Bacterial protein signals are associated with Crohn’s disease

Juste, Catherine; Kreil, David P.; Beauvallet, Christian; Guillot, Alain; Vaca, Sebastian; Carapito, Christine; Mondot, Stanislas; Sykacek, Peter; Sokol, Harry; Blon, Florence; Lepercq, Pascale; Levenez, Florence; Valot, Benoı̂t; Carré, Wilfrid; Loux, Valentin; Pons, Nicolas; David, Olivier; Schaeffer, Brigitte; Lepage, Patricia; Martin, Patrice; Monnet, Véronique; Seksik, Philippe; Beaugerie, Laurent; Ehrlich, S. Dusko; Gibrat, Jean‐François; Dorsselaer, Alain Van; Doré, Joël

doi:10.1136/gutjnl-2012-303786

Cited by 80 publications

(69 citation statements)

References 54 publications

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“…Blautia has the ability to ferment a large variety of organic substrates, enabling flexible growth in the colon. Bacteria in the Blautia genus have been associated with both decreased and increased obesity and Crohn’s disease [53, 54]. Our data also showed increased abundance of Blautia in individuals with high BMI levels (Fig.…”

Section: Discussionsupporting

confidence: 64%

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort

et al. 2017

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BackgroundThe gut microbiome is a complex and metabolically active community that directly influences host phenotypes. In this study, we profile gut microbiota using 16S rRNA gene sequencing in 531 well-phenotyped Finnish men from the Metabolic Syndrome In Men (METSIM) study.ResultsWe investigate gut microbiota relationships with a variety of factors that have an impact on the development of metabolic and cardiovascular traits. We identify novel associations between gut microbiota and fasting serum levels of a number of metabolites, including fatty acids, amino acids, lipids, and glucose. In particular, we detect associations with fasting plasma trimethylamine N-oxide (TMAO) levels, a gut microbiota-dependent metabolite associated with coronary artery disease and stroke. We further investigate the gut microbiota composition and microbiota–metabolite relationships in subjects with different body mass index and individuals with normal or altered oral glucose tolerance. Finally, we perform microbiota co-occurrence network analysis, which shows that certain metabolites strongly correlate with microbial community structure and that some of these correlations are specific for the pre-diabetic state.ConclusionsOur study identifies novel relationships between the composition of the gut microbiota and circulating metabolites and provides a resource for future studies to understand host–gut microbiota relationships.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1194-2) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 64%

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort

et al. 2017

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“…Previous proteomic data suggests that certain opportunistic Bacteroides sp. pathogens are increased in IBD subjects, at the expense of Prevotella species, which could explain the shifts within Bacteroidetes in our observations [53].…”

Section: Resultssupporting

confidence: 49%

Meta‐analyses of human gut microbes associated with obesity and IBD

2014

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Recent studies have linked human gut microbes to obesity and inflammatory bowel disease, but consistent signals have been difficult to identify. Here we test for indicator taxa and general features of the microbiota that are generally consistent across studies of obesity and of IBD, focusing on studies involving high-throughput sequencing of the 16S rRNA gene (which we could process using a common computational pipeline). We find that IBD has a consistent signature across studies and allows high classification accuracy of IBD from non-IBD subjects, but that although subjects can be classified as lean or obese within each individual study with statistically significant accuracy, consistent with the ability of the microbiota to experimentally transfer this phenotype, signatures of obesity are not consistent between studies even when the data are analyzed with consistent methods. The results suggest that correlations between microbes and clinical conditions with different effect sizes (e.g. the large effect size of IBD versus the small effect size of obesity) may require different cohort selection and analysis strategies.

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“…In Proteobacteria , Pseudomonas , Parasuterella , Haemophilus , Bilophila , Escherichia and Desulfovibrio were the highest contributors to protein group abundances. Our results are in agreement and further extend previous reports on the phylogenetic diversity of microbial proteins within the human gut (Klaassens et al ., ; Verberkmoes et al ., ; Rooijers et al ., ; Kolmeder et al ., ; Ferrer et al ., ; Perez‐Cobas et al ., ; Juste et al ., ; Brooks et al ., ; Kolmeder et al ., ; Tanca et al ., ; Zwittink et al ., ).…”

Section: Resultsmentioning

confidence: 98%

Gut microbial functional maturation and succession during human early life

Cerdó

Ruiz

Acuña

et al. 2018

Environmental Microbiology

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The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional diversity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and fermentation strategies from milk and mucin-derived monosaccharide catabolism feeding acetate/propanoate synthesis to complex food-derived hexoses fuelling butanoate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life.

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Bacterial protein signals are associated with Crohn’s disease

Cited by 80 publications

References 54 publications

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort

Relationships between gut microbiota, plasma metabolites, and metabolic syndrome traits in the METSIM cohort

Meta‐analyses of human gut microbes associated with obesity and IBD

Gut microbial functional maturation and succession during human early life

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