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Tap J, Lejzerowicz F, Cotillard A, Pichaud M, McDonald D, Song SJ, Knight R, Veiga P, Derrien M. Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors. Nat Commun 2023; 14:3310. [PMID: 37339957 DOI: 10.1038/s41467-023-38558-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 05/04/2023] [Indexed: 06/22/2023] Open
Abstract
The gut microbiome is important for human health, yet modulation requires more insight into inter-individual variation. Here, we explored latent structures of the human gut microbiome across the human lifespan, applying partitioning, pseudotime, and ordination approaches to >35,000 samples. Specifically, three major gut microbiome branches were identified, within which multiple partitions were observed in adulthood, with differential abundances of species along branches. Different compositions and metabolic functions characterized the branches' tips, reflecting ecological differences. An unsupervised network analysis from longitudinal data from 745 individuals showed that partitions exhibited connected gut microbiome states rather than over-partitioning. Stability in the Bacteroides-enriched branch was associated with specific ratios of Faecalibacterium:Bacteroides. We also showed that associations with factors (intrinsic and extrinsic) could be generic, branch- or partition-specific. Our ecological framework for cross-sectional and longitudinal data allows a better understanding of overall variation in the human gut microbiome and disentangles factors associated with specific configurations.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France.
| | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Section for Aquatic Biology and Toxicology, University of Oslo, Oslo, Norway
| | | | | | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Patrick Veiga
- Danone Nutricia Research, Gif-sur-Yvette, France
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, France
| | - Muriel Derrien
- Danone Nutricia Research, Gif-sur-Yvette, France.
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium.
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2
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Rodriguez CI, Keshavarzian A, Hamaker BR, Liu F, Lunken GR, Rasmussen H, Zhou H, Tap J, Swanson KS, Ukhanova M, Leclerc M, Gotteland M, Navarrete P, Kovatcheva-Datchary P, Dahl WJ, Martiny JBH. Curated and harmonized gut microbiome 16S rRNA amplicon data from dietary fiber intervention studies in humans. Sci Data 2023; 10:346. [PMID: 37268699 DOI: 10.1038/s41597-023-02254-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/19/2023] [Indexed: 06/04/2023] Open
Abstract
Next generation amplicon sequencing has created a plethora of data from human microbiomes. The accessibility to this scientific data and its corresponding metadata is important for its reuse, to allow for new discoveries, verification of published results, and serving as path for reproducibility. Dietary fiber consumption has been associated with a variety of health benefits that are thought to be mediated by gut microbiota. To enable direct comparisons of the response of the gut microbiome to fiber, we obtained 16S rRNA sequencing data and its corresponding metadata from 11 fiber intervention studies for a total of 2,368 samples. We provide curated and pre-processed genetic data and common metadata for comparison across the different studies.
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Affiliation(s)
- Cynthia I Rodriguez
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, USA.
| | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology, Rush University Medical Center, Chicago, USA
| | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research and Department of Food Science, Purdue University, West Lafayette, USA
| | - Feitong Liu
- H&H Group, H&H Research, China Research and Innovation Center, Beijing, China
| | | | - Heather Rasmussen
- University of Nebraska-Lincoln, Department of Nutrition and Health Sciences, Lincoln, USA
| | - Hongwei Zhou
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, USA
- State Key Laboratory of Organ Failure Research, Southern Medical University, Guangzhou, China
| | - Julien Tap
- Universite Paris-Saclay, INRAE, MICALIS Institute, Yvette, Jouy-en-Josas, France
| | - Kelly S Swanson
- University of Illinois at Urbana-Champaign, Department of Animal Sciences, Champaign, USA
| | - Maria Ukhanova
- University of Florida, School of Medicine, Gainesville, USA
| | - Marion Leclerc
- Universite Paris-Saclay, INRAE, MICALIS Institute, Yvette, Jouy-en-Josas, France
- Pendulum therapeutics, San Francisco, USA
| | - Martin Gotteland
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
- Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | - Paola Navarrete
- Laboratory of Microbiology and Probiotics, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
| | | | - Wendy J Dahl
- University of Florida, Food Science and Human Nutrition Department, Gainesville, USA
| | - Jennifer B H Martiny
- Dept. of Ecology and Evolutionary Biology, University of California, Irvine, USA
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3
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Ladeira R, Tap J, Derrien M. Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy. Microbiome Res Rep 2023; 2:9. [PMID: 38047280 PMCID: PMC10688807 DOI: 10.20517/mrr.2023.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 12/05/2023]
Abstract
Aim: The human gut Bifidobacterium community has been studied in detail in infants and following dietary interventions in adults. However, the variability of the distribution of Bifidobacterium species and intra-species functions have been little studied, particularly beyond infancy. Here, we explore the ecology of Bifidobacterium communities in a large public dataset of human gut metagenomes, mostly corresponding to adults. Methods: We selected 9.515 unique gut metagenomes from curatedMetagenomicData. Samples were partitioned by applying Dirichlet's multinomial mixture to Bifidobacterium species. A functional analysis was performed on > 2.000 human-associated Bifidobacterium metagenome-assembled genomes (MAGs) paired with participant gut microbiome and health features. Results: We identified several Bifidobacterium-based partitions in the human gut microbiome differing in terms of the presence and abundance of Bifidobacterium species. The partitions enriched in both B. longum and B. adolescentis were associated with gut microbiome diversity and a higher abundance of butyrate producers and were more prevalent in healthy individuals. B. bifidum MAGs harboring a set of genes potentially related to phages were more prevalent in partitions associated with a lower gut microbiome diversity and were genetically more closely related. Conclusion: This study expands our knowledge of the ecology and variability of the Bifidobacterium community, particularly in adults, and its specific association with the gut microbiota and health. Its findings may guide the rational selection of Bifidobacterium strains for gut microbiome complementation according to the individual's endogenous Bifidobacterium community. Our results also suggest that gut microbiome stratification for particular genera may be relevant for studies of variations of species and associations with the gut microbiome and health.
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Affiliation(s)
- Ruben Ladeira
- Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France
| | - Julien Tap
- Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas 78350, France
| | - Muriel Derrien
- Advanced Health & Science, Danone Global Research & Innovation Center, Gif-sur-Yvette 91190, France
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Litwin N, Cantrell K, Cotillard A, Derrien M, Johnson A, Knight R, Lejzerowicz F, McDonald D, Nowinski B, Song SJ, Tap J, Veiga P. Representing Diet in a Tree-Based Format for Interactive and Exploratory Assessment of Dietary Intake Data. Curr Dev Nutr 2022. [PMCID: PMC9193992 DOI: 10.1093/cdn/nzac063.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Objectives
We assessed the utility of representing dietary intake data in hierarchical tree structures that consider relationships among foods.
Methods
Dietary intake was collected from 1909 adults (≥18 years) using a food frequency questionnaire (FFQ; VioScreen) from the American Gut Project. FFQ food items were formatted into hierarchical tree structures based on 1) USDA's Food Nutrient and Database for Dietary Studies (FNDDS) classifications, 2) nutrient content, and 3) molecular compound information detected via mass spectrometry to capture the non-nutrient composition of foods. Next, we compared how well representing dissimilarities (or distances) between individuals based on their diet corresponded with indices such as the Healthy Eating Index (HEI-2015), when those distances are calculated using tree-based versus non-tree-based metrics. We performed an Adonis test (PERMANOVA) to measure the amount of variation explained (R2) in these diet-based distances by HEI-2015.
Results
We observed that dietary ordinations generated using tree-based relationships between foods have better agreement with HEI than ordinations generated without considering relatedness between foods. The variation explained by HEI-2015 increased by 35% when using the FNDDS tree compared to using a non-tree based quantitative metric (Bray-Curtis (not tree-based) R2 = 0.02931 vs. Weighted UniFrac (tree-based) R2 = 0.03969), by >20% when using the nutrient tree (vs. Weighted UniFrac R2 = 0.03627), and only marginally (6%) when using the molecular compound tree (vs. Weighted UniFrac R2 = 0.03116).
Conclusions
We show that tree-based measurements of dietary similarity lead to better agreement with diet indices (e.g., HEI) than when relationships among foods are not considered. We also show that representing dietary intake in a tree-like structure can offer interactive visualizations of data that can be used to inform hypotheses regarding dietary characteristics.
Funding Sources
Danone Nutricia Research.
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Affiliation(s)
- Nicole Litwin
- Center for Microbiome Innovation, University of California, San Diego
| | - Kalen Cantrell
- Center for Microbiome Innovation, University of California, San Diego
| | | | | | | | - Rob Knight
- Center for Microbiome Innovation, University of California, San Diego
| | | | | | - Brent Nowinski
- Center for Microbiome Innovation, University of California, San Diego
| | - Se Jin Song
- Center for Microbiome Innovation, University of California, San Diego
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Oyarzun I, Le Nevé B, Yañez F, Xie Z, Pichaud M, Serrano-Gómez G, Roca J, Veiga P, Azpiroz F, Tap J, Manichanh C. Human gut metatranscriptome changes induced by a fermented milk product are associated with improved tolerance to a flatulogenic diet. Comput Struct Biotechnol J 2022; 20:1632-1641. [PMID: 35465165 PMCID: PMC9014321 DOI: 10.1016/j.csbj.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/02/2022] [Accepted: 04/02/2022] [Indexed: 11/29/2022] Open
Abstract
Healthy plant-based diets rich in fermentable residues may induce gas-related symptoms, possibly mediated by the gut microbiota. We previously showed that consumption of a fermented milk product (FMP) containing Bifidobacterium animalis subsp. lactis CNCM I-2494 and lactic acid bacteria improved gastrointestinal (GI) comfort in response to a flatulogenic dietary challenge in healthy individuals. To study the effects of the FMP on gut microbiota activity from those participants, we conducted a metatranscriptomic analysis of fecal samples (n = 262), which were collected during the ingestion of a habitual diet and two series of a 3-day high-residue challenge diet, before and following 28-days of FMP consumption. Most of the FMP species were detected or found enriched upon consumption of the product. FMP mitigated the effect of a flatulogenic diet on gas-related symptoms in several ways. First, FMP consumption was associated with the depletion of gas-producing bacteria and increased hydrogen to methane conversion. It also led to the upregulation of activities such as replication and downregulation of functions related to motility and chemotaxis. Furthermore, upon FMP intake, metabolic activities such as carbohydrate metabolism, attributed to B. animalis and S. thermophilus, were enriched; these activities were coincidentally found to be negatively associated with several GI symptoms. Finally, a more connected microbial ecosystem or mutualistic relationship among microbes was found in responders to the FMP intervention. Taken together, these findings suggest that consumption of the FMP improved the tolerance of a flatulogenic diet through active interactions with the resident gut microbiota.
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Affiliation(s)
- Iñigo Oyarzun
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Francisca Yañez
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Zixuan Xie
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | | | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | | | - Fernando Azpiroz
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | - Chaysavanh Manichanh
- Microbiome Lab, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
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Vanhaecke T, Bretin O, Poirel M, Tap J. Drinking Water Source and Intake Are Associated with Distinct Gut Microbiota Signatures in US and UK Populations. J Nutr 2021; 152:171-182. [PMID: 34642755 PMCID: PMC8754568 DOI: 10.1093/jn/nxab312] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/28/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The microbiome of the digestive tract exerts fundamental roles in host physiology. Extrinsic factors including lifestyle and diet are widely recognized as key drivers of gut and oral microbiome compositions. Although drinking water is among the food items consumed in the largest amount, little is known about its potential impact on the microbiome. OBJECTIVES We explored the associations of plain drinking water source and intake with gut and oral microbiota compositions in a population-based cohort. METHODS Microbiota, health, lifestyle, and food intake data were extracted from the American Gut Project public database. Associations of drinking water source (bottled, tap, filtered, or well water) and intake with global microbiota composition were evaluated using linear and logistic models adjusted for anthropometric, diet, and lifestyle factors in 3413 and 3794 individuals, respectively (fecal samples; 56% female, median [IQR] age: 48 [36-59] y; median [IQR] BMI: 23.3 [20.9-26.3] kg/m2), and in 283 and 309 individuals, respectively (oral samples). RESULTS Drinking water source ranked among the key contributing factors explaining the gut microbiota variation, accounting for 13% [Faith's phylogenetic diversity (Faith's PD)] and 47% (Bray-Curtis dissimilarity) of the age effect size. Drinking water source was associated with differences in gut microbiota signatures, as revealed by β diversity analyses (P < 0.05; Bray-Curtis dissimilarity, weighted UniFrac distance). Subjects drinking mostly well water had higher fecal α diversity (P < 0.05; Faith's PD, observed amplicon sequence variants), higher Dorea, and lower Bacteroides, Odoribacter, and Streptococcus than the other groups. Low water drinkers also exhibited gut microbiota differences compared with high water drinkers (P < 0.05; Bray-Curtis dissimilarity, unweighted UniFrac distance) and a higher abundance of Campylobacter. No associations were found between oral microbiota composition and drinking water consumption. CONCLUSIONS Our results indicate that drinking water may be an important factor in shaping the human gut microbiome and that integrating drinking water source and intake as covariates in future microbiome analyses is warranted.
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Cotillard A, Cartier-Meheust A, Litwin NS, Chaumont S, Saccareau M, Lejzerowicz F, Tap J, Koutnikova H, Lopez DG, McDonald D, Song SJ, Knight R, Derrien M, Veiga P. A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project. Am J Clin Nutr 2021; 115:432-443. [PMID: 34617562 PMCID: PMC8827078 DOI: 10.1093/ajcn/nqab332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/27/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Individual diet components and specific dietary regimens have been shown to impact the gut microbiome. OBJECTIVES Here, we explored the contribution of long-term diet by searching for dietary patterns that would best associate with the gut microbiome in a population-based cohort. METHODS Using a priori and a posteriori approaches, we constructed dietary patterns from an FFQ completed by 1800 adults in the American Gut Project. Dietary patterns were defined as groups of participants or combinations of food variables (factors) driven by criteria ranging from individual nutrients to overall diet. We associated these patterns with 16S ribosomal RNA-based gut microbiome data for a subset of 744 participants. RESULTS Compared to individual features (e.g., fiber and protein), or to factors representing a reduced number of dietary features, 5 a posteriori dietary patterns based on food groups were best associated with gut microbiome beta diversity (P ≤ 0.0002). Two patterns followed Prudent-like diets-Plant-Based and Flexitarian-and exhibited the highest Healthy Eating Index 2010 (HEI-2010) scores. Two other patterns presented Western-like diets with a gradient in HEI-2010 scores. A fifth pattern consisted mostly of participants following an Exclusion diet (e.g., low carbohydrate). Notably, gut microbiome alpha diversity was significantly lower in the most Western pattern compared to the Flexitarian pattern (P ≤ 0.009), and the Exclusion diet pattern was associated with low relative abundance of Bifidobacterium (P ≤ 1.2 × 10-7), which was better explained by diet than health status. CONCLUSIONS We demonstrated that global-diet a posteriori patterns were more associated with gut microbiome variations than individual dietary features among adults in the United States. These results confirm that evaluating diet as a whole is important when studying the gut microbiome. It will also facilitate the design of more personalized dietary strategies in general populations.
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Affiliation(s)
| | | | - Nicole S Litwin
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | | | | | - Franck Lejzerowicz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | | | - Diana Gutierrez Lopez
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Se Jin Song
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
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Cotillard A, Chaumont S, Saccareau M, Litwin NS, Lopez DG, Tap J, Lejzerowicz F, Demaretz L, McDonald D, Song SJ, Knight R, Cartier-Meheust A, Veiga P. Unsupervised Diet Partitions Better Explain Variations of the Gut Microbiome Compared to Individual Dietary Markers in U.S. Adults of the American Gut Project Cohort. Curr Dev Nutr 2021. [DOI: 10.1093/cdn/nzab038_009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Objectives
Eating habits have been shown to impact the gut microbiome. Here we aimed to define several types of dietary patterns in a U.S. adult cohort and test their associations with the gut microbiome.
Methods
Using supervised and unsupervised approaches, we built dietary patterns based on a food frequency questionnaire of the American Gut Project database. Focusing on 1800 adult participants living in the United States, we defined patterns as partitions (groups of participants) or factors (combinations of food variables) driven by specific dietary criteria: fibers, proteins, Healthy Eating Index (HEI 2010), food items, food groups and micronutrients. We then associated these patterns with 16S gut microbiome data for 744 participants, excluding those reporting antibiotic intake in the last year or specific diseases. Analyses were adjusted for age, sex and BMI.
Results
Compared to individual features like fibers and proteins, or to factors representing reduced numbers of features, five unsupervised partitions based on food groups were best associated with gut microbiome beta-diversity. Two partitions presented a lower consumption of animal products, with one being almost completely exclusive and the other, close to a flexitarian diet, presenting the best diet quality as measured by HEI. A third one consisted mostly of participants under low carbohydrate diets with nearly no consumption of starchy foods or sweet products. Finally, the last two partitions presented Western-like diets with increased consumption of mixed dishes, sweet products and refined cereals, one of them being more diverse with increased nuts and whole cereals. Gut microbiome alpha-diversity was slightly increased in the flexitarian partition compared to the most westernized one. Strikingly, the low carbohydrate partition was associated with low levels of the Bifidobacterium genus.
Conclusions
We showed in a U.S. adult cohort that a global diet may be more associated with gut microbiome variations than individual features like fibers or proteins. Five diet partitions were identified and their specific associations with gut microbiome were studied. These results confirm the importance to consider diet as a whole when studying gut microbiota diversity.
Funding Sources
Danone Research.
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Affiliation(s)
| | | | | | - Nicole S Litwin
- Center for Microbiome Innovation & Department of Pediatrics, School of Medicine - University of California San Diego
| | | | | | - Franck Lejzerowicz
- Center for Microbiome Innovation & Department of Pediatrics, School of Medicine - University of California San Diego
| | | | - Daniel McDonald
- Department of Pediatrics, School of Medicine - University of California San Diego
| | - Se Jin Song
- Center for Microbiome Innovation - University of California San Diego
| | - Rob Knight
- Center for Microbiome Innovation & Department of Pediatrics, School of Medicine & Department of Bioengineering & Department of Computer Science and Engineering & Scripps Institution of Oceanography - University of California San Diego
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Tap J, Störsrud S, Le Nevé B, Cotillard A, Pons N, Doré J, Öhman L, Törnblom H, Derrien M, Simrén M. Diet and gut microbiome interactions of relevance for symptoms in irritable bowel syndrome. Microbiome 2021; 9:74. [PMID: 33771219 PMCID: PMC8004395 DOI: 10.1186/s40168-021-01018-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/02/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND While several studies have documented associations between dietary habits and microbiota composition and function in healthy individuals, no study explored these associations in patients with irritable bowel syndrome (IBS), and especially with symptoms. METHODS Here, we used a novel approach that combined data from a 4-day food diary, integrated into a food tree, together with gut microbiota (shotgun metagenomic) for individuals with IBS (N = 149) and healthy controls (N = 52). Paired microbiota and food-based trees allowed us to detect new associations between subspecies and diet. Combining co-inertia analysis and linear regression models, exhaled gas levels and symptom severity could be predicted from metagenomic and dietary data. RESULTS We showed that individuals with severe IBS are characterized by a higher intake of poorer-quality food items during their main meals. Our analysis suggested that covariations between gut microbiota at subspecies level and diet could be explained with IBS symptom severity, exhaled gas, glycan metabolism, and meat/plant ratio. We provided evidence that IBS severity is associated with altered gut microbiota hydrogen function in correlation with microbiota enzymes involved in animal carbohydrate metabolism. CONCLUSIONS Our study provides an unprecedented resolution of diet-microbiota-symptom interactions and ultimately guides new interventional studies that aim to identify gut microbiome-based nutritional recommendations for the management of gastrointestinal symptoms. TRIAL REGISTRATION This trial was registered on the ClinicalTrials.gov, with the registration number NCT01252550 , on 3rd December 2010. Video abstract.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Palaiseau, France.
| | - Stine Störsrud
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Nicolas Pons
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Joël Doré
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Lena Öhman
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
- Department of Immunology and Microbiology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden
| | | | - Magnus Simrén
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg, Sweden.
- Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina, Chapel Hill, NC, USA.
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10
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Polster A, Öhman L, Tap J, Derrien M, Le Nevé B, Sundin J, Törnblom H, Cvijovic M, Simrén M. A novel stepwise integrative analysis pipeline reveals distinct microbiota-host interactions and link to symptoms in irritable bowel syndrome. Sci Rep 2021; 11:5521. [PMID: 33750831 PMCID: PMC7943560 DOI: 10.1038/s41598-021-84686-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 02/15/2021] [Indexed: 12/15/2022] Open
Abstract
Although incompletely understood, microbiota-host interactions are assumed to be altered in irritable bowel syndrome (IBS). We, therefore, aimed to develop a novel analysis pipeline tailored for the integrative analysis of microbiota-host interactions and association to symptoms and prove its utility in a pilot cohort. A multilayer stepwise integrative analysis pipeline was developed to visualize complex variable associations. Application of the pipeline was demonstrated on a dataset of IBS patients and healthy controls (HC), using the R software package to analyze colonic host mRNA and mucosal microbiota (16S rRNA gene sequencing), as well as gastrointestinal (GI) and psychological symptoms. In total, 42 IBS patients (57% female, mean age 33.6 (range 18–58)) and 20 HC (60% female, mean age 26.8 (range 23–41)) were included. Only in IBS patients, mRNA expression of Toll-like receptor 4 and genes associated with barrier function (PAR2, OCLN, TJP1) intercorrelated closely, suggesting potential functional relationships. This host genes-based “permeability cluster” was associated to mucosa-adjacent Chlamydiae and Lentisphaerae, and furthermore associated to satiety as well as to anxiety, depression and fatigue. In both IBS patients and HC, chromogranins, secretogranins and TLRs clustered together. In IBS patients, this host genes-based “immune-enteroendocrine cluster” was associated to specific members of Firmicutes, and to depression and fatigue, whereas in HC no significant association to microbiota was identified. We have developed a stepwise integrative analysis pipeline that allowed identification of unique host-microbiota intercorrelation patterns and association to symptoms in IBS patients. This analysis pipeline may aid in advancing the understanding of complex variable associations in health and disease.
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Affiliation(s)
- Annikka Polster
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska University Hospital, Sahlgrenska Academy, University of Gothenburg, 41345, Göteborg, Sweden.
| | - Lena Öhman
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska University Hospital, Sahlgrenska Academy, University of Gothenburg, 41345, Göteborg, Sweden.,Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | | | | | - Johanna Sundin
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska University Hospital, Sahlgrenska Academy, University of Gothenburg, 41345, Göteborg, Sweden.,Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Göteborg, Sweden
| | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska University Hospital, Sahlgrenska Academy, University of Gothenburg, 41345, Göteborg, Sweden
| | - Marija Cvijovic
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Göteborg, Sweden
| | - Magnus Simrén
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska University Hospital, Sahlgrenska Academy, University of Gothenburg, 41345, Göteborg, Sweden.,Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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11
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Le Nevé B, Derrien M, Tap J, Brazeilles R, Cools Portier S, Guyonnet D, Ohman L, Störsrud S, Törnblom H, Simrén M. Fasting breath H2 and gut microbiota metabolic potential are associated with the response to a fermented milk product in irritable bowel syndrome. PLoS One 2019; 14:e0214273. [PMID: 30946757 PMCID: PMC6448848 DOI: 10.1371/journal.pone.0214273] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 02/25/2019] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES Aim of this study was to assess the effect of a fermented milk product containing Bifidobacterium lactis CNCM I-2494 (FMP) on gastrointestinal (GI) symptoms and exhaled H2 and CH4 during a nutrient and lactulose challenge in patients with irritable bowel syndrome (IBS). METHODS We included 125 patients with IBS (Rome III). Fasted subjects were served a 400ml liquid test meal containing 25g lactulose. The intensity of eight GI symptoms and the amount of exhaled H2 and CH4 were assessed before and during 4h after meal intake. The challenge was repeated after 14 days consumption of FMP or a control product in a double-blind, randomized, parallel design. The metabolic potential of fecal microbiota was profiled using 16S MiSeq analysis of samples obtained before and after the intervention. RESULTS 106 patients with IBS were randomized. No difference between FMP or control groups was found on GI symptoms or breath H2 and CH4 in the whole cohort. A post-hoc analysis in patients stratified according to their fasting H2 levels showed that in high H2 producers (fasting H2 level≥10ppm, n = 35), FMP consumption reduced fasting H2 levels (p = 0.003) and H2 production during the challenge (p = 0.002) and tended to decrease GI discomfort (p = 0.05) vs. control product. The Prevotella/Bacteroides metabolic potential at baseline was higher in high H2 producers (p<0.05) vs. low H2 producers and FMP consumption reduced this ratio (p<0.05) vs. control product. CONCLUSIONS The response to a fermented milk product containing Bifidobacterium lactis CNCM I-2494 (FMP) in patients with IBS seems to be associated with the metabolic potential of the gut microbiota. TRIAL REGISTRATION ClinicalTrial.gov NCT01252550. These results were presented as congress posters at Digestive Disease Week 2016 in San Diego, USA and United European Gastroenterology Week 2016 in Vienna, Austria.
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Affiliation(s)
| | | | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | | | | | | | - Lena Ohman
- Department of Immunology and Microbiology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Stine Störsrud
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina, Chapel Hill, North Carolina, United States of America
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12
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Labus JS, Osadchiy V, Hsiao EY, Tap J, Derrien M, Gupta A, Tillisch K, Le Nevé B, Grinsvall C, Ljungberg M, Öhman L, Törnblom H, Simren M, Mayer EA. Evidence for an association of gut microbial Clostridia with brain functional connectivity and gastrointestinal sensorimotor function in patients with irritable bowel syndrome, based on tripartite network analysis. Microbiome 2019; 7:45. [PMID: 30898151 PMCID: PMC6429755 DOI: 10.1186/s40168-019-0656-z] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 03/07/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND AND AIMS Evidence from preclinical and clinical studies suggests that interactions among the brain, gut, and microbiota may affect the pathophysiology of irritable bowel syndrome (IBS). As disruptions in central and peripheral serotonergic signaling pathways have been found in patients with IBS, we explored the hypothesis that the abundance of serotonin-modulating microbes of the order Clostridiales is associated with functional connectivity of somatosensory brain regions and gastrointestinal (GI) sensorimotor function. METHODS We performed a prospective study of 65 patients with IBS and 21 healthy individuals (controls) recruited from 2011 through 2013 at a secondary/tertiary care outpatient clinic in Sweden. Study participants underwent functional brain imaging, rectal balloon distension, a nutrient and lactulose challenge test, and assessment of oroanal transit time within a month. They also submitted stool samples, which were analyzed by 16S ribosomal RNA gene sequencing. A tripartite network analysis based on graph theory was used to investigate the interactions among bacteria in the order Clostridiales, connectivity of brain regions in the somatosensory network, and GI sensorimotor function. RESULTS We found associations between GI sensorimotor function and gut microbes in stool samples from controls, but not in samples from IBS patients. The largest differences between controls and patients with IBS were observed in the Lachnospiraceae incertae sedis, Clostridium XIVa, and Coprococcus subnetworks. We found connectivity of subcortical (thalamus, caudate, and putamen) and cortical (primary and secondary somatosensory cortices) regions to be involved in mediating interactions among these networks. CONCLUSIONS In a comparison of patients with IBS and controls, we observed disruptions in the interactions between the brain, gut, and gut microbial metabolites in patients with IBS-these involve mainly subcortical but also cortical regions of brain. These disruptions may contribute to altered perception of pain in patients with IBS and may be mediated by microbial modulation of the gut serotonergic system.
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Affiliation(s)
- Jennifer S Labus
- G. Oppenheimer Center for Neurobiology of Stress & Resilience, UCLA Vatche and Tamar Manoukian Division of Digestive Diseases, UCLA CHS 42-210, MC737818, 10833 Le Conte Avenue, Los Angeles, CA, 90095-7378, USA
| | - Vadim Osadchiy
- G. Oppenheimer Center for Neurobiology of Stress & Resilience, UCLA Vatche and Tamar Manoukian Division of Digestive Diseases, UCLA CHS 42-210, MC737818, 10833 Le Conte Avenue, Los Angeles, CA, 90095-7378, USA
| | - Elaine Y Hsiao
- G. Oppenheimer Center for Neurobiology of Stress & Resilience, UCLA Vatche and Tamar Manoukian Division of Digestive Diseases, UCLA CHS 42-210, MC737818, 10833 Le Conte Avenue, Los Angeles, CA, 90095-7378, USA
- UCLA Department of Integrative Biology and Physiology, Los Angeles, USA
| | - Julien Tap
- Danone Nutricia Research, Innovation, Science and Nutrition, Palaiseau, France
| | - Muriel Derrien
- Danone Nutricia Research, Innovation, Science and Nutrition, Palaiseau, France
| | - Arpana Gupta
- G. Oppenheimer Center for Neurobiology of Stress & Resilience, UCLA Vatche and Tamar Manoukian Division of Digestive Diseases, UCLA CHS 42-210, MC737818, 10833 Le Conte Avenue, Los Angeles, CA, 90095-7378, USA
| | - Kirsten Tillisch
- G. Oppenheimer Center for Neurobiology of Stress & Resilience, UCLA Vatche and Tamar Manoukian Division of Digestive Diseases, UCLA CHS 42-210, MC737818, 10833 Le Conte Avenue, Los Angeles, CA, 90095-7378, USA
| | - Boris Le Nevé
- Danone Nutricia Research, Innovation, Science and Nutrition, Palaiseau, France
| | - Cecilia Grinsvall
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria Ljungberg
- Department of Radiation Physics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Lena Öhman
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Immunology and Microbiology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simren
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina, Chapel Hill, NC, USA
| | - Emeran A Mayer
- G. Oppenheimer Center for Neurobiology of Stress & Resilience, UCLA Vatche and Tamar Manoukian Division of Digestive Diseases, UCLA CHS 42-210, MC737818, 10833 Le Conte Avenue, Los Angeles, CA, 90095-7378, USA.
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13
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Tap J, Cools-Portier S, Pavan S, Druesne A, Öhman L, Törnblom H, Simren M, Derrien M. Effects of the long-term storage of human fecal microbiota samples collected in RNAlater. Sci Rep 2019; 9:601. [PMID: 30679604 PMCID: PMC6345939 DOI: 10.1038/s41598-018-36953-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/23/2018] [Indexed: 12/14/2022] Open
Abstract
The adequate storage of fecal samples from clinical trials is crucial if analyses are to be performed later and in long-term studies. However, it is unknown whether the composition of the microbiota is preserved during long-term stool storage (>1 year). We therefore evaluated the influence of long-term storage on the microbiota composition of human stool samples collected in RNAlater and stored for approximately five years at −80 °C. We compared storage effects on stool samples from 24 subjects with the effects of technical variation due to different sequencing runs and biological variation (intra- and inter-subject), in another 101 subjects, based on alpha-diversity, beta-diversity and taxonomic composition. We also evaluated the impact of initial alpha-diversity and fecal microbiota composition on beta-diversity instability upon storage. Overall, long-term stool storage at −80 °C had only limited effects on the microbiota composition of human feces. The magnitude of changes in alpha- and beta- diversity and taxonomic composition after long-term storage was similar to inter-sequencing variation and smaller than biological variation (both intra- and inter-subject). The likelihood of fecal samples being affected by long-term storage correlated with the initial relative abundance of some genera and tend to be affected by initial taxonomic richness.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Innovation, Science and Nutrition Department, RD 128 - Avenue de la Vauve, 91767, Palaiseau, France
| | - Stéphanie Cools-Portier
- Danone Nutricia Research, Innovation, Science and Nutrition Department, RD 128 - Avenue de la Vauve, 91767, Palaiseau, France
| | | | - Anne Druesne
- Danone Nutricia Research, Innovation, Science and Nutrition Department, RD 128 - Avenue de la Vauve, 91767, Palaiseau, France
| | - Lena Öhman
- Department of Immunology and Microbiology, Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Internal Medicine and Clinical Nutrition, Inst. Of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, Inst. Of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simren
- Department of Internal Medicine and Clinical Nutrition, Inst. Of Medicine, University of Gothenburg, Gothenburg, Sweden.,Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Muriel Derrien
- Danone Nutricia Research, Innovation, Science and Nutrition Department, RD 128 - Avenue de la Vauve, 91767, Palaiseau, France.
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14
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Bennet SMP, Sundin J, Magnusson MK, Strid H, Tap J, Derrien M, Le Nevé B, Doré J, Törnblom H, Simrén M, Öhman L. Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation. Neurogastroenterol Motil 2018; 30:e13468. [PMID: 30230134 DOI: 10.1111/nmo.13468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/25/2018] [Accepted: 08/16/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Immune activity and gut microbiota may impact the pathophysiology of irritable bowel syndrome (IBS). We aimed to determine whether antibacterial gene expression of immune activity-defined IBS patients differed compared to healthy subjects (HS) and ulcerative colitis (UC) patients and whether antibacterial profiles reflected gut microbiota composition and IBS symptoms. METHODS Expression of 84 antibacterial genes in biopsies from HS, IBS patients (clustered according to immune activity (systemic and intestinal cytokines): immunonormal or immunoactive), and UC patients was assessed by Human Antibacterial Response RT2 Profiler PCR Array. In IBS patients, 16S rRNA gene sequencing of fecal and mucosal bacteria was performed and symptom pattern and severity were assessed. KEY RESULTS Intestinal antibacterial gene expression profiles differed between IBS patients (n = 31) and HS (n = 16), but did not differ between IBS subgroups based on bowel habit predominance or symptom severity. Based on previously identified IBS clusters, IBS patients with normal (n = 15) and enhanced immune activity (n = 16) had clearly separate antibacterial gene expression profiles from active UC patients (n = 12) and differed compared to each other and to HS. The differences in antibacterial gene expression profiles between immunonormal and immunoactive IBS patients were also reflected in distinct fecal and mucosal microbiota composition profiles, but not in symptom pattern or severity. CONCLUSIONS & INFERENCES This study demonstrates an altered antibacterial gene expression profile in IBS patients compared to HS and UC patients. While not linked to symptoms, immune activity-defined IBS clusters showed different intestinal antibacterial gene expression and distinct fecal and mucosal bacterial profiles.
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Affiliation(s)
- Sean M P Bennet
- Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Johanna Sundin
- Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Maria K Magnusson
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Julien Tap
- Danone Nutricia Research, Palaiseau, France
| | | | | | - Joël Doré
- French National Institute for Agricultural Research (INRA) MetaGenoPolis, Jouy-en-Josas, France
| | - Hans Törnblom
- Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Centre for Person-Centred Care, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Centre for Person-Centred Care, University of Gothenburg, Gothenburg, Sweden.,Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina, Chapel Hill, North Carolina
| | - Lena Öhman
- Institute of Medicine, University of Gothenburg, Gothenburg, Sweden.,Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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15
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Ruppé E, Ghozlane A, Tap J, Pons N, Alvarez AS, Maziers N, Cuesta T, Hernando-Amado S, Clares I, Martínez JL, Coque TM, Baquero F, Lanza VF, Máiz L, Goulenok T, de Lastours V, Amor N, Fantin B, Wieder I, Andremont A, van Schaik W, Rogers M, Zhang X, Willems RJL, de Brevern AG, Batto JM, Blottière HM, Léonard P, Léjard V, Letur A, Levenez F, Weiszer K, Haimet F, Doré J, Kennedy SP, Ehrlich SD. Prediction of the intestinal resistome by a three-dimensional structure-based method. Nat Microbiol 2018; 4:112-123. [PMID: 30478291 DOI: 10.1038/s41564-018-0292-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 10/11/2018] [Indexed: 12/21/2022]
Abstract
The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens via mobile genetic elements. Yet, this assumption is poorly supported by empirical evidence due to the distant homologies between known ARDs (mostly from culturable bacteria) and ARDs from the intestinal microbiota. Consequently, an accurate census of intestinal ARDs (that is, the intestinal resistome) has not yet been fully determined. For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. We found that the majority of predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino acid identity 29.8%) and found little evidence supporting their transfer between species. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n = 663) into six resistotypes that were connected to the previously described enterotypes. Finally, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results indicate that the majority of intestinal microbiota ARDs can be considered intrinsic to the dominant commensal microbiota and that these genes are rarely shared with bacterial pathogens.
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Affiliation(s)
- Etienne Ruppé
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France. .,IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.
| | - Amine Ghozlane
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Institut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS, Paris, France.,Institut Pasteur - Biomics - CITECH, Paris, France
| | - Julien Tap
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Danone Nutricia Research, Palaiseau, France
| | - Nicolas Pons
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | - Nicolas Maziers
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | | | | | - Irene Clares
- Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | | | - Teresa M Coque
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Fernando Baquero
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana, Madrid, Spain
| | - Val F Lanza
- Servicio de Microbiología Instituto, Ramón y Cajal de Investigación Sanitaria, Madrid, Spain.,CIBER en Epidemiología y Salud Pública, Madrid, Spain
| | - Luis Máiz
- Unit for Cystic Fibrosis, Ramon y Cajal University Hospital, Madrid, Spain
| | - Tiphaine Goulenok
- Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Victoire de Lastours
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Nawal Amor
- Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Bruno Fantin
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Internal Medicine Department, Beaujon Hospital, AP-HP, Clichy, France
| | - Ingrid Wieder
- Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Antoine Andremont
- IAME, UMR 1137, INSERM, Paris Diderot University, Sorbonne Paris Cité, Paris, France.,Bacteriology Laboratory, Bichat-Claude Bernard Hospital, AP-HP, Paris, France
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands.,Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, UK
| | - Malbert Rogers
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Xinglin Zhang
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Alexandre G de Brevern
- INSERM UMR_S 1134, Paris Diderot University, Sorbonne Paris Cité, Université de la Réunion, Université des Antilles, INTS, GR-Ex, Paris, France
| | - Jean-Michel Batto
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Hervé M Blottière
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Pierre Léonard
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Véronique Léjard
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Aline Letur
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Florence Levenez
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Kevin Weiszer
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Florence Haimet
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Joël Doré
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France
| | - Sean P Kennedy
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Institut Pasteur - Biomics - CITECH, Paris, France
| | - S Dusko Ehrlich
- MGP MetaGénoPolis, INRA, Université Paris-Saclay, Jouy en Josas, France.,Centre of Host Microbiome Interactions, King's College, London, UK
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16
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Breban M, Tap J, Leboime A, Said-Nahal R, Langella P, Chiocchia G, Furet JP, Sokol H. Faecal microbiota study reveals specific dysbiosis in spondyloarthritis. Ann Rheum Dis 2017; 76:1614-1622. [PMID: 28606969 DOI: 10.1136/annrheumdis-2016-211064] [Citation(s) in RCA: 215] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/23/2017] [Accepted: 05/10/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Altered microbiota composition or dysbiosis is suspected to be implicated in the pathogenesis of chronic inflammatory diseases, such as spondyloarthritis (SpA) and rheumatoid arthritis (RA). METHODS 16S ribosomal RNA gene sequencing was performed on faecal DNA isolated from stool samples in two consecutive cross-sectional cohorts, each comprising three groups of adult volunteers: SpA, RA and healthy controls (HCs). In the second study, HCs comprised a majority of aged-matched siblings of patients with known HLA-B27 status. Alpha and beta diversities were assessed using QIIME, and comparisons were performed using linear discriminant analysis effect size to examine differences between groups. RESULTS In both cohorts, dysbiosis was evidenced in SpA and RA, as compared with HCs, and was disease specific. A restriction of microbiota biodiversity was detected in both disease groups. The most striking change was a twofold to threefold increased abundance of Ruminococcus gnavus in SpA, as compared with both RA and HCs that was significant in both studies and positively correlated with disease activity in patients having a history of inflammatory bowel disease (IBD). Among HCs, significant difference in microbiota composition were also detected between HLA-B27+ and HLA-B27 negative siblings, suggesting that genetic background may influence gut microbiota composition. CONCLUSION Our results suggest that distinctive dysbiosis characterise both SpA and RA and evidence a reproducible increase in R. gnavus that appears specific for SpA and a marker of disease activity. This observation is consistent with the known proinflammatory role of this bacteria and its association with IBD. It may provide an explanation for the link that exists between SpA and IBD.
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Affiliation(s)
- Maxime Breban
- Université de Versailles-Saint-Quentin, Montigny-le-Bretonneux, France.,Université Paris Descartes, Sorbonne Paris Cité, Laboratoire d'Excellence Inflamex, Paris, France.,Service de Rhumatologie, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris, Boulogne, France
| | - Julien Tap
- Micalis Institute, INRA, AgroParisTech, Université ParisSaclay, Jouy-en-Josas, France.,MetaGenoPolis, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Ariane Leboime
- Service de Rhumatologie, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris, Boulogne, France
| | - Roula Said-Nahal
- Service de Rhumatologie, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris, Boulogne, France
| | - Philippe Langella
- Micalis Institute, INRA, AgroParisTech, Université ParisSaclay, Jouy-en-Josas, France
| | - Gilles Chiocchia
- Université de Versailles-Saint-Quentin, Montigny-le-Bretonneux, France.,Université Paris Descartes, Sorbonne Paris Cité, Laboratoire d'Excellence Inflamex, Paris, France.,Department of Gastroenterology, Saint Antoine Hospital, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Jean-Pierre Furet
- Micalis Institute, INRA, AgroParisTech, Université ParisSaclay, Jouy-en-Josas, France
| | - Harry Sokol
- Micalis Institute, INRA, AgroParisTech, Université ParisSaclay, Jouy-en-Josas, France.,Sorbonne University-UPMC Univ Paris 06, INSERM ERL 1157, Avenir Team Gut Microbiota and Immunity, Paris, France.,Service d'Immunologie, Hôpital Ambroise Paré, Assistance Publique - Hôpitaux de Paris, Boulogne, France
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Tap J, Derrien M, Törnblom H, Brazeilles R, Cools-Portier S, Doré J, Störsrud S, Le Nevé B, Öhman L, Simrén M. Identification of an Intestinal Microbiota Signature Associated With Severity of Irritable Bowel Syndrome. Gastroenterology 2017; 152:111-123.e8. [PMID: 27725146 DOI: 10.1053/j.gastro.2016.09.049] [Citation(s) in RCA: 371] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS We have limited knowledge about the association between the composition of the intestinal microbiota and clinical features of irritable bowel syndrome (IBS). We collected information on the fecal and mucosa-associated microbiota of patients with IBS and evaluated whether these were associated with symptoms. METHODS We collected fecal and mucosal samples from adult patients who met the Rome III criteria for IBS at a secondary/tertiary care outpatient clinics in Sweden, as well as from healthy subjects. The exploratory set comprised 149 subjects (110 with IBS and 39 healthy subjects); 232 fecal samples and 59 mucosal biopsy samples were collected and analyzed by 16S ribosomal RNA targeted pyrosequencing. The validation set comprised 46 subjects (29 with IBS and 17 healthy subjects); 46 fecal samples, but no mucosal samples, were collected and analyzed. For each subject, we measured exhaled H2 and CH4, oro-anal transit time, and the severity of psychological and gastrointestinal symptoms. Fecal methanogens were measured by quantitative polymerase chain reaction. Numerical ecology analyses and a machine learning procedure were used to analyze the data. RESULTS Fecal microbiota showed covariation with mucosal adherent microbiota. By using classic approaches, we found no differences in fecal microbiota abundance or composition between patients with IBS vs healthy patients. A machine learning procedure, a computational statistical technique, allowed us to reduce the 16S ribosomal RNA data complexity into a microbial signature for severe IBS, consisting of 90 bacterial operational taxonomic units. We confirmed the robustness of the intestinal microbial signature for severe IBS in the validation set. The signature was able to discriminate between patients with severe symptoms, patients with mild/moderate symptoms, and healthy subjects. By using this intestinal microbiota signature, we found IBS symptom severity to be associated negatively with microbial richness, exhaled CH4, presence of methanogens, and enterotypes enriched with Clostridiales or Prevotella species. This microbiota signature could not be explained by differences in diet or use of medications. CONCLUSIONS In analyzing fecal and mucosal microbiota from patients with IBS and healthy individuals, we identified an intestinal microbiota profile that is associated with the severity of IBS symptoms. TRIAL REGISTRATION NUMBER NCT01252550.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Palaiseau, France; French National Institute for Agricultural Research (INRA) MetaGenoPolis, Jouy en Josas, France
| | | | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Person-Centered Care, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Joël Doré
- French National Institute for Agricultural Research (INRA) MetaGenoPolis, Jouy en Josas, France
| | - Stine Störsrud
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Lena Öhman
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Microbiology and Immunology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; School of Health and Education, University of Skövde, Skövde, Sweden
| | - Magnus Simrén
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Centre for Person-Centered Care, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Center for Functional GI and Motility Disorders, University of North Carolina, Chapel Hill, North Carolina.
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Abstract
Modern life is associated with changes in gut microbial communities, believed to be involved in the emergence of non-communicable chronic diseases. While there is an increasing effort of the scientific community towards designing microbiota-targeting therapies aiming to restore the microbiota of diseased patients, there is a lack of approaches designed to prevent the disruption of the symbiosis between human and its microbial symbionts. We discuss in this review how new technologies, tools and models will contribute to identify diet-derived health-relevant microbial metabolites, possible targets for dietary recommendations tailored to individuals' physiology, diet, genetics, lifestyle and gut microbiota.
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Affiliation(s)
- Patrick Veiga
- Danone Nutricia Research, Avenue de la Vauve, 91120 Palaiseau, France
| | - Julien Tap
- Danone Nutricia Research, Avenue de la Vauve, 91120 Palaiseau, France
| | - Muriel Derrien
- Danone Nutricia Research, Avenue de la Vauve, 91120 Palaiseau, France
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19
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Le Nevé B, Brazeilles R, Derrien M, Tap J, Guyonnet D, Ohman L, Törnblom H, Simrén M. Reply. Clin Gastroenterol Hepatol 2016; 14:1222-3. [PMID: 27041478 DOI: 10.1016/j.cgh.2016.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Boris Le Nevé
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France
| | - Rémi Brazeilles
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France
| | - Muriel Derrien
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France
| | - Julien Tap
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France; Institut National de la Recherche Agronomique MetaGenoPolis, Jouy en Josas, France
| | - Denis Guyonnet
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France
| | - Lena Ohman
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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20
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Le Nevé B, Brazeilles R, Derrien M, Tap J, Guyonnet D, Ohman L, Törnblom H, Simrén M. Lactulose Challenge Determines Visceral Sensitivity and Severity of Symptoms in Patients With Irritable Bowel Syndrome. Clin Gastroenterol Hepatol 2016; 14:226-33.e1-3. [PMID: 26492847 DOI: 10.1016/j.cgh.2015.09.039] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/23/2015] [Accepted: 09/29/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Patients with irritable bowel syndrome (IBS) can be assigned to groups with different gastrointestinal (GI) symptoms based on results from a combined nutrient and lactulose challenge. We aimed to identify factors that predict outcomes to this challenge and to determine whether this can be used in noninvasive assessment of visceral sensitivity in patients with IBS. METHODS We performed a prospective study of 100 patients with IBS diagnosed according to Rome III criteria (all subtypes) and seen at a secondary or tertiary care center. After an overnight fast, subjects were given a liquid breakfast (400 mL; Nutridrink) that contained 25 g lactulose. Before the challenge, we assessed visceral sensitivity (via rectal barostat), oro-anal transit time, and fecal microbiota composition (via 16S ribosomal RNA pyrosequencing); we determined IBS severity using questionnaires. The intensity of 8 GI symptoms, the level of digestive comfort, and the amount of exhaled H2 and CH4 in breath were measured before and during a 4-hour period after the liquid breakfast. RESULTS Based on the intensity of 8 GI symptoms and level of digestive comfort during the challenge, patients were assigned to groups with high-intensity GI symptoms (HGS; n = 39) or low-intensity GI symptoms (LGS; n = 61); patients with HGS had more severe IBS (P < .0001), higher somatization (P < .01), and lower quality of life (P < .05-.01) than patients with LGS. Patients with HGS also had significantly higher rectal sensitivity to random phasic distensions (P < .05-.001, compared with patients with LGS). There were no significant differences between groups in fecal microbiota composition, exhaled gas in breath, or oro-anal transit time. CONCLUSIONS We found, in a prospective study, that results from a lactulose challenge test could be used to determine visceral sensitivity and severity of IBS. The intensity of patient symptoms did not correlate with the composition of the fecal microbiota. The lactulose challenge test may help better characterize patients with IBS and evaluate the efficacy of new treatments. ClinicalTrial.gov no: NCT01252550.
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Affiliation(s)
- Boris Le Nevé
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France.
| | - Rémi Brazeilles
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France
| | - Muriel Derrien
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France
| | - Julien Tap
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France; INRA (Institut National de la Recherche Agronomique) MetaGenoPolis, Jouy en Josas, France
| | - Denis Guyonnet
- Danone Nutricia Research, Life Sciences Department, Palaiseau, France
| | - Lena Ohman
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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Tap J, Furet J, Bensaada M, Philippe C, Roth H, Rabot S, Lakhdari O, Lombard V, Henrissat B, Corthier G, Fontaine E, Doré J, Leclerc M. Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environ Microbiol 2015; 17:4954-64. [DOI: 10.1111/1462-2920.13006] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 07/27/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Julien Tap
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | | | | | | | - Hubert Roth
- CHU Grenoble Bioénergétique‐INSERM U1055 Université J. Fourier Grenoble 38000 France
- CRNH Rhône‐Alpes Pierre Benite 69310 France
| | - Sylvie Rabot
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | - Omar Lakhdari
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques Aix‐Marseille Université CNRS UMR 7257, 163 Avenue de Luminy Marseille F‐13288 France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques Aix‐Marseille Université CNRS UMR 7257, 163 Avenue de Luminy Marseille F‐13288 France
| | | | - Eric Fontaine
- CHU Grenoble Bioénergétique‐INSERM U1055 Université J. Fourier Grenoble 38000 France
- CRNH Rhône‐Alpes Pierre Benite 69310 France
| | - Joël Doré
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
| | - Marion Leclerc
- INRA Micalis Institute UMR1319 Jouy‐en‐Josas 78350 France
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22
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Enck P, Campbell K, Tap J, Arnoux P, Antoine J. The Gut Microbiota for Health Experts Exchange: An Online Network for Sharing Knowledge. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.909.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Paul Enck
- Psychosomatic Medicine and Psychotherapy University Hospital TübingenGermany
| | | | - Julien Tap
- MetaGenopolis Laboratory Research Institute in Agricultural Sciences, INRAJouy‐en‐JosasFrance
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23
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Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, Amiot A, Böhm J, Brunetti F, Habermann N, Hercog R, Koch M, Luciani A, Mende DR, Schneider MA, Schrotz-King P, Tournigand C, Tran Van Nhieu J, Yamada T, Zimmermann J, Benes V, Kloor M, Ulrich CM, von Knebel Doeberitz M, Sobhani I, Bork P. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol 2014; 10:766. [PMID: 25432777 PMCID: PMC4299606 DOI: 10.15252/msb.20145645] [Citation(s) in RCA: 710] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Several bacterial species have been implicated in the development of colorectal carcinoma (CRC), but CRC-associated changes of fecal microbiota and their potential for cancer screening remain to be explored. Here, we used metagenomic sequencing of fecal samples to identify taxonomic markers that distinguished CRC patients from tumor-free controls in a study population of 156 participants. Accuracy of metagenomic CRC detection was similar to the standard fecal occult blood test (FOBT) and when both approaches were combined, sensitivity improved > 45% relative to the FOBT, while maintaining its specificity. Accuracy of metagenomic CRC detection did not differ significantly between early- and late-stage cancer and could be validated in independent patient and control populations (N = 335) from different countries. CRC-associated changes in the fecal microbiome at least partially reflected microbial community composition at the tumor itself, indicating that observed gene pool differences may reveal tumor-related host-microbe interactions. Indeed, we deduced a metabolic shift from fiber degradation in controls to utilization of host carbohydrates and amino acids in CRC patients, accompanied by an increase of lipopolysaccharide metabolism.
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Affiliation(s)
- Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julien Tap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Anita Y Voigt
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Paul I Costea
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Aurélien Amiot
- Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Jürgen Böhm
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Francesco Brunetti
- Department of Surgery, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Nina Habermann
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rajna Hercog
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Moritz Koch
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Alain Luciani
- Department of Radiology, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Daniel R Mende
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Martin A Schneider
- Department of General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Petra Schrotz-King
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christophe Tournigand
- Department of Medical Oncology, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Jeanne Tran Van Nhieu
- Department of Pathology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Takuji Yamada
- Department of Biological Information, Tokyo Institute of Technology, Tokyo, Japan
| | - Jürgen Zimmermann
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Cornelia M Ulrich
- Division of Preventive Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany German Cancer Research Center (DKFZ), Heidelberg, Germany Fred Hutchinson Cancer Research Center (FHCRC), Seattle, WA, USA
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology University Hospital Heidelberg, Heidelberg, Germany Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
| | - Iradj Sobhani
- Department of Gastroenterology and LIC-EA4393-EC2M3, APHP and UPEC Université Paris-Est Créteil, Créteil, France
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany Molecular Medicine Partnership Unit (MMPU), University Hospital Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany Max Delbrück Centre for Molecular Medicine, Berlin, Germany
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Sunagawa S, Schloissnig S, Arumugam M, Forslund K, Mitreva M, Tap J, Zhu A, Waller A, Mende DR, Kultima JR, Martin J, Kota K, Sunyaev SR, Typas A, Weinstock GM, Bork P. Individuality and temporal stability of the human gut microbiome. Cent Asian J Glob Health 2014; 2:120. [PMID: 29805877 PMCID: PMC5960903 DOI: 10.5195/cajgh.2013.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Introduction The breakthrough of next generation sequencing-technologies has enabled large-scale studies of natural microbial communities and the 16S rRNA genes have been widely used as a phylogenetic marker to study community structure. However, major limitations of this approach are that neither strain-level resolution nor genomic context of microorganisms can be provided. This information, however, is crucial to answer fundamental questions about the temporal stability and distinctiveness of natural microbial communities. Material and methods We developed a methodological framework for metagenomic single nucleotide polymorphism (SNP) variation analysis and applied it to publicly available data from 252 human fecal samples from 207 European and North American individuals. We further analyzed samples from 43 healthy subjects that were sampled at least twice over time intervals of up to one year and measured population similarities of dominant gut species. Results We detected 10.3 million SNPs in 101 species, which nearly amounts to the number identified in more than 1,000 humans. Conclusion The most striking result was that host-specific strains appear to be retained over long time periods. This indicates that individual-specific strains are not easily exchanged with the environment and furthermore, that an individuals appear to have a unique metagenomic genotype. This, in turn, is linked to implications for human gut physiology, such as the stability of antibiotic resistance potential.
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Affiliation(s)
| | | | | | | | | | - Julien Tap
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ana Zhu
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alison Waller
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Daniel R Mende
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - John Martin
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Karthik Kota
- European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | - Peer Bork
- European Molecular Biology Laboratory, Heidelberg, Germany
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25
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Consortium M, Weissenbach J, Ehrlich SD, Bork P. Addendum: Enterotypes of the human gut microbiome. Nature 2014. [DOI: 10.1038/nature13075] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger SA, Kultima JR, Coelho LP, Arumugam M, Tap J, Nielsen HB, Rasmussen S, Brunak S, Pedersen O, Guarner F, de Vos WM, Wang J, Li J, Doré J, Ehrlich SD, Stamatakis A, Bork P. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods 2013; 10:1196-9. [PMID: 24141494 DOI: 10.1038/nmeth.2693] [Citation(s) in RCA: 315] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 09/24/2013] [Indexed: 12/11/2022]
Abstract
To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/.
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27
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Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, Almeida M, Arumugam M, Batto JM, Kennedy S, Leonard P, Li J, Burgdorf K, Grarup N, Jørgensen T, Brandslund I, Nielsen HB, Juncker AS, Bertalan M, Levenez F, Pons N, Rasmussen S, Sunagawa S, Tap J, Tims S, Zoetendal EG, Brunak S, Clément K, Doré J, Kleerebezem M, Kristiansen K, Renault P, Sicheritz-Ponten T, de Vos WM, Zucker JD, Raes J, Hansen T, Bork P, Wang J, Ehrlich SD, Pedersen O. Richness of human gut microbiome correlates with metabolic markers. Nature 2013; 500:541-6. [DOI: 10.1038/nature12506] [Citation(s) in RCA: 2791] [Impact Index Per Article: 253.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 07/26/2013] [Indexed: 02/07/2023]
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28
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Kong LC, Tap J, Aron-Wisnewsky J, Pelloux V, Basdevant A, Bouillot JL, Zucker JD, Doré J, Clément K. Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes. Am J Clin Nutr 2013; 98:16-24. [PMID: 23719559 DOI: 10.3945/ajcn.113.058743] [Citation(s) in RCA: 284] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Roux-en-Y gastric bypass (RYGB) surgery is one of the most efficient procedures for treating morbid obesity and results in weight-loss and improvements in metabolism and inflammation. OBJECTIVE We examined the impact of RYGB on modifications of gut microbiota and its potential associations with changes in gene expression in white adipose tissue (WAT). DESIGN Gut microbiota were profiled from fecal samples by using pyrosequencing in morbidly obese individuals, explored before (0 mo), 3 mo after, and 6 mo after RYGB. WAT gene expression was studied at 0 and 3 mo. We explored associations between microbial genera and differentially expressed genes in WAT and clinical markers. RESULTS The richness of gut microbiota increased after RYGB; 37% of increased bacteria belonged to Proteobacteria. The associations between gut microbiota composition and WAT gene expression increased after RYGB. Fourteen discriminant bacterial genera (7 were dominant and 7 were subdominant) and 202 WAT genes changed after RYGB. Variations in bacterial genera correlated with changes in both clinical phenotype and adipose tissue gene expression. Some genes encode metabolic and inflammatory genes. Almost half of the correlations were independent of the change in calorie intake. CONCLUSION These results show an increase in gut microbiota richness and in the number of associations between gut microbiota and WAT genes after RYGB in obesity. Variations of gut microbiota were associated with changes in WAT gene expression. These findings stimulate deeper explorations of the mechanisms linking gut microbiome and WAT pathological alterations in human obesity and its changes after weight loss.
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Affiliation(s)
- Ling-Chun Kong
- Institute of Cardiometabolism and Nutrition, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Heart and Metabolism Department, Centre de Recherche Nutrition Humaine, Paris, France 1319 Micalis, Jouy-en-Josas, France
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Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley SD, Stinear TP, Brisse S, Médigue C, Parkhill J, Cruveiller S, Brosch R. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nat Genet 2013; 45:172-9. [PMID: 23291586 PMCID: PMC3856870 DOI: 10.1038/ng.2517] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 12/06/2012] [Indexed: 11/09/2022]
Abstract
Global spread and genetic monomorphism are hallmarks of Mycobacterium tuberculosis, the agent of human tuberculosis. In contrast, Mycobacterium canettii, and related tubercle bacilli that also cause human tuberculosis and exhibit unusual smooth colony morphology, are restricted to East-Africa. Here, we sequenced and analyzed the genomes of five representative strains of smooth tubercle bacilli (STB) using Sanger (4-5x coverage), 454/Roche (13-18x coverage) and/or Illumina DNA sequencing (45-105x coverage). We show that STB are highly recombinogenic and evolutionary early-branching, with larger genome sizes, 25-fold more SNPs, fewer molecular scars and distinct CRISPR-Cas systems relative to M. tuberculosis. Despite the differences, all tuberculosis-causing mycobacteria share a highly conserved core genome. Mouse-infection experiments revealed that STB are less persistent and virulent than M. tuberculosis. We conclude that M. tuberculosis emerged from an ancestral, STB-like pool of mycobacteria by gain of persistence and virulence mechanisms and we provide genome-wide insights into the molecular events involved.
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Affiliation(s)
- Philip Supply
- Institut National de la Santé et de la Recherche Médicale INSERM U1019, Center for Infection and Immunity of Lille, Lille, France.
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, JunWang, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Consortium M, Weissenbach J, Ehrlich SD, Bork P. Erratum: Enterotypes of the human gut microbiome. Nature 2011. [DOI: 10.1038/nature10187] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Antolín M, Artiguenave F, Blottiere HM, Almeida M, Brechot C, Cara C, Chervaux C, Cultrone A, Delorme C, Denariaz G, Dervyn R, Foerstner KU, Friss C, van de Guchte M, Guedon E, Haimet F, Huber W, van Hylckama-Vlieg J, Jamet A, Juste C, Kaci G, Knol J, Lakhdari O, Layec S, Le Roux K, Maguin E, Mérieux A, Melo Minardi R, M'rini C, Muller J, Oozeer R, Parkhill J, Renault P, Rescigno M, Sanchez N, Sunagawa S, Torrejon A, Turner K, Vandemeulebrouck G, Varela E, Winogradsky Y, Zeller G, Weissenbach J, Ehrlich SD, Bork P. Enterotypes of the human gut microbiome. Nature 2011; 473:174-80. [PMID: 21508958 DOI: 10.1038/nature09944] [Citation(s) in RCA: 4489] [Impact Index Per Article: 345.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 12/18/2010] [Indexed: 02/06/2023]
Abstract
Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.
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Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, Fernandes GR, Tap J, Bruls T, Batto JM, Bertalan M, Borruel N, Casellas F, Fernandez L, Gautier L, Hansen T, Hattori M, Hayashi T, Kleerebezem M, Kurokawa K, Leclerc M, Levenez F, Manichanh C, Nielsen HB, Nielsen T, Pons N, Poulain J, Qin J, Sicheritz-Ponten T, Tims S, Torrents D, Ugarte E, Zoetendal EG, Wang J, Guarner F, Pedersen O, de Vos WM, Brunak S, Doré J, Weissenbach J, Ehrlich SD, Bork P. Enterotypes of the human gut microbiome. Nature 2011. [DOI: 78495111110.1038/nature09944' target='_blank'>'"<>78495111110.1038/nature09944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [78495111110.1038/nature09944','', 'Julien Tap')">Reference Citation Analysis] [78495111110.1038/nature09944', 32)">What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
78495111110.1038/nature09944" />
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Sobhani I, Tap J, Roudot-Thoraval F, Roperch JP, Letulle S, Langella P, Corthier G, Tran Van Nhieu J, Furet JP. Microbial dysbiosis in colorectal cancer (CRC) patients. PLoS One 2011; 6:e16393. [PMID: 21297998 PMCID: PMC3029306 DOI: 10.1371/journal.pone.0016393] [Citation(s) in RCA: 566] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 12/14/2010] [Indexed: 12/11/2022] Open
Abstract
UNLABELLED The composition of the human intestinal microbiota is linked to health status. The aim was to analyze the microbiota of normal and colon cancer patients in order to establish cancer-related dysbiosis. PATIENTS AND METHODS Stool bacterial DNA was extracted prior to colonoscopy from 179 patients: 60 with colorectal cancer, and 119 with normal colonoscopy. Bacterial genes obtained by pyrosequencing of 12 stool samples (6 Normal and 6 Cancer) were subjected to a validated Principal Component Analysis (PCA) test. The dominant and subdominant bacterial population (C. leptum, C. coccoides, Bacteroides/Prevotella, Lactobacillus/Leuconostoc/Pediococcus groups, Bifidobacterium genus, and E. coli, and Faecalibacterium prausnitzii species) were quantified in all individuals using qPCR and specific IL17 producer cells in the intestinal mucosa were characterized using immunohistochemistry. FINDINGS Pyrosequencing (Minimal sequence 200 nucleotide reads) revealed 80% of all sequences could be assigned to a total of 819 taxa based on default parameter of Classifier software. The phylogenetic core in Cancer individuals was different from that in Normal individuals according to the PCA analysis, with trends towards differences in the dominant and subdominant families of bacteria. Consequently, All-bacteria [log(10) (bacteria/g of stool)] in Normal, and Cancer individuals were similar [11.88±0.35, and 11.80±0.56, respectively, (P = 0.16)], according to qPCR values whereas among all dominant and subdominant species only those of Bacteroides/Prevotella were higher (All bacteria-specific bacterium; P = 0.009) in Cancer (-1.04±0.55) than in Normal (-1.40±0.83) individuals. IL17 immunoreactive cells were significantly expressed more in the normal mucosa of cancer patients than in those with normal colonoscopy. CONCLUSION This is the first large series to demonstrate a composition change in the microbiota of colon cancer patients with possible impact on mucosal immune response. These data open new filed for mass screening and pathophysiology investigations.
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Affiliation(s)
- Iradj Sobhani
- Department of Gastroenterology and LIC-EA4393, APHP and UPEC Université Paris-Est Créteil, Créteil, France.
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Furet JP, Kong LC, Tap J, Poitou C, Basdevant A, Bouillot JL, Mariat D, Corthier G, Doré J, Henegar C, Rizkalla S, Clément K. Differential adaptation of human gut microbiota to bariatric surgery-induced weight loss: links with metabolic and low-grade inflammation markers. Diabetes 2010; 59:3049-57. [PMID: 20876719 PMCID: PMC2992765 DOI: 10.2337/db10-0253] [Citation(s) in RCA: 831] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Obesity alters gut microbiota ecology and associates with low-grade inflammation in humans. Roux-en-Y gastric bypass (RYGB) surgery is one of the most efficient procedures for the treatment of morbid obesity resulting in drastic weight loss and improvement of metabolic and inflammatory status. We analyzed the impact of RYGB on the modifications of gut microbiota and examined links with adaptations associated with this procedure. RESEARCH DESIGN AND METHODS Gut microbiota was profiled from fecal samples by real-time quantitative PCR in 13 lean control subjects and in 30 obese individuals (with seven type 2 diabetics) explored before (M0), 3 months (M3), and 6 months (M6) after RYGB. RESULTS Four major findings are highlighted: 1) Bacteroides/Prevotella group was lower in obese subjects than in control subjects at M0 and increased at M3. It was negatively correlated with corpulence, but the correlation depended highly on caloric intake; 2) Escherichia coli species increased at M3 and inversely correlated with fat mass and leptin levels independently of changes in food intake; 3) lactic acid bacteria including Lactobacillus/Leuconostoc/Pediococcus group and Bifidobacterium genus decreased at M3; and 4) Faecalibacterium prausnitzii species was lower in subjects with diabetes and associated negatively with inflammatory markers at M0 and throughout the follow-up after surgery independently of changes in food intake. CONCLUSIONS These results suggest that components of the dominant gut microbiota rapidly adapt in a starvation-like situation induced by RYGB while the F. prausnitzii species is directly linked to the reduction in low-grade inflammation state in obesity and diabetes independently of calorie intake.
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Affiliation(s)
- Jean-Pierre Furet
- French National Institute for Agricultural Research, U910, Unité d'Ecologie et de Physiologie du Système Digestif, Jouy-en-Josas, France
| | - Ling-Chun Kong
- Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Nutrition et d'Endocrinologie, Paris, France, and the Centre de Recherche Nutrition Humaine, Ile de France, Paris, France
- INSERM, U872, équipe 7 Nutriomique, Paris, France, and the Université Pierre et Marie Curie-Paris, Centre de Recherche des Cordeliers, UMR S 872, Paris, France; and the
| | - Julien Tap
- French National Institute for Agricultural Research, U910, Unité d'Ecologie et de Physiologie du Système Digestif, Jouy-en-Josas, France
| | - Christine Poitou
- Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Nutrition et d'Endocrinologie, Paris, France, and the Centre de Recherche Nutrition Humaine, Ile de France, Paris, France
- INSERM, U872, équipe 7 Nutriomique, Paris, France, and the Université Pierre et Marie Curie-Paris, Centre de Recherche des Cordeliers, UMR S 872, Paris, France; and the
| | - Arnaud Basdevant
- Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Nutrition et d'Endocrinologie, Paris, France, and the Centre de Recherche Nutrition Humaine, Ile de France, Paris, France
- INSERM, U872, équipe 7 Nutriomique, Paris, France, and the Université Pierre et Marie Curie-Paris, Centre de Recherche des Cordeliers, UMR S 872, Paris, France; and the
| | - Jean-Luc Bouillot
- Assistance Publique Hôpitaux de Paris, Département de Chirurgie, Hôpital Hôtel-Dieu, Paris, France
| | - Denis Mariat
- French National Institute for Agricultural Research, U910, Unité d'Ecologie et de Physiologie du Système Digestif, Jouy-en-Josas, France
| | - Gérard Corthier
- French National Institute for Agricultural Research, U910, Unité d'Ecologie et de Physiologie du Système Digestif, Jouy-en-Josas, France
| | - Joël Doré
- French National Institute for Agricultural Research, U910, Unité d'Ecologie et de Physiologie du Système Digestif, Jouy-en-Josas, France
| | - Corneliu Henegar
- Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Nutrition et d'Endocrinologie, Paris, France, and the Centre de Recherche Nutrition Humaine, Ile de France, Paris, France
| | - Salwa Rizkalla
- Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Nutrition et d'Endocrinologie, Paris, France, and the Centre de Recherche Nutrition Humaine, Ile de France, Paris, France
- INSERM, U872, équipe 7 Nutriomique, Paris, France, and the Université Pierre et Marie Curie-Paris, Centre de Recherche des Cordeliers, UMR S 872, Paris, France; and the
| | - Karine Clément
- Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Nutrition et d'Endocrinologie, Paris, France, and the Centre de Recherche Nutrition Humaine, Ile de France, Paris, France
- INSERM, U872, équipe 7 Nutriomique, Paris, France, and the Université Pierre et Marie Curie-Paris, Centre de Recherche des Cordeliers, UMR S 872, Paris, France; and the
- Corresponding author: Karine Clément,
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Tasse L, Bercovici J, Pizzut-Serin S, Robe P, Tap J, Klopp C, Cantarel BL, Coutinho PM, Henrissat B, Leclerc M, Doré J, Monsan P, Remaud-Simeon M, Potocki-Veronese G. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 2010; 20:1605-12. [PMID: 20841432 PMCID: PMC2963823 DOI: 10.1101/gr.108332.110] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 07/29/2010] [Indexed: 12/13/2022]
Abstract
The human gut microbiome is a complex ecosystem composed mainly of uncultured bacteria. It plays an essential role in the catabolism of dietary fibers, the part of plant material in our diet that is not metabolized in the upper digestive tract, because the human genome does not encode adequate carbohydrate active enzymes (CAZymes). We describe a multi-step functionally based approach to guide the in-depth pyrosequencing of specific regions of the human gut metagenome encoding the CAZymes involved in dietary fiber breakdown. High-throughput functional screens were first applied to a library covering 5.4 × 10(9) bp of metagenomic DNA, allowing the isolation of 310 clones showing beta-glucanase, hemicellulase, galactanase, amylase, or pectinase activities. Based on the results of refined secondary screens, sequencing efforts were reduced to 0.84 Mb of nonredundant metagenomic DNA, corresponding to 26 clones that were particularly efficient for the degradation of raw plant polysaccharides. Seventy-three CAZymes from 35 different families were discovered. This corresponds to a fivefold target-gene enrichment compared to random sequencing of the human gut metagenome. Thirty-three of these CAZy encoding genes are highly homologous to prevalent genes found in the gut microbiome of at least 20 individuals for whose metagenomic data are available. Moreover, 18 multigenic clusters encoding complementary enzyme activities for plant cell wall degradation were also identified. Gene taxonomic assignment is consistent with horizontal gene transfer events in dominant gut species and provides new insights into the human gut functional trophic chain.
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Affiliation(s)
- Lena Tasse
- Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, CNRS, INRA, F-31400 Toulouse, France
| | - Juliette Bercovici
- Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, CNRS, INRA, F-31400 Toulouse, France
| | - Sandra Pizzut-Serin
- Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, CNRS, INRA, F-31400 Toulouse, France
| | | | - Julien Tap
- INRA UEPSD, bat 405, Domaine de Vilvert, F-78352 Jouy en Josas Cedex, France
| | - Christophe Klopp
- Plateforme Bio-informatique Toulouse Genopole, UBIA INRA, BP 52627, F-31326 Castanet-Tolosan Cedex, France
| | - Brandi L. Cantarel
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, F-13288 Marseille, France
| | - Pedro M. Coutinho
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, F-13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS, Universités Aix-Marseille I & II, F-13288 Marseille, France
| | - Marion Leclerc
- INRA UEPSD, bat 405, Domaine de Vilvert, F-78352 Jouy en Josas Cedex, France
| | - Joël Doré
- INRA UEPSD, bat 405, Domaine de Vilvert, F-78352 Jouy en Josas Cedex, France
| | - Pierre Monsan
- Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, CNRS, INRA, F-31400 Toulouse, France
| | - Magali Remaud-Simeon
- Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, CNRS, INRA, F-31400 Toulouse, France
| | - Gabrielle Potocki-Veronese
- Université de Toulouse, INSA, UPS, INP, LISBP, F-31077 Toulouse, France
- UMR5504, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, CNRS, INRA, F-31400 Toulouse, France
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Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, Lefèvre F, Doré J, Blottière HM. Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-κB modulation in the human gut. PLoS One 2010; 5. [PMID: 20927194 PMCID: PMC2948039 DOI: 10.1371/journal.pone.0013092] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2010] [Accepted: 09/09/2010] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND/AIM The human intestinal microbiota plays an important role in modulation of mucosal immune responses. To study interactions between intestinal epithelial cells (IECs) and commensal bacteria, a functional metagenomic approach was developed. One interest of metagenomics is to provide access to genomes of uncultured microbes. We aimed at identifying bacterial genes involved in regulation of NF-κB signaling in IECs. A high throughput cell-based screening assay allowing rapid detection of NF-κB modulation in IECs was established using the reporter-gene strategy to screen metagenomic libraries issued from the human intestinal microbiota. METHODS A plasmid containing the secreted alkaline phosphatase (SEAP) gene under the control of NF-κB binding elements was stably transfected in HT-29 cells. The reporter clone HT-29/kb-seap-25 was selected and characterized. Then, a first screening of a metagenomic library from Crohn's disease patients was performed to identify NF-κB modulating clones. Furthermore, genes potentially involved in the effect of one stimulatory metagenomic clone were determined by sequence analysis associated to mutagenesis by transposition. RESULTS The two proinflammatory cytokines, TNF-α and IL-1β, were able to activate the reporter system, translating the activation of the NF-κB signaling pathway and NF-κB inhibitors, BAY 11-7082, caffeic acid phenethyl ester and MG132 were efficient. A screening of 2640 metagenomic clones led to the identification of 171 modulating clones. Among them, one stimulatory metagenomic clone, 52B7, was further characterized. Sequence analysis revealed that its metagenomic DNA insert might belong to a new Bacteroides strain and we identified 2 loci encoding an ABC transport system and a putative lipoprotein potentially involved in 52B7 effect on NF-κB. CONCLUSIONS We have established a robust high throughput screening assay for metagenomic libraries derived from the human intestinal microbiota to study bacteria-driven NF-κB regulation. This opens a strategic path toward the identification of bacterial strains and molecular patterns presenting a potential therapeutic interest.
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Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Li S, Jian M, Zhou Y, Li Y, Zhang X, Li S, Qin N, Yang H, Wang J, Brunak S, Doré J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010; 464:59-65. [PMID: 20203603 DOI: 10.1038/nature08821] [Citation(s) in RCA: 7136] [Impact Index Per Article: 509.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Accepted: 12/23/2009] [Indexed: 11/09/2022]
Abstract
To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe the Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals. The gene set, approximately 150 times larger than the human gene complement, contains an overwhelming majority of the prevalent (more frequent) microbial genes of the cohort and probably includes a large proportion of the prevalent human intestinal microbial genes. The genes are largely shared among individuals of the cohort. Over 99% of the genes are bacterial, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species, which are also largely shared. We define and describe the minimal gut metagenome and the minimal gut bacterial genome in terms of functions present in all individuals and most bacteria, respectively.
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Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Muñoz-Tamayo R, Paslier DLE, Nalin R, Dore J, Leclerc M. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 2009; 11:2574-84. [PMID: 19601958 DOI: 10.1111/j.1462-2920.2009.01982.x] [Citation(s) in RCA: 593] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The paradox of a host specificity of the human faecal microbiota otherwise acknowledged as characterized by global functionalities conserved between humans led us to explore the existence of a phylogenetic core. We investigated the presence of a set of bacterial molecular species that would be altogether dominant and prevalent within the faecal microbiota of healthy humans. A total of 10 456 non-chimeric bacterial 16S rRNA sequences were obtained after cloning of PCR-amplified rDNA from 17 human faecal DNA samples. Using alignment or tetranucleotide frequency-based methods, 3180 operational taxonomic units (OTUs) were detected. The 16S rRNA sequences mainly belonged to the phyla Firmicutes (79.4%), Bacteroidetes (16.9%), Actinobacteria (2.5%), Proteobacteria (1%) and Verrumicrobia (0.1%). Interestingly, while most of OTUs appeared individual-specific, 2.1% were present in more than 50% of the samples and accounted for 35.8% of the total sequences. These 66 dominant and prevalent OTUs included members of the genera Faecalibacterium, Ruminococcus, Eubacterium, Dorea, Bacteroides, Alistipes and Bifidobacterium. Furthermore, 24 OTUs had cultured type strains representatives which should be subjected to genome sequence with a high degree of priority. Strikingly, 52 of these 66 OTUs were detected in at least three out of four recently published human faecal microbiota data sets, obtained with very different experimental procedures. A statistical model confirmed these OTUs prevalence. Despite the species richness and a high individual specificity, a limited number of OTUs is shared among individuals and might represent the phylogenetic core of the human intestinal microbiota. Its role in human health deserves further study.
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Affiliation(s)
- Julien Tap
- INRA, UEPSD, UR910, 78350 Jouy en Josas, France
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Furet JP, Firmesse O, Gourmelon M, Bridonneau C, Tap J, Mondot S, Doré J, Corthier G. Comparative assessment of human and farm animal faecal microbiota using real-time quantitative PCR. FEMS Microbiol Ecol 2009; 68:351-62. [PMID: 19302550 DOI: 10.1111/j.1574-6941.2009.00671.x] [Citation(s) in RCA: 292] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pollution of the environment by human and animal faecal pollution affects the safety of shellfish, drinking water and recreational beaches. To pinpoint the origin of contaminations, it is essential to define the differences between human microbiota and that of farm animals. A strategy based on real-time quantitative PCR (qPCR) assays was therefore developed and applied to compare the composition of intestinal microbiota of these two groups. Primers were designed to quantify the 16S rRNA gene from dominant and subdominant bacterial groups. TaqMan probes were defined for the qPCR technique used for dominant microbiota. Human faecal microbiota was compared with that of farm animals using faecal samples collected from rabbits, goats, horses, pigs, sheep and cows. Three dominant bacterial groups (Bacteroides/Prevotella, Clostridium coccoides and Bifidobacterium) of the human microbiota showed differential population levels in animal species. The Clostridium leptum group showed the lowest differences among human and farm animal species. Human subdominant bacterial groups were highly variable in animal species. Partial least squares regression indicated that the human microbiota could be distinguished from all farm animals studied. This culture-independent comparative assessment of the faecal microbiota between humans and farm animals will prove useful in identifying biomarkers of human and animal faecal contaminations that can be applied to microbial source tracking methods.
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Affiliation(s)
- Jean-Pierre Furet
- INRA, U910, Unité d'Ecologie et de Physiologie du Système Digestif, Jouy-en-Josas, France.
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Pinguet F, Favre G, Canal P, Tap J, Soula G. [Injectable anti-cancer drugs. Stocking, preparation and administration]. Soins 1990:44-8. [PMID: 2237542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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