH, Chen HL. Gut Bifidobacterium longum is associated with better native liver survival in patients with biliary atresia. JHEP Rep 2024; 6:101090. [PMID: 39006502 PMCID: PMC11246047 DOI: 10.1016/j.jhepr.2024.101090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 03/08/2024] [Accepted: 04/03/2024] [Indexed: 07/16/2024] Open
Abstract
Background & Aims The gut microbiome plays an important role in liver diseases, but its specific impact on biliary atresia (BA) remains to be explored. We aimed to investigate the microbial signature in the early life of patients with BA and to analyze its influence on long-term outcomes. Methods Fecal samples (n = 42) were collected from infants with BA before and after Kasai portoenterostomy (KPE). The stool microbiota was analyzed using 16S rRNA next-generation sequencing and compared with that of age-matched healthy controls (HCs). Shotgun metagenomic sequencing analysis was employed to confirm the bacterial composition in 10 fecal samples before KPE. The correlation of the microbiome signature with liver function and long-term outcomes was assessed. Results In the 16S rRNA next-generation sequencing analysis of fecal microbiota, the alpha and beta diversity analyses revealed significant differences between HCs and patients with BA before and after KPE. The difference in microbial composition analyzed by linear discriminant analysis and random forest classification revealed that the abundance of Bifidobacterium longum (B. longum) was significantly lower in patients before and after KPE than in HCs. The abundance of B. longum was negatively correlated with the gamma-glutamyltransferase level after KPE (p <0.05). Patients with early detectable B. longum had significantly lower total and direct bilirubin 3 months after KPE (p <0.005) and had a significantly lower liver transplantation rate (hazard ratio: 0.16, 95% CI 0.03-0.83, p = 0.029). Shotgun metagenomic sequencing also revealed that patients with BA and detectable B. longum had reduced total and direct bilirubin after KPE. Conclusion The gut microbiome of patients with BA differed from that of HCs, with a notable abundance of B. longum in early infancy correlating with better long-term outcomes. Impact and implications Bifidobacterium longum (B. longum) is a beneficial bacterium commonly found in the human gut. It has been studied for its potential impacts on various health conditions. In patients with biliary atresia, we found that a greater abundance of B. longum in the fecal microbiome is associated with improved clinical outcomes. This suggests that early colonization and increasing B. longum levels in the gut could be a therapeutic strategy to improve the prognosis of patients with biliary atresia.
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Affiliation(s)
- Chee-Seng Lee
- Department of Pediatrics, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Ray Lin
- Department of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, Taipei, Taiwan
| | - Huey-Huey Chua
- Department of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, Taipei, Taiwan
| | - Jia-Feng Wu
- Department of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, Taipei, Taiwan
| | - Kai-Chi Chang
- Department of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, Taipei, Taiwan
| | - Yen-Hsuan Ni
- Department of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, Taipei, Taiwan
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
- Center of Genomic and Precision Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
- Medical Microbiota Center, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mei-Hwei Chang
- Department of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, Taipei, Taiwan
| | - Huey-Ling Chen
- Department of Pediatrics, National Taiwan University College of Medicine and Children's Hospital, Taipei, Taiwan
- Hepatitis Research Center, National Taiwan University Hospital, Taipei, Taiwan
- Department and Graduate Institute of Medical Education and Bioethics, National Taiwan University College of Medicine, Taipei, Taiwan
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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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47
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Bermingham KM, Linenberg I, Polidori L, Asnicar F, Arrè A, Wolf J, Badri F, Bernard H, Capdevila J, Bulsiewicz WJ, Gardner CD, Ordovas JM, Davies R, Hadjigeorgiou G, Hall WL, Delahanty LM, Valdes AM, Segata N, Spector TD, Berry SE. Effects of a personalized nutrition program on cardiometabolic health: a randomized controlled trial. Nat Med 2024; 30:1888-1897. [PMID: 38714898 PMCID: PMC11271409 DOI: 10.1038/s41591-024-02951-6] [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: 10/18/2023] [Accepted: 03/26/2024] [Indexed: 05/15/2024]
Abstract
Large variability exists in people's responses to foods. However, the efficacy of personalized dietary advice for health remains understudied. We compared a personalized dietary program (PDP) versus general advice (control) on cardiometabolic health using a randomized clinical trial. The PDP used food characteristics, individual postprandial glucose and triglyceride (TG) responses to foods, microbiomes and health history, to produce personalized food scores in an 18-week app-based program. The control group received standard care dietary advice (US Department of Agriculture Guidelines for Americans, 2020-2025) using online resources, check-ins, video lessons and a leaflet. Primary outcomes were serum low-density lipoprotein cholesterol and TG concentrations at baseline and at 18 weeks. Participants (n = 347), aged 41-70 years and generally representative of the average US population, were randomized to the PDP (n = 177) or control (n = 170). Intention-to-treat analysis (n = 347) between groups showed significant reduction in TGs (mean difference = -0.13 mmol l-1; log-transformed 95% confidence interval = -0.07 to -0.01, P = 0.016). Changes in low-density lipoprotein cholesterol were not significant. There were improvements in secondary outcomes, including body weight, waist circumference, HbA1c, diet quality and microbiome (beta-diversity) (P < 0.05), particularly in highly adherent PDP participants. However, blood pressure, insulin, glucose, C-peptide, apolipoprotein A1 and B, and postprandial TGs did not differ between groups. No serious intervention-related adverse events were reported. Following a personalized diet led to some improvements in cardiometabolic health compared to standard dietary advice. ClinicalTrials.gov registration: NCT05273268 .
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Affiliation(s)
- Kate M Bermingham
- Department of Nutritional Sciences, King's College London, London, UK
- Zoe Ltd, London, UK
| | - Inbar Linenberg
- Department of Nutritional Sciences, King's College London, London, UK
- Zoe Ltd, London, UK
| | | | - Francesco Asnicar
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | | | | | | | | | | | | | | | - Jose M Ordovas
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, USA
- IMDEA Food Institute, Campus of International Excellence, Universidad Autónoma de Madrid, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Universidad Camilo José Cela, Madrid, Spain
| | | | | | - Wendy L Hall
- Department of Nutritional Sciences, King's College London, London, UK
| | - Linda M Delahanty
- Diabetes Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ana M Valdes
- School of Medicine, University of Nottingham, Nottingham, UK
- Nottingham National Institute for Health and Care Research Biomedical Research Centre, Nottingham, UK
| | - Nicola Segata
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Tim D Spector
- Department of Nutritional Sciences, King's College London, London, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sarah E Berry
- Department of Nutritional Sciences, King's College London, London, UK.
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48
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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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49
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Maki KA, Wallen GR, Bastiaanssen TF, Hsu LY, Valencia ME, Ramchandani VA, Schwandt ML, Diazgranados N, Cryan JF, Momenan R, Barb JJ. The gut-brain axis in individuals with alcohol use disorder: An exploratory study of associations among clinical symptoms, brain morphometry, and the gut microbiome. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2024; 48:1261-1277. [PMID: 38982564 PMCID: PMC11239122 DOI: 10.1111/acer.15346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 07/11/2024]
Abstract
BACKGROUND Alcohol use disorder (AUD) is commonly associated with distressing psychological symptoms. Pathologic changes associated with AUD have been described in both the gut microbiome and brain, but the mechanisms underlying gut-brain signaling in individuals with AUD are unknown. This study examined associations among the gut microbiome, brain morphometry, and clinical symptoms in treatment-seeking individuals with AUD. METHODS We performed a secondary analysis of data collected during inpatient treatment for AUD in subjects who provided gut microbiome samples and had structural brain magnetic resonance imaging (MRI; n = 16). Shotgun metagenomics sequencing was performed, and the morphometry of brain regions of interest was calculated. Clinical symptom severity was quantified using validated instruments. Gut-brain modules (GBMs) used to infer neuroactive signaling potential from the gut microbiome were generated in addition to microbiome features (e.g., alpha diversity and bacterial taxa abundance). Bivariate correlations were performed between MRI and clinical features, microbiome and clinical features, and MRI and microbiome features. RESULTS Amygdala volume was significantly associated with alpha diversity and the abundance of several bacteria including taxa classified to Blautia, Ruminococcus, Bacteroides, and Phocaeicola. There were moderate associations between amygdala volume and GBMs, including butyrate synthesis I, glutamate synthesis I, and GABA synthesis I & II, but these relationships were not significant after false discovery rate (FDR) correction. Other bacterial taxa with shared associations to MRI features and clinical symptoms included Escherichia coli and Prevotella copri. CONCLUSIONS We identified gut microbiome features associated with MRI morphometry and AUD-associated symptom severity. Given the small sample size and bivariate associations performed, these results require confirmation in larger samples and controls to provide meaningful clinical inferences. Nevertheless, these results will inform targeted future research on the role of the gut microbiome in gut-brain communication and how signaling may be altered in patients with AUD.
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Affiliation(s)
- Katherine A. Maki
- Translational Biobehavioral and Health Disparities Branch, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Gwenyth R. Wallen
- Translational Biobehavioral and Health Disparities Branch, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Thomaz F.S. Bastiaanssen
- APC Microbiome Ireland and Department of Anatomy & Neuroscience, University College Cork, Cork, Ireland
| | - Li-Yueh Hsu
- Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael E. Valencia
- Translational Biobehavioral and Health Disparities Branch, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Vijay A. Ramchandani
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Melanie L. Schwandt
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Nancy Diazgranados
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - John F. Cryan
- APC Microbiome Ireland and Department of Anatomy & Neuroscience, University College Cork, Cork, Ireland
| | - Reza Momenan
- Clinical NeuroImaging Research Core, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer J. Barb
- Translational Biobehavioral and Health Disparities Branch, Clinical Center, National Institutes of Health, Bethesda, MD, USA
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50
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Leech SM, Borg DJ, Rae KM, Kumar S, Clifton VL, Dekker Nitert M. Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics. Microb Genom 2024; 10. [PMID: 38995243 DOI: 10.1099/mgen.0.001269] [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] [Indexed: 07/13/2024] Open
Abstract
Background. Previous research has shown that delivery mode can shape infant gut microbiome composition. However, mothers delivering by caesarean section routinely receive prophylactic antibiotics prior to delivery, resulting in antibiotic exposure to the infant via the placenta. Previously, only a small number of studies have examined the effect of delivery mode versus antibiotic exposure on the infant gut microbiome with mixed findings.Objective. We aimed to determine the effect of delivery mode compared to antibiotic use during labour and delivery on the infant and maternal gut microbiome at 6 weeks post-partum.Methodology. Twenty-five mother-infant dyads were selected from the longitudinal Queensland Family Cohort Study. The selected dyads comprised nine vaginally delivered infants without antibiotics, seven vaginally delivered infants exposed to antibiotics and nine infants born by caesarean section with routine maternal prophylactic antibiotics. Shotgun-metagenomic sequencing of DNA from stool samples collected at 6 weeks post-partum from mother and infant was used to assess microbiome composition.Results. Caesarean section infants exhibited decreases in Bacteroidetes (ANCOM-BC q<0.0001, MaAsLin 2 q=0.041), changes to several functional pathways and altered beta diversity (R 2=0.056, P=0.029), while minimal differences due to antibiotic exposure were detected. For mothers, caesarean delivery (P=0.0007) and antibiotic use (P=0.016) decreased the evenness of the gut microbiome at 6 weeks post-partum without changing beta diversity. Several taxa in the maternal microbiome were altered in association with antibiotic use, with few differentially abundant taxa associated with delivery mode.Conclusion. For infants, delivery mode appears to have a larger effect on gut microbiome composition at 6 weeks post-partum than intrapartum antibiotic exposure. For mothers, both delivery mode and intrapartum antibiotic use have a small effect on gut microbiome composition at 6 weeks post-partum.
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Affiliation(s)
- Sophie M Leech
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Danielle J Borg
- Pregnancy and Development Group, Mater Research Institute, South Brisbane, QLD, Australia
- Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
| | - Kym M Rae
- Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
- Indigenous Health Group, Mater Research Institute, South Brisbane, QLD, Australia
| | - Sailesh Kumar
- Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
- Mater Mothers' Hospital, Brisbane, QLD, Australia
| | - Vicki L Clifton
- Pregnancy and Development Group, Mater Research Institute, South Brisbane, QLD, Australia
- Faculty of Medicine, The University of Queensland, St Lucia, QLD, Australia
| | - Marloes Dekker Nitert
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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