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Li Y, Chen G, Hu X, Bao Y, Wu C, Zeng N, Jiang F. Assessing causal relationships between gut microbiota and psoriasis: evidence from two sample Mendelian randomization analysis. Sci Rep 2024; 14:8831. [PMID: 38632320 PMCID: PMC11024213 DOI: 10.1038/s41598-024-59603-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/12/2024] [Indexed: 04/19/2024] Open
Abstract
Mounting data hints that the gut microbiota's role may be pivotal in understanding the emergence of psoriasis. However, discerning a direct causal link is yet elusive. In this exploration, we adopted a Mendelian randomization (MR) strategy to probe the prospective causal interplay between the gut's microbial landscape and the predisposition to psoriasis. Genetic markers acting as instrumental variables for gut microbiota were extrapolated from a genome-wide association study (GWAS) encompassing 18,340 individuals. A separate GWAS yielded summary data for psoriasis, which covered 337,159 patients and 433,201 control subjects. The primary analysis hinged on inverse variance weighting (IVW). Additional methods like the weighted median approach and MR-Egger regression were employed to validate the integrity of our findings. Intriguing correlations emerged between psoriasis risk and eight specific bacterial traits. To illustrate: Mollicutes presented an odds ratio (OR) of 1.003 with a 95% confidence interval (CI) spanning 1.001-1.005 (p = 0.016), while the family. Victivallaceae revealed an OR of 0.998 with CI values between 0.997 and 0.999 (p = 0.023). Eubacterium (coprostanoligenes group) revealed an OR of 0.997 with CI values between 0.994 and 0.999 (p = 0.027). Eubacterium (fissicatena group) revealed an OR of 0.997 with CI values between 0.996 and 0.999 (p = 0.005). Holdemania revealed an OR of 1.001 with CI values 1-1.003 (p = 0.034). Lachnospiraceae (NK4A136 group) revealed an OR of 0.997 with CI values between 0.995 and 0.999 (p = 0.046). Lactococcus revealed an OR of 0.998 with CI values between 0.996 and 0.999 (p = 0.008). Tenericutes revealed an OR of 1.003 with CI values between 1.001 and 1.006 (p = 0.016). Sensitivity analysis for these bacterial features yielded congruent outcomes, reinforcing statistically significant ties between the eight bacterial entities and psoriasis. This comprehensive probe underscores emerging evidence pointing towards a plausible causal nexus between diverse gut microbiota and the onset of psoriasis. It beckons further research to unravel the intricacies of how the gut's microbial constituents might sway psoriasis's pathogenesis.
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Affiliation(s)
- Yuan Li
- Department of Dermatology, The Fifth People's Hospital of Hainan Province, Haikou, China
| | - Gaihe Chen
- Department of Dermatology, The Fifth People's Hospital of Hainan Province, Haikou, China
| | - Xiaohuan Hu
- Department of Dermatology, The Fifth People's Hospital of Hainan Province, Haikou, China
| | - Yunlei Bao
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chuyan Wu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
| | - Ni Zeng
- Department of Dermatology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, China.
| | - Feng Jiang
- Department of Neonatology, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China.
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Calle-García J, Ramayo-Caldas Y, Zingaretti LM, Quintanilla R, Ballester M, Pérez-Enciso M. On the holobiont 'predictome' of immunocompetence in pigs. Genet Sel Evol 2023; 55:29. [PMID: 37127575 PMCID: PMC10150480 DOI: 10.1186/s12711-023-00803-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/07/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Gut microbial composition plays an important role in numerous traits, including immune response. Integration of host genomic information with microbiome data is a natural step in the prediction of complex traits, although methods to optimize this are still largely unexplored. In this paper, we assess the impact of different modelling strategies on the predictive capacity for six porcine immunocompetence traits when both genotype and microbiota data are available. METHODS We used phenotypic data on six immunity traits and the relative abundance of gut bacterial communities on 400 Duroc pigs that were genotyped for 70 k SNPs. We compared the predictive accuracy, defined as the correlation between predicted and observed phenotypes, of a wide catalogue of models: reproducing kernel Hilbert space (RKHS), Bayes C, and an ensemble method, using a range of priors and microbial clustering strategies. Combined (holobiont) models that include both genotype and microbiome data were compared with partial models that use one source of variation only. RESULTS Overall, holobiont models performed better than partial models. Host genotype was especially relevant for predicting adaptive immunity traits (i.e., concentration of immunoglobulins M and G), whereas microbial composition was important for predicting innate immunity traits (i.e., concentration of haptoglobin and C-reactive protein and lymphocyte phagocytic capacity). None of the models was uniformly best across all traits. We observed a greater variability in predictive accuracies across models when microbiability (the variance explained by the microbiome) was high. Clustering microbial abundances did not necessarily increase predictive accuracy. CONCLUSIONS Gut microbiota information is useful for predicting immunocompetence traits, especially those related to innate immunity. Modelling microbiome abundances deserves special attention when microbiability is high. Clustering microbial data for prediction is not recommended by default.
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Affiliation(s)
- Joan Calle-García
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain
| | - Yuliaxis Ramayo-Caldas
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - Laura M Zingaretti
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain
| | - Raquel Quintanilla
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - María Ballester
- Animal Breeding and Genetics Program, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, 08140, Barcelona, Spain
| | - Miguel Pérez-Enciso
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Campus UAB, Edifici CRAG, 08193, Bellaterra, Spain.
- ICREA, Passeig Lluis Companys 23, 08010, Barcelona, Spain.
- Corteva Agriscience, Virtual Location, Bergen op Zoom, Indianapolis, 4611 BB, Netherlands.
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Aziz I, Noreen Z, Ijaz UZ, Gundogdu O, Hamid MH, Muhammad N, Khan A, Bokhari H. A prospective study on linking diarrheagenic E. coli with stunted childhood growth in relation to gut microbiome. Sci Rep 2023; 13:6802. [PMID: 37185286 PMCID: PMC10133260 DOI: 10.1038/s41598-023-32491-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 03/28/2023] [Indexed: 05/17/2023] Open
Abstract
Stunted growth is an emerging global challenge affecting children under the age of 5 years in low- and middle-income countries. Despite such a high global prevalence of stunting, the mechanism of pathogenesis and the role of associated gut microbiota is poorly understood. The present study was designed to investigate the association of pathogenic strains of E. coli with the residential gut microbiota of stunted growth children. A total of 64 stool sample were collected from children aged ≤ 5 years, and were processed for isolation and molecular characterization of diarrheagenic E. coli. Selected stool samples (n = 39 including three normal controls) were then analysed for microbial community profiling using 16S ribosomal RNA (rRNA) gene sequencing. Furthermore, associations between changes in the microbiota in the presence of different E. coli strains was explored. Pathotyping of the isolated E. coli (n = 64) has shown that 39.68% belonged to one of the five pathotypes of E. coli whilst the remaining ones were non-typeable. Amongst the different pathotypes, EPEC was found to be the most prevalent (52%; n = 13), followed by EAEC (20%; n = 5), EIEC (12%; n = 3), EHEC (8%; n = 2) and ETEC 2 (8%; n = 2). Phylogrouping analysis has shown that majority of the strains belonged to B2 (28.12%). Microbial diversity is shown to be significant and varied when the samples are organized under the recovered phylogroups. Moreover, based on predictive metabolism, the colonization of these strains were found to be significantly associated with energy utilization pathways such as Denovoprine-2 and glyoxylate-by. Differential analysis has shown that Escherichia-Shigella and Enterococcus were altered for the children with stunted growth.
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Affiliation(s)
- Israr Aziz
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | - Zobia Noreen
- Department of Biosciences, COMSATS University, Islamabad, Pakistan
| | | | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Muhammad Haroon Hamid
- Department of Pediatrics/Department of Preventive Pediatrics, Mayo Hospital, King Edward Medical University, Lahore, Pakistan
| | - Nazir Muhammad
- Department of Pediatrics/Department of Preventive Pediatrics, Mayo Hospital, King Edward Medical University, Lahore, Pakistan
| | - Abdullah Khan
- Paediatric Unit, Saidu Teaching Hospitals, Swat, Saidu Sharif, Pakistan
| | - Habib Bokhari
- Department of Biosciences, COMSATS University, Islamabad, Pakistan.
- Department of Biosciences, Kohsar University, Murree, Pakistan.
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Vijay-Kumar M, Bovilla VR, Yeoh BS, Golonka RM, Saha P, Joe B, Gewirtz AT. Bacterial flagellin is a dominant, stable innate immune activator in the gastrointestinal contents of mice and rats. Gut Microbes 2023; 15:2185031. [PMID: 36880647 PMCID: PMC10012918 DOI: 10.1080/19490976.2023.2185031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 02/21/2023] [Indexed: 03/08/2023] Open
Abstract
Intestinal contents comprise the largest repository of immunogenic ligands of microbial origin. We undertook this study to assess the predominant microbe-associated molecular patterns (MAMPs) present therein and the receptors) that mediate the innate immune responses to them. Here, we demonstrated that intestinal contents from conventional, but not germ-free, mice and rats triggered robust innate immune responses in vitro and in vivo. Such immune responses were abrogated in the absence of either myeloid differentiation factor 88 (MyD88) or Toll-like receptor (TLR) 5, but not TLR4, suggesting that the stimuli was flagellin (i.e., protein subunit of flagella that drives bacterial motility). Accordingly, pre-treating intestinal extracts with proteinase, thereby degrading flagellin, was sufficient to block their ability to activate innate immune responses. Taken together, this work serves to underscore flagellin as a major, heat-stable and bioactive MAMP in the intestinal content that confers this milieu strong potential to trigger innate immune responses.
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Affiliation(s)
- Matam Vijay-Kumar
- UT Microbiome Consortium, Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Venugopal R. Bovilla
- UT Microbiome Consortium, Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Beng San Yeoh
- UT Microbiome Consortium, Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Rachel M. Golonka
- UT Microbiome Consortium, Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Piu Saha
- UT Microbiome Consortium, Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Bina Joe
- UT Microbiome Consortium, Department of Physiology & Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Andrew T. Gewirtz
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
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Shaffer M, Thurimella K, Sterrett JD, Lozupone CA. SCNIC: Sparse correlation network investigation for compositional data. Mol Ecol Resour 2023; 23:312-325. [PMID: 36001047 PMCID: PMC9744196 DOI: 10.1111/1755-0998.13704] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 12/14/2022]
Abstract
Microbiome studies are often limited by a lack of statistical power due to small sample sizes and a large number of features. This problem is exacerbated in correlative studies of multi-omic datasets. Statistical power can be increased by finding and summarizing modules of correlated observations, which is one dimensionality reduction method. Additionally, modules provide biological insight as correlated groups of microbes can have relationships among themselves. To address these challenges, we developed SCNIC: Sparse Cooccurrence Network Investigation for compositional data. SCNIC is open-source software that can generate correlation networks and detect and summarize modules of highly correlated features. Modules can be formed using either the Louvain Modularity Maximization (LMM) algorithm or a Shared Minimum Distance algorithm (SMD) that we newly describe here and relate to LMM using simulated data. We applied SCNIC to two published datasets and we achieved increased statistical power and identified microbes that not only differed across groups, but also correlated strongly with each other, suggesting shared environmental drivers or cooperative relationships among them. SCNIC provides an easy way to generate correlation networks, identify modules of correlated features and summarize them for downstream statistical analysis. Although SCNIC was designed considering properties of microbiome data, such as compositionality and sparsity, it can be applied to a variety of data types including metabolomics data and used to integrate multiple data types. SCNIC allows for the identification of functional microbial relationships at scale while increasing statistical power through feature reduction.
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Affiliation(s)
- Michael Shaffer
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kumar Thurimella
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA,Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - John D. Sterrett
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | - Catherine A. Lozupone
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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Scarsella E, Jha A, Sandri M, Stefanon B. Network-based gut microbiome analysis in dogs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1080/1828051x.2022.2124932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Elisa Scarsella
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Aashish Jha
- Genetic Heritage Group, Program in Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Misa Sandri
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, Udine, Italy
| | - Bruno Stefanon
- Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, Udine, Italy
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Jebessa E, Guo L, Chen X, Bello SF, Cai B, Girma M, Hanotte O, Nie Q. Influence of Eimeria maxima coccidia infection on gut microbiome diversity and composition of the jejunum and cecum of indigenous chicken. Front Immunol 2022; 13:994224. [PMID: 36131927 PMCID: PMC9483182 DOI: 10.3389/fimmu.2022.994224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Coccidiosis is an economically significant protozoan disease and an intracellular parasite that significantly impacts poultry production. The gastrointestinal tract microbiota plays a central role in host health and metabolism, and these microbes enhance chickens’ immune systems and nutrient absorption. In this study, we analyzed the abundance and diversity of microbiota of the jejunum and cecum of a dual-purpose indigenous Horro chicken following Eimeria maxima infection. We compared microbial abundance, composition, and diversity at the 4- and 7- days post-infection using 16S rRNA gene sequencing. We obtained, on average, 147,742 and 132,986 high-quality sequences per sample for jejunum and cecum content, respectively. Firmicutes, Proteobacteria, Campilobacterota and Bacteroidota were the major microbial phylum detected in the jejunum content. Firmicutes were the dominant phylum for 4- and 7-days jejunum control groups accounting for (>60% of the sequences). In the infected group Campilobacterota was the dominant phylum in the jejunum (> 24% of sequences) at 4-and 7-days post-infection groups, while Proteobacteria was predominant at 4- and 7-days post-infection of the cecum (> 40% of the sequences). The microbial genus Lactobacillus and Helicobacter were found in the jejunum, while Alistipes, Barnesiella and Faecalibacterium were detected in the cecum. In the jejunum, Helicobacter was dominant at 4 -and-7 days post-infection (≥24%), and Lactobacillus was dominant at 4 -and 7- days in the control group (> 50%). In 4- and 7-days post-infection, Alistipes genus was the more prevalent (> 38%) in the cecum. Thus, clear differences were observed in the bacterial microbiota distribution and abundance between the jejunum and cecum, as well as between infected and control groups for both tissues. The results indicate that chicken intestinal microbial imbalance (dysbiosis) is associated with Eimeria parasite infection and will likely affect the host-microbial non-pathogenic and pathogenic molecular interactions.
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Affiliation(s)
- Endashaw Jebessa
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- LiveGene – Centre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Lijin Guo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Xiaolan Chen
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Bolin Cai
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
| | - Mekonnen Girma
- LiveGene – Centre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | - Olivier Hanotte
- LiveGene – Centre for Tropical Livestock Genetics and Health (CTLGH), International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
- School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
- *Correspondence: Qinghua Nie, ; Olivier Hanotte, ,
| | - Qinghua Nie
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou, China
- *Correspondence: Qinghua Nie, ; Olivier Hanotte, ,
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Impacts of Circadian Gene Period2 Knockout on Intestinal Metabolism and Hepatic Antioxidant and Inflammation State in Mice. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7896371. [PMID: 35910841 PMCID: PMC9325607 DOI: 10.1155/2022/7896371] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/19/2022] [Accepted: 06/17/2022] [Indexed: 11/26/2022]
Abstract
The period circadian regulator 2 (Per2) gene is important for the modulations of rhythmic homeostasis in the gut and liver; disruption will cause metabolic diseases, such as obesity, diabetes, and fatty liver. Herein, we investigated the alterations in intestinal metabolic and hepatic functions in Per2 knockout (Per2−/−, KO) and wild-type (Per2+/+, WT) mice. Growth indices, intestinal metabolomics, hepatic circadian rhythms, lipid metabolism, inflammation-related genes, antioxidant capacity, and transcriptome sequencing were performed after euthanasia. Data indicated that KO decreased the intestinal concentrations of amino acids such as γ-aminobutyric acid, aspartic acid, glycine, L-allothreonine, methionine, proline, serine, and valine while it increased the concentrations of carbohydrates such as cellobiose, D-talose, fucose, lyxose, and xylose compared with WT. Moreover, the imbalance of intestinal metabolism further seemed to induce liver dysfunction. Data indicated that Per2 knockout altered the expression of hepatic circadian rhythm genes, such as Clock, Bmal1, Per1, Per3, Cry1, and Cry2. KO also induced hepatic lipid metabolism, because of the increase of liver index and serum concentrations of low-density lipoprotein, and the upregulated expression of Pparα, Cyp7a1, and Cpt1. In addition, KO improved hepatic antioxidant capacity due to the increase activities of SOD and GSH-Px and the decrease in concentrations of MDA. Lastly, KO increased the relative expression levels of hepatic inflammation-related genes, such as Il-1β, Il-6, Tnf-α, Myd88, and Nf-κB p65, which may potentially lead to hepatic inflammation. Overall, Per2 knockout induces gut metabolic dysregulation and may potentially trigger alterations in hepatic antioxidant and inflammation responses.
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Moroishi Y, Gui J, Hoen AG, Morrison HG, Baker ER, Nadeau KC, Li H, Li Z, Madan JC, Karagas MR. The relationship between the gut microbiome and the risk of respiratory infections among newborns. COMMUNICATIONS MEDICINE 2022; 2:87. [PMID: 35847562 PMCID: PMC9283516 DOI: 10.1038/s43856-022-00152-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 06/27/2022] [Indexed: 12/15/2022] Open
Abstract
Background Emerging evidence points to a critical role of the developing gut microbiome in immune maturation and infant health; however, prospective studies are lacking. Methods We examined the occurrence of infections and associated symptoms during the first year of life in relation to the infant gut microbiome at six weeks of age using bacterial 16S rRNA V4-V5 gene sequencing (N = 465) and shotgun metagenomics (N = 185). We used generalized estimating equations to assess the associations between longitudinal outcomes and 16S alpha diversity and metagenomics species. Results Here we show higher infant gut microbiota alpha diversity was associated with an increased risk of infections or respiratory symptoms treated with a prescription medicine, and specifically upper respiratory tract infections. Among vaginally delivered infants, a higher alpha diversity was associated with an increased risk of all-cause wheezing treated with a prescription medicine and diarrhea involving a visit to a health care provider. Positive associations were specifically observed with Veillonella species among all deliveries and Haemophilus influenzae among cesarean-delivered infants. Conclusion Our findings suggest that intestinal microbial diversity and the relative abundance of key taxa in early infancy may influence susceptibility to respiratory infection, wheezing, and diarrhea.
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Affiliation(s)
- Yuka Moroishi
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH USA
| | - Hilary G. Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA USA
| | - Emily R. Baker
- Department of Obstetrics and Gynecology, Dartmouth-Hitchcock Medical Center, Lebanon, NH USA
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, CA USA
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Zhigang Li
- Department of Biostatistics, University of Florida, Gainesville, FL USA
| | - Juliette C. Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
- Department of Pediatrics, Children’s Hospital at Dartmouth, Lebanon, NH USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH USA
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The Gut Microbiota and Vascular Aging: A State-of-the-Art and Systematic Review of the Literature. J Clin Med 2022; 11:jcm11123557. [PMID: 35743626 PMCID: PMC9224769 DOI: 10.3390/jcm11123557] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 12/15/2022] Open
Abstract
The gut microbiota is a critical regulator of human physiology, deleterious changes to its composition and function (dysbiosis) have been linked to the development and progression of cardiovascular diseases. Vascular ageing (VA) is a process of progressive stiffening of the arterial tree associated with arterial wall remodeling, which can precede hypertension and organ damage, and is associated with cardiovascular risk. Arterial stiffness has become the preferred marker of VA. In our systematic review, we found an association between gut microbiota composition and arterial stiffness, with two patterns, in most animal and human studies: a direct correlation between arterial stiffness and abundances of bacteria associated with altered gut permeability and inflammation; an inverse relationship between arterial stiffness, microbiota diversity, and abundances of bacteria associated with most fit microbiota composition. Interventional studies were able to show a stable link between microbiota modification and arterial stiffness only in animals. None of the human interventional trials was able to demonstrate this relationship, and very few adjusted the analyses for determinants of arterial stiffness. We observed a lack of large randomized interventional trials in humans that test the role of gut microbiota modifications on arterial stiffness, and take into account BP and hemodynamic alterations.
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Abstract
Disturbances in the primary colonization of the infant gut can result in lifelong consequences and have been associated with a range of host conditions. Although early-life factors have been shown to affect infant gut microbiota development, our current understanding of human gut colonization in early life remains limited. To gain more insights into the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (n = 303 total samples). To evaluate the gut microbiota maturation transition toward an adult configuration, we compared the microbiome composition of the infants to that of the Flemish Gut Flora Project (FGFP) population (n = 1,106). We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, the genus predominance was observed to shift from Escherichia over Bifidobacterium to Bacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like constellations, microbiome community typing against the background of the FGFP cohort clustered all infant samples within the (in adults) potentially dysbiotic Bacteroides 2 (Bact2) enterotype. We confirmed the similarities between infant gut microbial colonization and adult dysbiosis. Profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected.
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Belkina TV, Averina OV, Savenkova EV, Danilenko VN. Human Intestinal Microbiome and the Immune System: The Role of Probiotics in Shaping an Immune System Unsusceptible to COVID-19 Infection. BIOLOGY BULLETIN REVIEWS 2021. [PMCID: PMC8365270 DOI: 10.1134/s2079086421040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- T. V. Belkina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - O. V. Averina
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - E. V. Savenkova
- International Institute for Strategic Development of Sectoral Economics, Peoples’ Friendship University of Russia (RUDN), Moscow, Russia
| | - V. N. Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- International Institute for Strategic Development of Sectoral Economics, Peoples’ Friendship University of Russia (RUDN), Moscow, Russia
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13
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Jin Y, Yu S, Kim DH, Yun EJ, Kim KH. Characterization of Neoagarooligosaccharide Hydrolase BpGH117 from a Human Gut Bacterium Bacteroides plebeius. Mar Drugs 2021; 19:md19050271. [PMID: 34068166 PMCID: PMC8152962 DOI: 10.3390/md19050271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 12/17/2022] Open
Abstract
α-Neoagarobiose (NAB)/neoagarooligosaccharide (NAO) hydrolase plays an important role as an exo-acting 3,6-anhydro-α-(1,3)-L-galactosidase in agarose utilization. Agarose is an abundant polysaccharide found in red seaweeds, comprising 3,6-anhydro-L-galactose (AHG) and D-galactose residues. Unlike agarose degradation, which has been reported in marine microbes, recent metagenomic analysis of Bacteroides plebeius, a human gut bacterium, revealed the presence of genes encoding enzymes involved in agarose degradation, including α-NAB/NAO hydrolase. Among the agarolytic enzymes, BpGH117 has been partially characterized. Here, we characterized the exo-acting α-NAB/NAO hydrolase BpGH117, originating from B. plebeius. The optimal temperature and pH for His-tagged BpGH117 activity were 35 °C and 9.0, respectively, indicative of its unique origin. His-tagged BpGH117 was thermostable up to 35 °C, and the enzyme activity was maintained at 80% of the initial activity at a pre-incubation temperature of 40 °C for 120 min. Km and Vmax values for NAB were 30.22 mM and 54.84 U/mg, respectively, and kcat/Km was 2.65 s−1 mM−1. These results suggest that His-tagged BpGH117 can be used for producing bioactive products such as AHG and agarotriose from agarose efficiently.
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Yun EJ, Yu S, Kim YA, Liu JJ, Kang NJ, Jin YS, Kim KH. In Vitro Prebiotic and Anti-Colon Cancer Activities of Agar-Derived Sugars from Red Seaweeds. Mar Drugs 2021; 19:md19040213. [PMID: 33921308 PMCID: PMC8070132 DOI: 10.3390/md19040213] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 01/09/2023] Open
Abstract
Numerous health benefits of diets containing red seaweeds or agar-derived sugar mixtures produced by enzymatic or acid hydrolysis of agar have been reported. However, among various agar-derived sugars, the key components that confer health-beneficial effects, such as prebiotic and anti-colon cancer activities, remain unclear. Here, we prepared various agar-derived sugars by multiple enzymatic reactions using an endo-type and an exo-type of β-agarase and a neoagarobiose hydrolase and tested their in vitro prebiotic and anti-colon cancer activities. Among various agar-derived sugars, agarotriose exhibited prebiotic activity that was verified based on the fermentability of agarotriose by probiotic bifidobacteria. Furthermore, we demonstrated the anti-colon cancer activity of 3,6-anhydro-l-galactose, which significantly inhibited the proliferation of human colon cancer cells and induced their apoptosis. Our results provide crucial information regarding the key compounds derived from red seaweeds that confer beneficial health effects, including prebiotic and anti-colon cancer activities, to the host.
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Affiliation(s)
- Eun Ju Yun
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Korea; (E.J.Y.); (S.Y.)
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Sora Yu
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Korea; (E.J.Y.); (S.Y.)
| | - Young-Ah Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (Y.-A.K.); (N.J.K.)
| | - Jing-Jing Liu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nam Joo Kang
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea; (Y.-A.K.); (N.J.K.)
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: (Y.-S.J.); (K.H.K.)
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02841, Korea; (E.J.Y.); (S.Y.)
- Correspondence: (Y.-S.J.); (K.H.K.)
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15
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Ma Z(S. Niche-neutral theoretic approach to mechanisms underlying the biodiversity and biogeography of human microbiomes. Evol Appl 2021; 14:322-334. [PMID: 33664779 PMCID: PMC7896709 DOI: 10.1111/eva.13116] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/05/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
The human microbiome consists of five major regional biomes distributed in or on our five body sites including skin, oral, lung, gut, and reproductive tract. Its biogeography (the spatial and temporal distribution of its biodiversity) has far-reaching implications to our health and diseases. Nevertheless, we currently have very limited understanding on the mechanisms shaping the biogeography, since it is often rather difficult to determine the relative importance of drift, dispersal, speciation, and selection, the four processes (mechanisms) determining the patterns of microbial biogeography and community dynamics according to a recent synthesis in community ecology and biogeography. To disentangle these mechanisms, I utilize multisite neutral (MSN) model and niche-neutral hybrid (NNH) model to analyze large number of truly multisite microbiome samples covering all five major human microbiome habitats, including 699 metacommunities and 5,420 local communities. Approximately 89% of metacommunities and 92% local communities exhibit patterns indistinguishable from neutral, and 20% indistinguishable from niche-neutral hybrid model, indicating the relative significance of stochastic neutral forces versus deterministic niche selection in shaping the biogeography of human microbiome. These findings cast supporting evidence to van der Gast's revision to classic Bass-Becking doctrine of microbial biogeography: "Some things are everywhere and some things are not. Sometimes the environment selects and sometimes it doesn't," offering the first educated guess for "some" and "sometimes" in the revised doctrine. Furthermore, the logistic/Cox regression models describing the relationships among community neutrality, niche differentiation, and key community/species characteristics (including community diversity, community/species dominance, speciation, and migration rates) were constructed to quantitatively describe the niche-neutral continuum and the influences of community/species properties on the continuum.
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Affiliation(s)
- Zhanshan (Sam) Ma
- Computational Biology and Medical Ecology LabState Key Laboratory of Genetic Resources and EvolutionKunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
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16
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Badri M, Kurtz ZD, Bonneau R, Müller CL. Shrinkage improves estimation of microbial associations under different normalization methods. NAR Genom Bioinform 2020; 2:lqaa100. [PMID: 33575644 PMCID: PMC7745771 DOI: 10.1093/nargab/lqaa100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 10/27/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Estimation of statistical associations in microbial genomic survey count data is fundamental to microbiome research. Experimental limitations, including count compositionality, low sample sizes and technical variability, obstruct standard application of association measures and require data normalization prior to statistical estimation. Here, we investigate the interplay between data normalization, microbial association estimation and available sample size by leveraging the large-scale American Gut Project (AGP) survey data. We analyze the statistical properties of two prominent linear association estimators, correlation and proportionality, under different sample scenarios and data normalization schemes, including RNA-seq analysis workflows and log-ratio transformations. We show that shrinkage estimation, a standard statistical regularization technique, can universally improve the quality of taxon-taxon association estimates for microbiome data. We find that large-scale association patterns in the AGP data can be grouped into five normalization-dependent classes. Using microbial association network construction and clustering as downstream data analysis examples, we show that variance-stabilizing and log-ratio approaches enable the most taxonomically and structurally coherent estimates. Taken together, the findings from our reproducible analysis workflow have important implications for microbiome studies in multiple stages of analysis, particularly when only small sample sizes are available.
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Affiliation(s)
- Michelle Badri
- Department of Biology, New York University, New York, NY 10012, USA
| | | | - Richard Bonneau
- Department of Biology, New York University, New York, NY 10012, USA
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Computer Science Department, Courant Institute, New York, NY 10012, USA
| | - Christian L Müller
- Center for Computational Mathematics, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg 85764, Germany
- Department of Statistics, Ludwig-Maximilians-Universität München, Munich 80539, Germany
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17
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Reider SJ, Moosmang S, Tragust J, Trgovec-Greif L, Tragust S, Perschy L, Przysiecki N, Sturm S, Tilg H, Stuppner H, Rattei T, Moschen AR. Prebiotic Effects of Partially Hydrolyzed Guar Gum on the Composition and Function of the Human Microbiota-Results from the PAGODA Trial. Nutrients 2020; 12:nu12051257. [PMID: 32354152 PMCID: PMC7281958 DOI: 10.3390/nu12051257] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 12/13/2022] Open
Abstract
(1) Background: Alterations in the structural composition of the human gut microbiota have been identified in various disease entities along with exciting mechanistic clues by reductionist gnotobiotic modeling. Improving health by beneficially modulating an altered microbiota is a promising treatment approach. Prebiotics, substrates selectively used by host microorganisms conferring a health benefit, are broadly used for dietary and clinical interventions. Herein, we sought to investigate the microbiota-modelling effects of the soluble fiber, partially hydrolyzed guar gum (PHGG). (2) Methods: We performed a 9 week clinical trial in 20 healthy volunteers that included three weeks of a lead-in period, followed by three weeks of an intervention phase, wherein study subjects received 5 g PHGG up to three times per day, and concluding with a three-week washout period. A stool diary was kept on a daily basis, and clinical data along with serum/plasma and stool samples were collected on a weekly basis. PHGG-induced alterations of the gut microbiota were studied by 16S metagenomics of the V1–V3 and V3–V4 regions. To gain functional insight, we further studied stool metabolites using nuclear magnetic resonance (NMR) spectroscopy. (3) Results: In healthy subjects, PHGG had significant effects on stool frequency and consistency. These effects were paralleled by changes in α- (species evenness) and β-diversity (Bray–Curtis distances), along with increasing abundances of metabolites including butyrate, acetate and various amino acids. On a taxonomic level, PHGG intake was associated with a bloom in Ruminococcus, Fusicatenibacter, Faecalibacterium and Bacteroides and a reduction in Roseburia, Lachnospiracea and Blautia. The majority of effects disappeared after stopping the prebiotic and most effects tended to be more pronounced in male participants. (4) Conclusions: Herein, we describe novel aspects of the prebiotic PHGG on compositional and functional properties of the healthy human microbiota.
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Affiliation(s)
- Simon J. Reider
- Christian Doppler Laboratory for Mucosal Immunology, Medical University Innsbruck, 6020 Innsbruck, Austria; (S.J.R.); (J.T.); (N.P.)
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University Innsbruck, 6020 Innsbruck, Austria;
| | - Simon Moosmang
- Institute of Pharmacy/Pharmacognosy & Center for Molecular Biosciences Innsbruck, Leopold-Franzens Universität, 6020 Innsbruck, Austria; (S.M.); (S.S.); (H.S.)
| | - Judith Tragust
- Christian Doppler Laboratory for Mucosal Immunology, Medical University Innsbruck, 6020 Innsbruck, Austria; (S.J.R.); (J.T.); (N.P.)
| | - Lovro Trgovec-Greif
- Division of Computational Systems Biology, Department of Microbiology, University of Vienna, 1010 Vienna, Austria; (L.T.-G.); (L.P.); (T.R.)
| | - Simon Tragust
- General Zoology Institute of Biology, University Halle, 06108 Halle, Germany;
| | - Lorenz Perschy
- Division of Computational Systems Biology, Department of Microbiology, University of Vienna, 1010 Vienna, Austria; (L.T.-G.); (L.P.); (T.R.)
| | - Nicole Przysiecki
- Christian Doppler Laboratory for Mucosal Immunology, Medical University Innsbruck, 6020 Innsbruck, Austria; (S.J.R.); (J.T.); (N.P.)
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University Innsbruck, 6020 Innsbruck, Austria;
| | - Sonja Sturm
- Institute of Pharmacy/Pharmacognosy & Center for Molecular Biosciences Innsbruck, Leopold-Franzens Universität, 6020 Innsbruck, Austria; (S.M.); (S.S.); (H.S.)
| | - Herbert Tilg
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University Innsbruck, 6020 Innsbruck, Austria;
| | - Hermann Stuppner
- Institute of Pharmacy/Pharmacognosy & Center for Molecular Biosciences Innsbruck, Leopold-Franzens Universität, 6020 Innsbruck, Austria; (S.M.); (S.S.); (H.S.)
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology, University of Vienna, 1010 Vienna, Austria; (L.T.-G.); (L.P.); (T.R.)
| | - Alexander R. Moschen
- Christian Doppler Laboratory for Mucosal Immunology, Medical University Innsbruck, 6020 Innsbruck, Austria; (S.J.R.); (J.T.); (N.P.)
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology & Metabolism, Medical University Innsbruck, 6020 Innsbruck, Austria;
- Correspondence:
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18
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Pan S, Hullar MAJ, Lai LA, Peng H, May DH, Noble WS, Raftery D, Navarro SL, Neuhouser ML, Lampe PD, Lampe JW, Chen R. Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach. Microorganisms 2020; 8:E379. [PMID: 32156071 PMCID: PMC7143255 DOI: 10.3390/microorganisms8030379] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 12/11/2022] Open
Abstract
Although the gut microbiome has been associated with dietary patterns linked to health, microbial metabolism is not well characterized. This ancillary study was a proof of principle analysis for a novel application of metaproteomics to study microbial protein expression in a controlled dietary intervention. We measured the response of the microbiome to diet in a randomized crossover dietary intervention of a whole-grain, low glycemic load diet (WG) and a refined-grain, high glycemic load diet (RG). Total proteins in stools from 9 participants at the end of each diet period (n = 18) were analyzed by LC MS/MS and proteins were identified using the Human Microbiome Project (HMP) human gut microbiome database and UniProt human protein databases. T-tests, controlling for false discovery rate (FDR) <10%, were used to compare the Gene Ontology (GO) biological processes and bacterial enzymes between the two interventions. Using shotgun proteomics, more than 53,000 unique peptides were identified including microbial (89%) and human peptides (11%). Forty-eight bacterial enzymes were statistically different between the diets, including those implicated in SCFA production and degradation of fatty acids. Enzymes associated with degradation of human mucin were significantly enriched in the RG diet. These results illustrate that the metaproteomic approach is a valuable tool to study the microbial metabolism of diets that may influence host health.
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Affiliation(s)
- Sheng Pan
- Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (S.P.); (H.P.)
| | - Meredith A. J. Hullar
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Lisa A. Lai
- Department of Medicine, University of Washington, Seattle, WA 98105, USA;
| | - Hong Peng
- Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (S.P.); (H.P.)
| | - Damon H. May
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA; (D.H.M.)
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA; (D.H.M.)
| | - Daniel Raftery
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA 98109 USA
| | - Sandi L. Navarro
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Marian L. Neuhouser
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Paul D. Lampe
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Johanna W. Lampe
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Ru Chen
- Division of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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19
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De Angelis M, Ferrocino I, Calabrese FM, De Filippis F, Cavallo N, Siragusa S, Rampelli S, Di Cagno R, Rantsiou K, Vannini L, Pellegrini N, Lazzi C, Turroni S, Lorusso N, Ventura M, Chieppa M, Neviani E, Brigidi P, O'Toole PW, Ercolini D, Gobbetti M, Cocolin L. Diet influences the functions of the human intestinal microbiome. Sci Rep 2020; 10:4247. [PMID: 32144387 PMCID: PMC7060259 DOI: 10.1038/s41598-020-61192-y] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 02/12/2020] [Indexed: 02/06/2023] Open
Abstract
Gut microbes programme their metabolism to suit intestinal conditions and convert dietary components into a panel of small molecules that ultimately affect host physiology. To unveil what is behind the effects of key dietary components on microbial functions and the way they modulate host-microbe interaction, we used for the first time a multi-omic approach that goes behind the mere gut phylogenetic composition and provides an overall picture of the functional repertoire in 27 fecal samples from omnivorous, vegan and vegetarian volunteers. Based on our data, vegan and vegetarian diets were associated to the highest abundance of microbial genes/proteins responsible for cell motility, carbohydrate- and protein-hydrolyzing enzymes, transport systems and the synthesis of essential amino acids and vitamins. A positive correlation was observed when intake of fiber and the relative fecal abundance of flagellin were compared. Microbial cells and flagellin extracted from fecal samples of 61 healthy donors modulated the viability of the human (HT29) colon carcinoma cells and the host response through the stimulation of the expression of Toll-like receptor 5, lectin RegIIIα and three interleukins (IL-8, IL-22 and IL-23). Our findings concretize a further and relevant milestone on how the diet may prevent/mitigate disease risk.
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Affiliation(s)
- Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Ilario Ferrocino
- Department of Agricultural, Forest and Food Science, University of Turin, Grugliasco, Italy
| | - Francesco Maria Calabrese
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy.,Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences and Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Noemi Cavallo
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Sonya Siragusa
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Raffaella Di Cagno
- Faculty of Science and Technology, Free University of Bozen, Bozen, Italy
| | - Kalliopi Rantsiou
- Department of Agricultural, Forest and Food Science, University of Turin, Grugliasco, Italy
| | - Lucia Vannini
- Department of Agricultural and Food Sciences, Alma Mater Studiorum University of Bologna, and Inter-Departmental Centre for Industrial Agri-Food Research, Alma Mater Studiorum University of Bologna, Cesena, Italy
| | | | - Camilla Lazzi
- Food and Drug Department, University of Parma, Parma, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Nicola Lorusso
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Mario Ventura
- Department of Biology, University of Bari Aldo Moro, Bari, Italy
| | - Marcello Chieppa
- National Institute of Gastroenterology "S. de Bellis", Castellana Grotte, Bari, Italy
| | - Erasmo Neviani
- Food and Drug Department, University of Parma, Parma, Italy
| | - Patrizia Brigidi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Paul W O'Toole
- Department of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Danilo Ercolini
- Department of Agricultural Sciences and Task Force on Microbiome Studies, University of Naples Federico II, Portici, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Free University of Bozen, Bozen, Italy.
| | - Luca Cocolin
- Department of Agricultural, Forest and Food Science, University of Turin, Grugliasco, Italy
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20
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Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole. Proc Natl Acad Sci U S A 2020; 117:6114-6120. [PMID: 32123098 DOI: 10.1073/pnas.1916974117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacterial chemotaxis to prominent microbiota metabolites such as indole is important in the formation of microbial communities in the gastrointestinal (GI) tract. However, the basis of chemotaxis to indole is poorly understood. Here, we exposed Escherichia coli to a range of indole concentrations and measured the dynamic responses of individual flagellar motors to determine the chemotaxis response. Below 1 mM indole, a repellent-only response was observed. At 1 mM indole and higher, a time-dependent inversion from a repellent to an attractant response was observed. The repellent and attractant responses were mediated by the Tsr and Tar chemoreceptors, respectively. Also, the flagellar motor itself mediated a repellent response independent of the receptors. Chemotaxis assays revealed that receptor-mediated adaptation to indole caused a bipartite response-wild-type cells were attracted to regions of high indole concentration if they had previously adapted to indole but were otherwise repelled. We propose that indole spatially segregates cells based on their state of adaptation to repel invaders while recruiting beneficial resident bacteria to growing microbial communities within the GI tract.
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21
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Abstract
Diet is an important risk factor for colorectal cancer (CRC), and several dietary constituents implicated in CRC are modified by gut microbial metabolism. Microbial fermentation of dietary fiber produces short-chain fatty acids, e.g., acetate, propionate, and butyrate. Dietary fiber has been shown to reduce colon tumors in animal models, and, in vitro, butyrate influences cellular pathways important to cancer risk. Furthermore, work from our group suggests that the combined effects of butyrate and omega-3 polyunsaturated fatty acids (n-3 PUFA) may enhance the chemopreventive potential of these dietary constituents. We postulate that the relatively low intakes of n-3 PUFA and fiber in Western populations and the failure to address interactions between these dietary components may explain why chemoprotective effects of n-3 PUFA and fermentable fibers have not been detected consistently in prospective cohort studies. In this review, we summarize the evidence outlining the effects of n-3 long-chain PUFA and highly fermentable fiber with respect to alterations in critical pathways important to CRC prevention, particularly intrinsic mitochondrial-mediated programmed cell death resulting from the accumulation of lipid reactive oxygen species (ferroptosis), and epigenetic programming related to lipid catabolism and beta-oxidation-associated genes.
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Abstract
Bacterial and archaeal flagellins are remarkable in having a shared region with variation in housekeeping proteins and a region with extreme diversity, perhaps greater than for any other protein. Analysis of the 113,285 available full-gene sequences of flagellin genes from published bacterial and archaeal sequences revealed the nature and enormous extent of flagellin diversity. There were 35,898 unique amino acid sequences that were resolved into 187 clusters. Analysis of the Escherichia coli and Salmonella enterica flagellins revealed that the variation occurs at two levels. The first is the division of the variable regions into sequence forms that are so divergent that there is no meaningful alignment even within species, and these corresponded to the E. coli or S. enterica H-antigen groups. The second level is variation within these groups, which is extensive in both species. Shared sequence would allow PCR of the variable regions and thus strain-level analysis of microbiome DNA. Flagellin, the agent of prokaryotic flagellar motion, is very widely distributed and is the H antigen of serology. Flagellin molecules have a variable region that confers serotype specificity, encoded by the middle of the gene, and also conserved regions encoded by the two ends of the gene. We collected all available prokaryotic flagellin protein sequences and found the variable region diversity to be at two levels. In each species investigated, there are hypervariable region (HVR) forms without detectable homology in protein sequences between them. There is also considerable variation within HVR forms, indicating that some have been diverging for thousands of years and that interphylum horizontal gene transfers make a major contribution to the evolution of such atypical diversity. IMPORTANCE Bacterial and archaeal flagellins are remarkable in having a shared region with variation in housekeeping proteins and a region with extreme diversity, perhaps greater than for any other protein. Analysis of the 113,285 available full-gene sequences of flagellin genes from published bacterial and archaeal sequences revealed the nature and enormous extent of flagellin diversity. There were 35,898 unique amino acid sequences that were resolved into 187 clusters. Analysis of the Escherichia coli and Salmonella enterica flagellins revealed that the variation occurs at two levels. The first is the division of the variable regions into sequence forms that are so divergent that there is no meaningful alignment even within species, and these corresponded to the E. coli or S. enterica H-antigen groups. The second level is variation within these groups, which is extensive in both species. Shared sequence would allow PCR of the variable regions and thus strain-level analysis of microbiome DNA.
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Jennings A, Koch M, Jensen MK, Bang C, Kassubek J, Müller HP, Nöthlings U, Franke A, Lieb W, Cassidy A. The role of the gut microbiome in the association between habitual anthocyanin intake and visceral abdominal fat in population-level analysis. Am J Clin Nutr 2020; 111:340-350. [PMID: 31826255 PMCID: PMC6997102 DOI: 10.1093/ajcn/nqz299] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/12/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Flavonoid intake modifies the composition of the gut microbiome, which contributes to the metabolism of flavonoids. Few studies have examined the contribution of the gut microbiome to the health benefits associated with flavonoid intake. OBJECTIVES We aimed to examine associations between habitual intakes of flavonoid subclasses and MRI-determined visceral (VAT) and subcutaneous (SAT) adipose tissue. Uniquely, we also identified associations between the aforementioned measurements and gut microbiome composition sequenced from 16S ribosomal RNA genes. METHODS We undertook cross-sectional analyses of 618 men and women (n = 368 male), aged 25-83 y, from the PopGen cohort. RESULTS Higher intake of anthocyanins was associated with lower amounts of VAT [tertile (T)3-T1: -0.49 dm3; β: -8.9%; 95% CI: -16.2%, -1.1%; P = 0.03] and VAT:SAT ratio (T3-T1: -0.04; β: -7.1%; 95% CI: -13.5%, -0.3%; P = 0.03). Higher intakes of anthocyanin-rich foods were also inversely associated with VAT [quantile (Q)4-Q1: -0.39 dm3; β: -9.9%; 95% CI: -17.4%, -1.6%; P = 0.02] and VAT:SAT ratio (Q4-Q1: -0.04; β: -6.5%; 95% CI: -13.3%, -0.9%; P = 0.03). Participants with the highest intakes of anthocyanin-rich foods also had higher microbial diversity (Q4-Q1: β: 0.18; 95% CI: 0.06, 0.31; P < 0.01), higher abundances of Clostridiales (Q4-Q1: β: 449; 95% CI: 96.3, 801; P = 0.04) and Ruminococcaceae (Q4-Q1: β: 313; 95% CI: 33.6, 591; P = 0.04), and lower abundance of Clostridium XIVa (Q4-Q1: β: -41.1; 95% CI: -72.4, -9.8; P = 0.04). Participants with the highest microbial diversity, abundances of Clostridiales and Ruminococcaceae, and lower abundance of Clostridium XIVa had lower amounts of VAT. Up to 18.5% of the association between intake of anthocyanin-rich foods and VAT could be explained by the gut microbiome. CONCLUSIONS These novel data suggest that higher microbial diversity and abundance of specific taxa in the Clostridiales order may contribute to the association between higher intake of anthocyanins and lower abdominal adipose tissue.
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Affiliation(s)
- Amy Jennings
- Department of Nutrition and Preventive Medicine, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Manja Koch
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Majken K Jensen
- Department of Nutrition, Harvard TH Chan School of Public Health, Boston, MA, USA
- Department of Medicine, Channing Division of Network Medicine, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Jan Kassubek
- Department of Neurology, University of Ulm, Ulm, Germany
| | | | - Ute Nöthlings
- Department of Nutrition and Food Sciences, University of Bonn, Bonn, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, Kiel, Germany
- Biobank PopGen, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Aedín Cassidy
- Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
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Dubinsky V, Reshef L, Bar N, Keizer D, Golan N, Rabinowitz K, Godny L, Yadgar K, Zonensain K, Tulchinsky H, Gophna U, Dotan I. Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy. Gastroenterology 2020; 158:610-624.e13. [PMID: 31605691 DOI: 10.1053/j.gastro.2019.10.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 09/29/2019] [Accepted: 10/01/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND & AIMS Pouchitis that develops in patients with ulcerative colitis after total proctocolectomy and ileal pouch anal anastomosis is usually treated with antibiotics. Some patients have recurrence of flares, or become antibiotic-dependent, and require repeated courses or prolonged periods of antibiotic therapy. We investigated microbial factors associated with response to antibiotic treatment and development of antibiotic dependence in patients with pouchitis. METHODS We performed a prospective study of 49 patients who had undergone pouch surgery at a tertiary center. Disease activity was determined based on clinical, endoscopic, and histologic criteria. Pouch phenotype was defined as recurrent-acute pouchitis (n = 6), chronic pouchitis and Crohn's-like disease of the pouch (n = 27), normal pouch from patient with ulcerative colitis (n = 10), and normal pouch from patient with familial adenomatous polyposis (n = 6). Fecal samples (n = 234) were collected over time during or in the absence of antibiotic treatment (ciprofloxacin and/or metronidazole). Thirty-three patients were treated with antibiotics, for a median of 425 days of cumulative antibiotic therapy, during follow-up. Calprotectin was measured and fecal DNA was sequenced using shotgun metagenomics and analyzed with specifically designed bioinformatic pipelines. Bacterial strains were isolated from fecal samples. We assessed their ciprofloxacin resistance and ability to induce secretion of inflammatory cytokines by HT-29 intestinal epithelial cells. RESULTS Most antibiotic-treated patients (79%) had a clinical response to each course of antibiotics; however, 89% of those who completed a 4-week course relapsed within 3 months. Median calprotectin levels decreased by 40% in response to antibiotics. Antibiotic treatment reduced disease-associated bacteria such as Clostridium perfringens, Ruminococcus gnavus, and Klebsiella pneumoniae, but also beneficial species, such as Faecalibacterium prausnitzii. The microbiomes of antibiotic-responsive patients were dominated by facultative anaerobic genera (Escherichia, Enterococcus, and Streptococcus), with multiple ciprofloxacin-resistance mutations in drug target genes and confirmed drug resistance. However, these strains had lower potential for virulence and did not induce secretion of inflammatory cytokines by epithelial cells. After antibiotic cessation, patients had an abrupt shift in microbiome composition, with blooms of oral and disease-associated bacteria. In addition, antibiotic treatment enriched for strains that acquired multidrug resistance loci, encoding enzymes that confer resistance to nonrelated antibiotics, including extended-spectrum beta-lactamases. CONCLUSIONS The efficacy of antibiotic treatment of pouchitis might be attributed to the establishment of an antibiotic-resistant microbiome with low inflammatory potential. This microbiome might provide resistance against colonization by bacteria that promote inflammation. To avoid progression to antibiotic-dependent disease and its consequences, strategies such as short-term alternating antibiotics and nutrition- and microbiome-based interventions should be considered.
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Affiliation(s)
- Vadim Dubinsky
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University
| | - Leah Reshef
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University
| | - Nir Bar
- Department of Gastroenterology and Liver Disease, Tel Aviv Sourasky Medical Center; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Danielle Keizer
- The Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel; Felsenstein Medical Research Center, Rabin Medical Center, Petah-Tikva, Israel
| | - Noam Golan
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University
| | - Keren Rabinowitz
- The Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel; Felsenstein Medical Research Center, Rabin Medical Center, Petah-Tikva, Israel
| | - Lihi Godny
- The Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel; Felsenstein Medical Research Center, Rabin Medical Center, Petah-Tikva, Israel
| | - Karin Yadgar
- The Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel; Felsenstein Medical Research Center, Rabin Medical Center, Petah-Tikva, Israel
| | - Keren Zonensain
- The Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel; Felsenstein Medical Research Center, Rabin Medical Center, Petah-Tikva, Israel
| | - Hagit Tulchinsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Proctology Unit, Division of Surgery, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Uri Gophna
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University.
| | - Iris Dotan
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.
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25
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Long-term administration of Lactobacillus casei Zhang stabilized gut microbiota of adults and reduced gut microbiota age index of older adults. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103682] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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26
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De Angelis M, Garruti G, Minervini F, Bonfrate L, Portincasa P, Gobbetti M. The Food-gut Human Axis: The Effects of Diet on Gut Microbiota and Metabolome. Curr Med Chem 2019; 26:3567-3583. [PMID: 28462705 DOI: 10.2174/0929867324666170428103848] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 02/08/2023]
Abstract
Gut microbiota, the largest symbiont community hosted in human organism, is emerging as a pivotal player in the relationship between dietary habits and health. Oral and, especially, intestinal microbes metabolize dietary components, affecting human health by producing harmful or beneficial metabolites, which are involved in the incidence and progression of several intestinal related and non-related diseases. Habitual diet (Western, Agrarian and Mediterranean omnivore diets, vegetarian, vegan and gluten-free diets) drives the composition of the gut microbiota and metabolome. Within the dietary components, polymers (mainly fibers, proteins, fat and polyphenols) that are not hydrolyzed by human enzymes seem to be the main leads of the metabolic pathways of gut microbiota, which in turn directly influence the human metabolome. Specific relationships between diet and microbes, microbes and metabolites, microbes and immune functions and microbes and/or their metabolites and some human diseases are being established. Dietary treatments with fibers are the most effective to benefit the metabolome profile, by improving the synthesis of short chain fatty acids and decreasing the level of molecules, such as p-cresyl sulfate, indoxyl sulfate and trimethylamine N-oxide, involved in disease state. Based on the axis diet-microbiota-health, this review aims at describing the most recent knowledge oriented towards a profitable use of diet to provide benefits to human health, both directly and indirectly, through the activity of gut microbiota.
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Affiliation(s)
- Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Gabriella Garruti
- Department of Emergency and Organ Transplants, Section of Endocrinology, Andrology and Metabolic Diseases, University of Bari Medical School, Bari, Italy
| | - Fabio Minervini
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Leonilde Bonfrate
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy.,Clinica Medica "A. Murri", Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy
| | - Piero Portincasa
- Clinica Medica "A. Murri", Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Free University of Bozen, Bolzano, Italy
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Oliphant K, Parreira VR, Cochrane K, Allen-Vercoe E. Drivers of human gut microbial community assembly: coadaptation, determinism and stochasticity. ISME JOURNAL 2019; 13:3080-3092. [PMID: 31477821 DOI: 10.1038/s41396-019-0498-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 07/21/2019] [Accepted: 08/14/2019] [Indexed: 02/07/2023]
Abstract
Microbial community assembly is a complex process shaped by multiple factors, including habitat filtering, species assortment and stochasticity. Understanding the relative importance of these drivers would enable scientists to design strategies initiating a desired reassembly for e.g., remediating low diversity ecosystems. Here, we aimed to examine if a human fecal-derived defined microbial community cultured in bioreactors assembled deterministically or stochastically, by completing replicate experiments under two growth medium conditions characteristic of either high fiber or high protein diets. Then, we recreated this defined microbial community by matching different strains of the same species sourced from distinct human donors, in order to elucidate whether coadaptation of strains within a host influenced community dynamics. Each defined microbial ecosystem was evaluated for composition using marker gene sequencing, and for behavior using 1H-NMR-based metabonomics. We found that stochasticity had the largest influence on the species structure when substrate concentrations varied, whereas habitat filtering greatly impacted the metabonomic output. Evidence of coadaptation was elucidated from comparisons of the two communities; we found that the artificial community tended to exclude saccharolytic Firmicutes species and was enriched for metabolic intermediates, such as Stickland fermentation products, suggesting overall that polysaccharide utilization by Firmicutes is dependent on cooperation.
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Affiliation(s)
- Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada.
| | - Valeria R Parreira
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Kyla Cochrane
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
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28
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Tran HQ, Mills RH, Peters NV, Holder MK, de Vries GJ, Knight R, Chassaing B, Gonzalez DJ, Gewirtz AT. Associations of the Fecal Microbial Proteome Composition and Proneness to Diet-induced Obesity. Mol Cell Proteomics 2019; 18:1864-1879. [PMID: 31262998 PMCID: PMC6731084 DOI: 10.1074/mcp.ra119.001623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Indexed: 12/16/2022] Open
Abstract
Consumption of refined high-fat, low-fiber diets promotes development of obesity and its associated consequences. Although genetics play an important role in dictating susceptibility to such obesogenic diets, mice with nearly uniform genetics exhibit marked heterogeneity in their extent of obesity in response to such diets. This suggests non-genetic determinants play a role in diet-induced obesity. Hence, we sought to identify parameters that predict, and/or correlate with, development of obesity in response to an obesogenic diet. We assayed behavior, metabolic parameters, inflammatory markers/cytokines, microbiota composition, and the fecal metaproteome, in a cohort of mice (n = 50) prior to, and the 8 weeks following, administration of an obesogenic high-fat low-fiber diet. Neither behavioral testing nor quantitation of inflammatory markers broadly predicted severity of diet-induced obesity. Although, the small subset of mice that exhibited basal elevations in serum IL-6 (n = 5) were among the more obese mice in the cohort. While fecal microbiota composition changed markedly in response to the obesogenic diet, it lacked the ability to predict which mice were relative prone or resistant to obesity. In contrast, fecal metaproteome analysis revealed functional and taxonomic differences among the proteins associated with proneness to obesity. Targeted interrogation of microbiota composition data successfully validated the taxonomic differences seen in the metaproteome. Although future work will be needed to determine the breadth of applicability of these associations to other cohorts of animals and humans, this study nonetheless highlights the potential power of gut microbial proteins to predict and perhaps impact development of obesity.
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Affiliation(s)
- Hao Q Tran
- ‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA
| | - Robert H Mills
- §Department of Pharmacology, University of California, San Diego, CA; ¶Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA; ‖Department of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, CA; **Center for Microbiome Innovation, University of California, San Diego, CA
| | - Nicole V Peters
- ‡‡Neuroscience Institute, Georgia State University, Atlanta, GA
| | - Mary K Holder
- ‡‡Neuroscience Institute, Georgia State University, Atlanta, GA; §§School of Psychology, Georgia Institute of Technology, Atlanta, GA 30332
| | | | - Rob Knight
- ‖Department of Pediatrics, and Department of Computer Science and Engineering, University of California, San Diego, CA; **Center for Microbiome Innovation, University of California, San Diego, CA
| | - Benoit Chassaing
- ‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA; ‡‡Neuroscience Institute, Georgia State University, Atlanta, GA
| | - David J Gonzalez
- §Department of Pharmacology, University of California, San Diego, CA; ¶Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA; **Center for Microbiome Innovation, University of California, San Diego, CA.
| | - Andrew T Gewirtz
- ‡Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA.
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Abstract
The gut microbiome is a complex microbial community that plays a key role in human health. Diet is an important factor dictating gut microbiome composition. This is mediated by multiple microbe-microbe interactions that result in the fermentation of nondigestible carbohydrates and the production of short-chain fatty acids. Certain species play key metabolic roles in the microbiome, and their disappearance could result in dysbiosis. In this work, a synthetic consortium of 14 gut microbes was studied during the utilization of prebiotic inulin in batch bioreactors. Fermentations were repeated leaving one species out every time, in order to evaluate the impact of their elimination on the system. Substrate consumption, microbial composition, and metabolite production were determined. Single deletions never resulted in a complete loss of bacterial growth or inulin consumption, suggesting functional redundancy. Deletions of Bacteroides dorei and Lachnoclostridium clostridioforme resulted in lower biomass and higher residual inulin. The absence of B. dorei impacted the abundance of the other 10 species negatively. Lachnoclostridium symbiosum, a butyrate producer, appeared to be the most sensitive species to deletions, being stimulated by the presence of Escherichia coli, Bifidobacterium adolescentis, B. dorei, and Lactobacillus plantarum Conversely, bioreactors without these species did not show butyrate production. L. clostridioforme was observed to be essential for propionate production, and B. dorei for lactate production. Our analysis identified specific members that were essential for the function of the consortium. In conclusion, species deletions from microbial consortia could be a useful approach to identify relevant interactions between microorganisms and defining metabolic roles in the gut microbiome.IMPORTANCE Gut microbes associate, compete for, and specialize in specific metabolic tasks. These interactions are dictated by the cross-feeding of degradation or fermentation products. However, the individual contribution of microbes to the function of the gut microbiome is difficult to evaluate. It is essential to understand the complexity of microbial interactions and how the presence or absence of specific microorganisms affects the stability and functioning of the gut microbiome. The experimental approach of this study could be used for identifying keystone species, in addition to redundant functions and conditions that contribute to community stability. Redundancy is an important feature of the microbiome, and its reduction could be useful for the design of microbial consortia with desired metabolic properties enhancing the tasks of the keystone species.
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Trait-based community assembly and succession of the infant gut microbiome. Nat Commun 2019; 10:512. [PMID: 30710083 PMCID: PMC6358638 DOI: 10.1038/s41467-019-08377-w] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/31/2018] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiome develops over early childhood and aids in food digestion and immunomodulation, but the mechanisms driving its development remain elusive. Here we use data curated from literature and online repositories to examine trait-based patterns of gut microbiome succession in 56 infants over their first three years of life. We also develop a new phylogeny-based approach of inferring trait values that can extend readily to other microbial systems and questions. Trait-based patterns suggest that infant gut succession begins with a functionally variable cohort of taxa, adept at proliferating rapidly within hosts, which gradually matures into a more functionally uniform cohort of taxa adapted to thrive in the anoxic gut and disperse between anoxic patches as oxygen-tolerant spores. Trait-based composition stabilizes after the first year, while taxonomic turnover continues unabated, suggesting functional redundancy in the traits examined. Trait-based approaches powerfully complement taxonomy-based approaches to understanding the mechanisms of microbial community assembly and succession. Recent efforts have been made to apply ecological theory on succession to understand the dynamics of human microbiomes throughout development. Here, Guittar et al. use a trait-based approach to show how microbial traits putatively related to dispersal and environmental tolerance shift in the infant microbiome over the first three years of life.
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31
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Shigeno Y, Toyama M, Nakamura M, Niimi K, Takahashi E, Benno Y. Comparison of gut microbiota composition between laboratory-bred marmosets (Callithrix jacchus) with chronic diarrhea and healthy animals using terminal restriction fragment length polymorphism analysis. Microbiol Immunol 2018; 62:702-710. [DOI: 10.1111/1348-0421.12655] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Yuko Shigeno
- Benno Laboratory; RIKEN Baton Zone Program; RIKEN Cluster for Science Technology and Innovation Hub; 2-1 Hirosawa, Wako-shi Saitama Japan
| | - Mutsumi Toyama
- Benno Laboratory; RIKEN Baton Zone Program; RIKEN Cluster for Science Technology and Innovation Hub; 2-1 Hirosawa, Wako-shi Saitama Japan
| | - Mutsumi Nakamura
- Benno Laboratory; RIKEN Baton Zone Program; RIKEN Cluster for Science Technology and Innovation Hub; 2-1 Hirosawa, Wako-shi Saitama Japan
| | - Kimie Niimi
- Research Resources Division; RIKEN Center for Brain Science; 2-1 Hirosawa, Wako-shi Saitama Japan
| | - Eiki Takahashi
- Research Resources Division; RIKEN Center for Brain Science; 2-1 Hirosawa, Wako-shi Saitama Japan
| | - Yoshimi Benno
- Benno Laboratory; RIKEN Baton Zone Program; RIKEN Cluster for Science Technology and Innovation Hub; 2-1 Hirosawa, Wako-shi Saitama Japan
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Dugas LR, Bernabé BP, Priyadarshini M, Fei N, Park SJ, Brown L, Plange-Rhule J, Nelson D, Toh EC, Gao X, Dong Q, Sun J, Kliethermes S, Gottel N, Luke A, Gilbert JA, Layden BT. Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women. Sci Rep 2018; 8:17135. [PMID: 30459320 PMCID: PMC6244201 DOI: 10.1038/s41598-018-35230-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/28/2018] [Indexed: 02/07/2023] Open
Abstract
We compared the gut microbial populations in 100 women, from rural Ghana and urban US [50% lean (BMI < 25 kg/m2) and 50% obese (BMI ≥ 30 kg/m2)] to examine the ecological co-occurrence network topology of the gut microbiota as well as the relationship of short chain fatty acids (SCFAs) with obesity. Ghanaians consumed significantly more dietary fiber, had greater microbial alpha-diversity, different beta-diversity, and had a greater concentration of total fecal SCFAs (p-value < 0.002). Lean Ghanaians had significantly greater network density, connectivity and stability than either obese Ghanaians, or lean and obese US participants (false discovery rate (FDR) corrected p-value ≤ 0.01). Bacteroides uniformis was significantly more abundant in lean women, irrespective of country (FDR corrected p < 0.001), while lean Ghanaians had a significantly greater proportion of Ruminococcus callidus, Prevotella copri, and Escherichia coli, and smaller proportions of Lachnospiraceae, Bacteroides and Parabacteroides. Lean Ghanaians had a significantly greater abundance of predicted microbial genes that catalyzed the production of butyric acid via the fermentation of pyruvate or branched amino-acids, while obese Ghanaians and US women (irrespective of BMI) had a significantly greater abundance of predicted microbial genes that encoded for enzymes associated with the fermentation of amino-acids such as alanine, aspartate, lysine and glutamate. Similar to lean Ghanaian women, mice humanized with stool from the lean Ghanaian participant had a significantly lower abundance of family Lachnospiraceae and genus Bacteroides and Parabacteroides, and were resistant to obesity following 6-weeks of high fat feeding (p-value < 0.01). Obesity-resistant mice also showed increased intestinal transcriptional expression of the free fatty acid (Ffa) receptor Ffa2, in spite of similar fecal SCFAs concentrations. We demonstrate that the association between obesity resistance and increased predicted ecological connectivity and stability of the lean Ghanaian microbiota, as well as increased local SCFA receptor level, provides evidence of the importance of robust gut ecologic network in obesity.
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Affiliation(s)
- Lara R Dugas
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA.
| | | | - Medha Priyadarshini
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL, USA
| | - Na Fei
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Seo Jin Park
- Department of Microbiology-Immunology, Northwestern University, Chicago, Illinois, USA
| | - Laquita Brown
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | | | - David Nelson
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, USA
| | - Evelyn C Toh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, USA
| | - Xiang Gao
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Qunfeng Dong
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Jun Sun
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Stephanie Kliethermes
- Department of Orthopedics and Rehabilitation, University of Wisconsin School of Medicine and Public Health, Wisconsin, USA
| | - Neil Gottel
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Amy Luke
- Public Health Sciences, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, USA
| | - Jack A Gilbert
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, USA
| | - Brian T Layden
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL, USA.,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
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Lopez-Siles M, Enrich-Capó N, Aldeguer X, Sabat-Mir M, Duncan SH, Garcia-Gil LJ, Martinez-Medina M. Alterations in the Abundance and Co-occurrence of Akkermansia muciniphila and Faecalibacterium prausnitzii in the Colonic Mucosa of Inflammatory Bowel Disease Subjects. Front Cell Infect Microbiol 2018; 8:281. [PMID: 30245977 PMCID: PMC6137959 DOI: 10.3389/fcimb.2018.00281] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 07/25/2018] [Indexed: 12/21/2022] Open
Abstract
Akkermansia muciniphila and Faecalibacterium prausnitzii, cohabitants in the intestinal mucosa, are considered members of a healthy microbiota and reduction of both species occurs in several intestinal disorders, including inflammatory bowel disease. Little is known however about a possible link between the reduction in quantity of these species, and in which circumstances this may occur. This study aims to determine the abundances and co-occurrence of the two species in order to elucidate conditions that may compromise their presence in the gut. Loads of A. muciniphila, total F. prausnitzii and its two phylogroup (16S rRNA gene copies) were determined by quantitative polymerase chain reaction in colonic biopsies from 17 healthy controls (H), 23 patients with ulcerative colitis (UC), 31 patients with Crohn's disease (CD), 3 with irritable bowel syndrome (IBS) and 3 with colorectal cancer (CRC). Data were normalized to total bacterial 16S rRNA gene copies in the same sample. Prevalence, relative abundances and correlation analyses were performed according to type of disease and considering relevant clinical characteristics of patients such as IBD location, age of disease onset, CD behavior, current medication and activity status. Co-occurrence of both species was found in 29% of H, 65% of UC and 29% of CD. Lower levels of total F. prausnitzii and phylogroups were found in subjects with CD, compared with H subjects (P ≤ 0.044). In contrast, no differences were found with the regard to A. muciniphila abundance across different disease states, but CD patients with disease onset below 16 years of age featured a marked depletion of this species. In CD patients, correlation between A. muciniphila and total F. prausnitzii (ρ = 0.362, P = 0.045) was observed, and particularly in those with non-stricturing, non-penetrating disease behavior and under moderate immunosuppressants therapy. Altogether, this study revealed that co-occurrence of both species differs between disease status. In addition, IBD patients featured a reduction of F. prausnitzii but similar loads of A. muciniphila when compared to H subjects, with the exception of those with early onset CD. Depletion of A. muciniphila in this subgroup of subjects suggests that it could be a potential biomarker to assist in pediatric CD diagnosis.
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Affiliation(s)
- Mireia Lopez-Siles
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Núria Enrich-Capó
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
| | - Xavier Aldeguer
- Department of Gastroenterology, Hospital Dr. Josep Trueta, Girona, Spain
| | - Miriam Sabat-Mir
- Department of Gastroenterology, Hospital Santa Caterina, Girona, Spain
| | - Sylvia H Duncan
- Microbiology Group, Rowett Institute of Nutrition and Health, Aberdeen, United Kingdom
| | - L Jesús Garcia-Gil
- Laboratory of Molecular Microbiology, Biology Department, Universitat de Girona, Girona, Spain
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Variability of core microbiota in newly diagnosed treatment-naïve paediatric inflammatory bowel disease patients. PLoS One 2018; 13:e0197649. [PMID: 30102706 PMCID: PMC6089417 DOI: 10.1371/journal.pone.0197649] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 07/24/2018] [Indexed: 12/30/2022] Open
Abstract
Background & aims Intestinal microbiota is considered to play a crucial role in the aetiology of inflammatory bowel disease (IBD). We aimed to describe faecal microbiota composition and dynamics in a large cohort of children with de novo (naïve) IBD, in comparison to healthy paediatric controls (HC). Methods In this prospective study, performed at two tertiary centres, faecal samples from newly diagnosed, treatment-naïve paediatric IBD patients were collected prior to bowel cleansing for colonoscopy (t0) and 1, 3 and 6 weeks and 3 months after initiation of therapy. The microbial profiles of Crohn’s disease (CD) and Ulcerative colitis (UC) patients were compared with HC and linked to therapeutic response. Microbiota composition was analysed by IS-pro technology. Results Microbial profiles of 104 new IBD-patients (63 CD, 41 UC, median age 14.0 years) were compared to 61 HC (median 7.8 years). IBD was mainly characterised by decreased abundance of Alistipes finegoldii and Alistipes putredinis, which characterize a healthy state microbial core. The classifier including these core species as predictors achieved an AUC of the ROC curve of .87. Core bacteria tended to regain abundance during treatment, but did not reach healthy levels. Conclusion Faecal microbiota profiles of children with de novo CD and UC can be discriminated from HC with high accuracy, mainly driven by a decreased abundance of species shaping the microbial core in the healthy state. Paediatric IBD can therefore be characterized by decreased abundance of certain bacterial species reflecting the healthy state rather than by the introduction of pathogens.
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35
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Lu J, Shi P, Li H. Generalized linear models with linear constraints for microbiome compositional data. Biometrics 2018; 75:235-244. [PMID: 30039859 DOI: 10.1111/biom.12956] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 01/04/2023]
Abstract
Motivated by regression analysis for microbiome compositional data, this article considers generalized linear regression analysis with compositional covariates, where a group of linear constraints on regression coefficients are imposed to account for the compositional nature of the data and to achieve subcompositional coherence. A penalized likelihood estimation procedure using a generalized accelerated proximal gradient method is developed to efficiently estimate the regression coefficients. A de-biased procedure is developed to obtain asymptotically unbiased and normally distributed estimates, which leads to valid confidence intervals of the regression coefficients. Simulations results show the correctness of the coverage probability of the confidence intervals and smaller variances of the estimates when the appropriate linear constraints are imposed. The methods are illustrated by a microbiome study in order to identify bacterial species that are associated with inflammatory bowel disease (IBD) and to predict IBD using fecal microbiome.
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Affiliation(s)
- Jiarui Lu
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A
| | - Pixu Shi
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, U.S.A
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Kriss M, Hazleton KZ, Nusbacher NM, Martin CG, Lozupone CA. Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery. Curr Opin Microbiol 2018; 44:34-40. [PMID: 30036705 DOI: 10.1016/j.mib.2018.07.003] [Citation(s) in RCA: 241] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/07/2018] [Accepted: 07/11/2018] [Indexed: 02/07/2023]
Abstract
Dysbiosis, an imbalance in microbial communities, is linked with disease when this imbalance disturbs microbiota functions essential for maintaining health or introduces processes that promote disease. Dysbiosis in disease is predicted when microbiota differ compositionally from a healthy control population, but only truly defined when these differences are mechanistically related to adverse phenotypes. For the human gut microbiota, dysbiosis varies across diseases. One common manifestation is replacement of the complex community of anaerobes typical of the healthy adult gut microbiome with a community of lower overall microbial diversity and increased facultative anaerobes. Here we review diseases in which low-diversity dysbiosis has been observed and mechanistically linked with disease, with a particular focus on liver disease, inflammatory bowel disease, and Clostridium difficile infection.
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Affiliation(s)
- Michael Kriss
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Colorado, 12700 East 19th Avenue, Campus Box B146, Aurora, CO 80045, USA
| | - Keith Z Hazleton
- Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Colorado, 13123 East 16th Avenue, Aurora, CO 80045, USA; Digestive Health Institute, Children's Hospital Colorado, 13123 East 16th Avenue, Aurora, CO 80045, USA
| | - Nichole M Nusbacher
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado, 12700 East 19th Avenue, Campus Box 8617, Aurora, CO 80045, USA
| | - Casey G Martin
- Department of Immunology and Microbiology, University of Colorado, 12700 East 19th Avenue,Campus Box 8617, Aurora, CO 80045, USA
| | - Catherine A Lozupone
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado, 12700 East 19th Avenue, Campus Box 8617, Aurora, CO 80045, USA.
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37
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Grieneisen LE, Livermore J, Alberts S, Tung J, Archie EA. Group Living and Male Dispersal Predict the Core Gut Microbiome in Wild Baboons. Integr Comp Biol 2018; 57:770-785. [PMID: 29048537 DOI: 10.1093/icb/icx046] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The mammalian gut microbiome plays a profound role in the physiology, metabolism, and overall health of its host. However, biologists have only a nascent understanding of the forces that drive inter-individual heterogeneity in gut microbial composition, especially the role of host social environment. Here we used 178 samples from 78 wild yellow baboons (Papio cynocephalus) living in two social groups to test how host social context, including group living, social interactions within groups, and transfer between social groups (e.g., dispersal) predict inter-individual variation in gut microbial alpha and beta diversity. We also tested whether social effects differed for prevalent "core" gut microbial taxa, which are thought to provide primary functions to hosts, versus rare "non-core" microbes, which may represent relatively transient environmental acquisitions. Confirming prior studies, we found that each social group harbored a distinct gut microbial community. These differences included both non-core and core gut microbial taxa, suggesting that these effects are not solely driven by recent gut microbial exposures. Within social groups, close grooming partners had more similar core microbiomes, but not non-core microbiomes, than individuals who rarely groomed each other, even controlling for kinship and diet similarity between grooming partners. Finally, in support of the idea that the gut microbiome can be altered by current social context, we found that the longer an immigrant male had lived in a given social group, the more closely his gut microbiome resembled the gut microbiomes of the group's long-term residents. Together, these results reveal the importance of a host's social context in shaping the gut microbiome and shed new light onto the microbiome-related consequences of male dispersal.
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Affiliation(s)
- Laura E Grieneisen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Josh Livermore
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Susan Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
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38
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Deaver JA, Eum SY, Toborek M. Circadian Disruption Changes Gut Microbiome Taxa and Functional Gene Composition. Front Microbiol 2018; 9:737. [PMID: 29706947 PMCID: PMC5909328 DOI: 10.3389/fmicb.2018.00737] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 03/29/2018] [Indexed: 12/22/2022] Open
Abstract
Disrupted circadian rhythms and alterations of the gut microbiome composition were proposed to affect host health. Therefore, the aim of this research was to identify whether these events are connected and if circadian rhythm disruption by abnormal light–dark (LD) cycles affects microbial community gene expression and host vulnerability to intestinal dysfunction. Mice were subjected to either a 4-week period of constant 24-h light or of normal 12-h LD cycles. Stool samples were collected at the beginning and after the circadian rhythm disruption. A metatranscriptomic analysis revealed an increase in Ruminococcus torques, a bacterial species known to decrease gut barrier integrity, and a decrease in Lactobacillus johnsonii, a bacterium that helps maintain the intestinal epithelial cell layer, after circadian rhythm disruption. In addition, genes involved in pathways promoting host beneficial immune responses were downregulated, while genes involved in the synthesis and transportation of the endotoxin lipopolysaccharide were upregulated in mice with disrupted circadian cycles. Importantly, these mice were also more prone to dysfunction of the intestinal barrier. These results further elucidate the impact of light-cycle disruption on the gut microbiome and its connection with increased incidence of disease in response to circadian rhythm disturbances.
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Affiliation(s)
- Jessica A Deaver
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sung Y Eum
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Michal Toborek
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, United States
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McKenney EA, O'Connell TM, Rodrigo A, Yoder AD. Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs. Gut Microbes 2018; 9:202-217. [PMID: 29182421 PMCID: PMC6219591 DOI: 10.1080/19490976.2017.1408762] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Many studies have demonstrated the effects of host diet on gut microbial membership, metagenomics, and fermentation individually; but few have attempted to interpret the relationship among these biological phenomena with respect to host features (e.g. gut morphology). We quantitatively compare the fecal microbial communities, metabolic pathways, and fermentation products associated with the nutritional intake of frugivorous (fruit-eating) and folivorous (leaf-eating) lemurs. Our results provide a uniquely multidimensional and comparative perspective on the adaptive dynamics between host and microbiome. Shotgun metagenomic sequencing revealed significant differential taxonomic and metabolic pathway enrichment, tailored to digest and detoxify different diets. Frugivorous metagenomes feature pathways to degrade simple carbohydrates and host-derived glycosaminoglycans, while folivorous metagenomes are equipped to break down phytic acid and other phytochemical compounds in an anaerobic environment. We used nuclear magnetic resonance based metabolic profiling of fecal samples to link metabolic pathways to fermentation products, confirming that the dissimilar substrates provided in each diet select for specific microbial functions. Fecal samples from frugivorous lemurs contained significantly different profiles of short chain fatty acids, alcohol fermentation products, amino acids, glucose, and glycerol compared to folivorous lemurs. We present the relationships between these datasets as an integrated visual framework, which we refer to as microbial geometry. We use microbial geometry to compare empirical gut microbial profiles across different feeding strategies, and suggest additional utility as a tool for hypothesis-generation.
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Affiliation(s)
- E. A. McKenney
- Biology Department, Duke University, Durham, NC, USA,CONTACT E. A. McKenney
| | | | - Allen Rodrigo
- Biology Department, Duke University, Durham, NC, USA,Research School of Biology, Australian National University, ACT, Australia
| | - Anne D. Yoder
- Biology Department, Duke University, Durham, NC, USA,Duke Lemur Center, Duke University, Durham, NC, USA
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40
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Jackson MA, Bonder MJ, Kuncheva Z, Zierer J, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Bell JT, Spector TD, Steves CJ. Detection of stable community structures within gut microbiota co-occurrence networks from different human populations. PeerJ 2018; 6:e4303. [PMID: 29441232 PMCID: PMC5807925 DOI: 10.7717/peerj.4303] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/10/2018] [Indexed: 12/20/2022] Open
Abstract
Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.
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Affiliation(s)
- Matthew A Jackson
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Marc Jan Bonder
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - Zhana Kuncheva
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Jonas Zierer
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jingyuan Fu
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands.,University Medical Center Groningen, Department of Pediatrics, University of Groningen, Groningen, Netherlands
| | - Alexander Kurilshikov
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands.,K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway
| | - Alexandra Zhernakova
- University Medical Center Groningen, Department of Genetics, University of Groningen, Groningen, Netherlands
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
| | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
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41
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Hugenholtz F, de Vos WM. Mouse models for human intestinal microbiota research: a critical evaluation. Cell Mol Life Sci 2018; 75:149-160. [PMID: 29124307 PMCID: PMC5752736 DOI: 10.1007/s00018-017-2693-8] [Citation(s) in RCA: 330] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 09/29/2017] [Indexed: 02/06/2023]
Abstract
Since the early days of the intestinal microbiota research, mouse models have been used frequently to study the interaction of microbes with their host. However, to translate the knowledge gained from mouse studies to a human situation, the major spatio-temporal similarities and differences between intestinal microbiota in mice and humans need to be considered. This is done here with specific attention for the comparative physiology of the intestinal tract, the effect of dietary patterns and differences in genetics. Detailed phylogenetic and metagenomic analysis showed that while many common genera are found in the human and murine intestine, these differ strongly in abundance and in total only 4% of the bacterial genes are found to share considerable identity. Moreover, a large variety of murine strains is available yet most of the microbiota research is performed in wild-type, inbred strains and their transgenic derivatives. It has become increasingly clear that the providers, rearing facilities and the genetic background of these mice have a significant impact on the microbial composition and this is illustrated with recent experimental data. This may affect the reproducibility of mouse microbiota studies and their conclusions. Hence, future studies should take these into account to truly show the effect of diet, genotype or environmental factors on the microbial composition.
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Affiliation(s)
- Floor Hugenholtz
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE, Wageningen, The Netherlands
- Division of Infectious Diseases, Department of Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, Building 124, 6708 WE, Wageningen, The Netherlands.
- Research Programme Unit Immunobiology, Department of Bacteriology and Immunology, Helsinki University, P.O. Box 21, 00014, Helsinki, Finland.
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42
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Haran JP, Bucci V, Dutta P, Ward D, McCormick B. The nursing home elder microbiome stability and associations with age, frailty, nutrition and physical location. J Med Microbiol 2017; 67:40-51. [PMID: 29134939 DOI: 10.1099/jmm.0.000640] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The microbiome from nursing home (NH) residents is marked by a loss in diversity that is associated with increased frailty. Our objective was to explore the associations of NH environment, frailty, nutritional status and residents' age to microbiome composition and potential metabolic function. METHODOLOGY We conducted a prospective longitudinal cohort study of 23 residents, 65 years or older, from one NH that had four floors: two separate medical intensive floors and two floors with active elders. Residents were assessed using the mini nutritional assessment tool and clinical frailty scale. Bacterial composition and metabolic potential of residents' stool samples was determined by metagenomic sequencing. We performed traditional unsupervised correspondence analysis and linear mixed effect modelling regression to assess the bacteria and functional pathways significantly affected by these covariates.Results/Key findings. NH resident microbiomes demonstrated temporal stability (PERMANOVA P=0.001) and differing dysbiotic associations with increasing age, frailty and malnutrition scores. As residents aged, the abundance of microbiota-encoded genes and pathways related to essential amino acid, nitrogenous base and vitamin B production declined. With increasing frailty, residents had lower abundances of butyrate-producing organisms, which are associated with increased health and higher abundances of known dysbiotic species. As residents became malnourished, butyrate-producing organisms declined and dysbiotic bacterial species increased. Finally, the microbiome of residents living in proximity shared similar species and, as demonstrated for Escherichia coli, similar strains. CONCLUSION These findings support the conclusion that a signature 'NH' microbiota may exist that is affected by the residents' age, frailty, nutritional status and physical location.
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Affiliation(s)
- John P Haran
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA.,Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA
| | - Vanni Bucci
- Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Biology, University of Massachusetts Dartmouth, Dartmouth, MA, USA
| | - Protiva Dutta
- Department of Emergency Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Doyle Ward
- Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Beth McCormick
- Center for Microbiome Research, University of Massachusetts Medical School, Worcester, MA, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
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Shaffer M, Armstrong AJS, Phelan VV, Reisdorph N, Lozupone CA. Microbiome and metabolome data integration provides insight into health and disease. Transl Res 2017; 189:51-64. [PMID: 28764956 PMCID: PMC5659916 DOI: 10.1016/j.trsl.2017.07.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 06/28/2017] [Accepted: 07/08/2017] [Indexed: 02/07/2023]
Abstract
For much of our history, the most basic information about the microbial world has evaded characterization. Next-generation sequencing has led to a rapid increase in understanding of the structure and function of host-associated microbial communities in diverse diseases ranging from obesity to autism. Through experimental systems such as gnotobiotic mice only colonized with known microbes, a causal relationship between microbial communities and disease phenotypes has been supported. Now, microbiome research must move beyond correlations and general demonstration of causality to develop mechanistic understandings of microbial influence, including through their metabolic activities. Similar to the microbiome field, advances in technologies for cataloguing small molecules have broadened our understanding of the metabolites that populate our bodies. Integration of microbial and metabolomics data paired with experimental validation has promise for identifying microbial influence on host physiology through production, modification, or degradation of bioactive metabolites. Realization of microbial metabolic activities that affect health is hampered by gaps in our understanding of (1) biological properties of microbes and metabolites, (2) which microbial enzymes/pathways produce which metabolites, and (3) the effects of metabolites on hosts. Capitalizing on known mechanistic relationships and filling gaps in our understanding has the potential to enable translational microbiome research across disease contexts.
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Affiliation(s)
- Michael Shaffer
- Department of Medicine, University of Colorado Denver, Aurora, Colo; Computational Bioscience Program, University of Colorado Denver, Aurora, Colo
| | - Abigail J S Armstrong
- Department of Medicine, University of Colorado Denver, Aurora, Colo; Department of Immunology and Microbiology, University of Colorado Denver, Aurora, Colo
| | - Vanessa V Phelan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colo
| | - Nichole Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Denver, Aurora, Colo
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Durand A, Maillard F, Foulon J, Gweon HS, Valot B, Chalot M. Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site. MICROBIAL ECOLOGY 2017; 74:795-809. [PMID: 28451743 DOI: 10.1007/s00248-017-0984-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/17/2017] [Indexed: 06/07/2023]
Abstract
Characterization of microbial communities in stressful conditions at a field level is rather scarce, especially when considering fungal communities from aboveground habitats. We aimed at characterizing fungal communities from different poplar habitats at a Hg-contaminated phytomanagement site by using Illumina-based sequencing, network analysis approach, and direct isolation of Hg-resistant fungal strains. The highest diversity estimated by the Shannon index was found for soil communities, which was negatively affected by soil Hg concentration. Among the significant correlations between soil operational taxonomic units (OTUs) in the co-occurrence network, 80% were negatively correlated revealing dominance of a pattern of mutual exclusion. The fungal communities associated with Populus roots mostly consisted of OTUs from the symbiotic guild, such as members of the Thelephoraceae, thus explaining the lowest diversity found for root communities. Additionally, root communities showed the highest network connectivity index, while rarely detected OTUs from the Glomeromycetes may have a central role in the root network. Unexpectedly high richness and diversity were found for aboveground habitats, compared to the root habitat. The aboveground habitats were dominated by yeasts from the Lalaria, Davidiella, and Bensingtonia genera, not detected in belowground habitats. Leaf and stem habitats were characterized by few dominant OTUs such as those from the Dothideomycete class producing mutual exclusion with other OTUs. Aureobasidium pullulans, one of the dominating OTUs, was further isolated from the leaf habitat, in addition to Nakazawaea populi species, which were found to be Hg resistant. Altogether, these findings will provide an improved point of reference for microbial research on inoculation-based programs of tailings dumps.
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Affiliation(s)
- Alexis Durand
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 Place Tharradin, BP 71427, 25211, Montbéliard, France
| | - François Maillard
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 Place Tharradin, BP 71427, 25211, Montbéliard, France
| | - Julie Foulon
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 Place Tharradin, BP 71427, 25211, Montbéliard, France
| | - Hyun S Gweon
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxon, OX10 8BB, UK
| | - Benoit Valot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 Place Tharradin, BP 71427, 25211, Montbéliard, France
| | - Michel Chalot
- Laboratoire Chrono-Environnement, UMR 6249, Université de Bourgogne Franche-Comté, Pôle Universitaire du Pays de Montbéliard, 4 Place Tharradin, BP 71427, 25211, Montbéliard, France.
- Faculté des Sciences et Technologies, Université de Lorraine, BP 70239, 54506, Vandoeuvre-les-Nancy, France.
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Stedtfeld RD, Chai B, Crawford RB, Stedtfeld TM, Williams MR, Xiangwen S, Kuwahara T, Cole JR, Kaminski NE, Tiedje JM, Hashsham SA. Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD. Front Microbiol 2017; 8:1708. [PMID: 28936204 PMCID: PMC5594080 DOI: 10.3389/fmicb.2017.01708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 08/23/2017] [Indexed: 12/17/2022] Open
Abstract
Environmental toxicants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AhR), are known to induce host toxicity and structural shifts in the gut microbiota. Key bacterial populations with similar or opposing functional responses to AhR ligand exposure may potentially help regulate expression of genes associated with immune dysfunction. To examine this question and the mechanisms for AhR ligand-induced bacterial shifts, C57BL/6 gnotobiotic mice were colonized with and without segmented filamentous bacteria (SFB) – an immune activator. Mice were also colonized with polysaccharide A producing Bacteroides fragilis – an immune suppressor to serve as a commensal background. Following colonization, mice were administered TCDD (30 μg/kg) every 4 days for 28 days by oral gavage. Quantified with the nCounter® mouse immunology panel, opposing responses in ileal gene expression (e.g., genes associated with T-cell differentiation via the class II major histocompatibility complex) as a result of TCDD dosing and SFB colonization were observed. Genes that responded to TCDD in the presence of SFB did not show a significant response in the absence of SFB, and vice versa. Regulatory T-cells examined in the mesenteric lymph-nodes, spleen, and blood were also less impacted by TCDD in mice colonized with SFB. TCDD-induced shifts in abundance of SFB and B. fragilis compared with previous studies in mice with a traditional gut microbiome. With regard to the mouse model colonized with individual populations, results indicate that TCDD-induced host response was significantly modulated by the presence of SFB in the gut microbiome, providing insight into therapeutic potential between AhR ligands and key commensals.
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Affiliation(s)
- Robert D Stedtfeld
- Department of Civil and Environmental Engineering, East LansingMI, United States
| | - Benli Chai
- Center for Microbial Ecology, Michigan State University, East LansingMI, United States
| | - Robert B Crawford
- Institute for Integrative Toxicology, Michigan State University, East LansingMI, United States.,Department of Pharmacology and Toxicology, Michigan State University, East LansingMI, United States
| | - Tiffany M Stedtfeld
- Department of Civil and Environmental Engineering, East LansingMI, United States
| | - Maggie R Williams
- Department of Civil and Environmental Engineering, East LansingMI, United States
| | - Shao Xiangwen
- Department of Civil and Environmental Engineering, East LansingMI, United States
| | - Tomomi Kuwahara
- Department of Molecular Bacteriology, Institute of Health Biosciences, University of Tokushima Graduate SchoolTokushima, Japan
| | - James R Cole
- Center for Microbial Ecology, Michigan State University, East LansingMI, United States
| | - Norbert E Kaminski
- Institute for Integrative Toxicology, Michigan State University, East LansingMI, United States.,Department of Pharmacology and Toxicology, Michigan State University, East LansingMI, United States
| | - James M Tiedje
- Center for Microbial Ecology, Michigan State University, East LansingMI, United States
| | - Syed A Hashsham
- Department of Civil and Environmental Engineering, East LansingMI, United States.,Center for Microbial Ecology, Michigan State University, East LansingMI, United States
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Casero D, Gill K, Sridharan V, Koturbash I, Nelson G, Hauer-Jensen M, Boerma M, Braun J, Cheema AK. Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome. MICROBIOME 2017; 5:105. [PMID: 28821301 PMCID: PMC5563039 DOI: 10.1186/s40168-017-0325-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 08/08/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Space travel is associated with continuous low dose rate exposure to high linear energy transfer (LET) radiation. Pathophysiological manifestations after low dose radiation exposure are strongly influenced by non-cytocidal radiation effects, including changes in the microbiome and host gene expression. Although the importance of the gut microbiome in the maintenance of human health is well established, little is known about the role of radiation in altering the microbiome during deep-space travel. RESULTS Using a mouse model for exposure to high LET radiation, we observed substantial changes in the composition and functional potential of the gut microbiome. These were accompanied by changes in the abundance of multiple metabolites, which were related to the enzymatic activity of the predicted metagenome by means of metabolic network modeling. There was a complex dynamic in microbial and metabolic composition at different radiation doses, suggestive of transient, dose-dependent interactions between microbial ecology and signals from the host's cellular damage repair processes. The observed radiation-induced changes in microbiota diversity and composition were analyzed at the functional level. A constitutive change in activity was found for several pathways dominated by microbiome-specific enzymatic reactions like carbohydrate digestion and absorption and lipopolysaccharide biosynthesis, while the activity in other radiation-responsive pathways like phosphatidylinositol signaling could be linked to dose-dependent changes in the abundance of specific taxa. CONCLUSIONS The implication of microbiome-mediated pathophysiology after low dose ionizing radiation may be an unappreciated biologic hazard of space travel and deserves experimental validation. This study provides a conceptual and analytical basis of further investigations to increase our understanding of the chronic effects of space radiation on human health, and points to potential new targets for intervention in adverse radiation effects.
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Affiliation(s)
- David Casero
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Kirandeep Gill
- Department of Oncology, Georgetown University Medical Center, Washington DC, 20057, USA
| | - Vijayalakshmi Sridharan
- Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Gregory Nelson
- Department of Radiation Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Martin Hauer-Jensen
- Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Marjan Boerma
- Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Jonathan Braun
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Amrita K Cheema
- Department of Oncology, Georgetown University Medical Center, Washington DC, 20057, USA.
- Department of Biochemistry and Molecular and & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20057, USA.
- GCD-7N Pre-Clinical Science Building, 3900 Reservoir Road NW, Washington DC, 20057, USA.
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Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2017; 2:mSphere00237-17. [PMID: 28776041 PMCID: PMC5541158 DOI: 10.1128/msphere.00237-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/17/2017] [Indexed: 01/01/2023] Open
Abstract
Cultivation in the laboratory is key for understanding the phenotypic characteristics, growth requirements, metabolism, and environmental preferences of bacteria. However, oftentimes, phenotypic information is not easily accessible. Here, we compiled phenotypic and environmental tolerance information for >5,000 bacterial strains described in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). We demonstrate how this database can be used to link bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and environmental preferences. The phenotypic database can be freely accessed (https://doi.org/10.6084/m9.figshare.4272392), and we have included instructions for researchers interested in adding new entries or curating existing ones. Cultivation in the laboratory is essential for understanding the phenotypic characteristics and environmental preferences of bacteria. However, basic phenotypic information is not readily accessible. Here, we compiled phenotypic and environmental tolerance information for >5,000 bacterial strains described in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) with all information made publicly available in an updatable database. Although the data span 23 different bacterial phyla, most entries described aerobic, mesophilic, neutrophilic strains from Proteobacteria (mainly Alpha- and Gammaproteobacteria), Actinobacteria, Firmicutes, and Bacteroidetes isolated from soils, marine habitats, and plants. Most of the routinely measured traits tended to show a significant phylogenetic signal, although this signal was weak for environmental preferences. We demonstrated how this database could be used to link genomic attributes to differences in pH and salinity optima. We found that adaptations to high salinity or high-pH conditions are related to cell surface transporter genes, along with previously uncharacterized genes that might play a role in regulating environmental tolerances. Together, this work highlights the utility of this database for associating bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and emphasizes the need for more comprehensive and consistent measurements of traits across a broader diversity of bacteria. IMPORTANCE Cultivation in the laboratory is key for understanding the phenotypic characteristics, growth requirements, metabolism, and environmental preferences of bacteria. However, oftentimes, phenotypic information is not easily accessible. Here, we compiled phenotypic and environmental tolerance information for >5,000 bacterial strains described in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). We demonstrate how this database can be used to link bacterial taxonomy, phylogeny, or specific genes to measured phenotypic traits and environmental preferences. The phenotypic database can be freely accessed (https://doi.org/10.6084/m9.figshare.4272392), and we have included instructions for researchers interested in adding new entries or curating existing ones.
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48
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McKenney EA, Greene LK, Drea CM, Yoder AD. Down for the count: Cryptosporidium infection depletes the gut microbiome in Coquerel's sifakas. MICROBIAL ECOLOGY IN HEALTH AND DISEASE 2017; 28:1335165. [PMID: 28740461 PMCID: PMC5508644 DOI: 10.1080/16512235.2017.1335165] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/17/2017] [Indexed: 12/12/2022]
Abstract
Background: The gut microbiome (GMB) is the first line of defense against enteric pathogens, which are a leading cause of disease and mortality worldwide. One such pathogen, the protozoan Cryptosporidium, causes a variety of digestive disorders that can be devastating and even lethal. The Coquerel’s sifaka (Propithecus coquereli) – an endangered, folivorous primate endemic to Madagascar – is precariously susceptible to cryptosporidiosis under captive conditions. If left untreated, infection can rapidly advance to morbidity and death. Objective: To gain a richer understanding of the pathophysiology of this pathogen while also improving captive management of endangered species, we examine the impact of cryptosporidiosis on the GMB of a flagship species known to experience a debilitating disease state upon infection. Design: Using 16S sequencing of DNA extracted from sifaka fecal samples, we compared the microbial communities of healthy sifakas to those of infected individuals, across infection and recovery periods. Results: Over the course of infection, we found that the sifaka GMB responds with decreased microbial diversity and increased community dissimilarity. Compared to the GMB of unaffected individuals, as well as during pre-infection and recovery periods, the GMB during active infection was enriched for microbial taxa associated with dysbiosis and rapid transit time. Time to recovery was inversely related to age, with young animals being slowest to recover GMB diversity and full community membership. Antimicrobial treatment during infection caused a significant depletion in GMB diversity. Conclusions: Although individual sifakas show unique trajectories of microbial loss and recolonization in response to infection, recovering sifakas exhibit remarkably consistent patterns, similar to initial community assembly of the GMB in infants. This observation, in particular, provides biological insight into the rules by which the GMB recovers from the disease state. Fecal transfaunation may prove effective in restoring a healthy GMB in animals with specialized diets.
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Affiliation(s)
| | - Lydia K Greene
- University Program in Ecology, Duke University, Durham, NC, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC
| | - Christine M Drea
- Department of Biology, Duke University, Durham, NC, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC
| | - Anne D Yoder
- Department of Biology, Duke University, Durham, NC, USA.,University Program in Ecology, Duke University, Durham, NC, USA.,Duke Lemur Center, Durham, NC, USA
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Connor N, Barberán A, Clauset A. Using null models to infer microbial co-occurrence networks. PLoS One 2017; 12:e0176751. [PMID: 28493918 PMCID: PMC5426617 DOI: 10.1371/journal.pone.0176751] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/12/2017] [Indexed: 12/21/2022] Open
Abstract
Although microbial communities are ubiquitous in nature, relatively little is known about the structural and functional roles of their constituent organisms' underlying interactions. A common approach to study such questions begins with extracting a network of statistically significant pairwise co-occurrences from a matrix of observed operational taxonomic unit (OTU) abundances across sites. The structure of this network is assumed to encode information about ecological interactions and processes, resistance to perturbation, and the identity of keystone species. However, common methods for identifying these pairwise interactions can contaminate the network with spurious patterns that obscure true ecological signals. Here, we describe this problem in detail and develop a solution that incorporates null models to distinguish ecological signals from statistical noise. We apply these methods to the initial OTU abundance matrix and to the extracted network. We demonstrate this approach by applying it to a large soil microbiome data set and show that many previously reported patterns for these data are statistical artifacts. In contrast, we find the frequency of three-way interactions among microbial OTUs to be highly statistically significant. These results demonstrate the importance of using appropriate null models when studying observational microbiome data, and suggest that extracting and characterizing three-way interactions among OTUs is a promising direction for unraveling the structure and function of microbial ecosystems.
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Affiliation(s)
- Nora Connor
- Department of Computer Science, University of Colorado, Boulder, Colorado, United States of America
- * E-mail:
| | - Albert Barberán
- Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona, United States of America
| | - Aaron Clauset
- Department of Computer Science, University of Colorado, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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50
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Stedtfeld RD, Stedtfeld TM, Fader KA, Williams MR, Bhaduri P, Quensen J, Zacharewski TR, Tiedje JM, Hashsham SA. TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome. FEMS Microbiol Ecol 2017; 93:3798199. [PMID: 28475713 PMCID: PMC5458050 DOI: 10.1093/femsec/fix058] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/02/2017] [Indexed: 02/06/2023] Open
Abstract
Dysbiosis of the gut microbiome via antibiotics, changes in diet and infection can select for bacterial groups that more frequently harbor antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). However, the impact of environmental toxicants on the reservoir of ARGs in the gut microbiome has received less attention. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a potent aryl hydrocarbon receptor (AhR) agonist with multiple toxic health effects including immune dysfunction. The selective pressure of TCDD on the abundance of ARG and MGE-harboring gut populations was examined using C57BL/6 mice exposed to 0-30 μg/kg TCDD for 28 and 92 days with the latter having a 30-day recovery period. DNA extracted from temporally collected fecal pellets was characterized using a qPCR array with 384 assays targeting ARGs and MGEs. Fourteen genes, typically observed in Enterobacteriaceae, increased significantly within 8 days of initial dosing, persisted throughout the treatment period, and remained induced 30 days post dosing. A qPCR primer set targeting Enterobacteriaceae also showed 10- to 100-fold higher abundance in TCDD-treated groups, which was further verified using metagenomics. Results show a bloom of ARG-harboring bacterial groups in the gut due to a xenobiotic compound that is not a metal, biocide or antimicrobial.
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Affiliation(s)
- Robert D. Stedtfeld
- Department of Civil and Environmental Engineering, East Lansing, MI 48824, USA
| | | | - Kelly A. Fader
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Maggie R. Williams
- Department of Civil and Environmental Engineering, East Lansing, MI 48824, USA
| | - Prianca Bhaduri
- Department of Civil and Environmental Engineering, East Lansing, MI 48824, USA
| | - John Quensen
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - Timothy R. Zacharewski
- Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - James M. Tiedje
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
| | - Syed A. Hashsham
- Department of Civil and Environmental Engineering, East Lansing, MI 48824, USA
- Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
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