Species-function relationships shape ecological properties of the human gut microbiome.

Vieira-Silva S; Falony G; Darzi Y; Lima-Mendez G; Garcia Yunta R; Okuda S; Vandeputte D; Valles-Colomer M; Hildebrand F; Chaffron S; Raes J

doi:10.1038/nmicrobiol.2016.88

Species-function relationships shape ecological properties of the human gut microbiome.

Vieira-Silva S ^{1,

2},

Falony G ^{1,

2},

Darzi Y ^{1,

2},

Lima-Mendez G ^{1,

2},

Garcia Yunta R ²,

Okuda S ³,

Vandeputte D ^{1,

2},

Valles-Colomer M ^{1,

2},

Hildebrand F ²,

Chaffron S ^{1,

2},

Raes J ^{1,

2}

Affiliations

1. Department of Microbiology and Immunology, KU Leuven-University of Leuven, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium.
Authors
Vieira-Silva S^{1,

2}
Falony G^{1,

2}
Darzi Y^{1,

2}
Lima-Mendez G^{1,

2}
Vandeputte D^{1,

2}
Valles-Colomer M^{1,

2}
Chaffron S^{1,

2}
Raes J^{1,

2}
(8 authors)
2. VIB, Center for the Biology of Disease, Herestraat 49, B-3000 Leuven, Belgium.
Authors
Vieira-Silva S^{1,

2}
Falony G^{1,

2}
Darzi Y^{1,

2}
Lima-Mendez G^{1,

2}
Garcia Yunta R²
Vandeputte D^{1,

2}
Valles-Colomer M^{1,

2}
Hildebrand F²
Chaffron S^{1,

2}
Raes J^{1,

2}
(10 authors)
3. Niigata University Graduate School of Medical and Dental Sciences 1-757 Asahimachi-dori, Chuo-ku, Niigata 951-8510, Japan.
Authors
Okuda S³
(1 author)

ORCIDs linked to this article

Show all (10)

Nature Microbiology, 13 Jun 2016, 1(8):16088
https://doi.org/10.1038/nmicrobiol.2016.88 PMID: 27573110

Abstract

Despite recent progress, the organization and ecological properties of the intestinal microbial ecosystem remain under-investigated. Here, using a manually curated metabolic module framework for (meta-)genomic data analysis, we studied species-function relationships in gut microbial genomes and microbiomes. Half of gut-associated species were found to be generalists regarding overall substrate preference, but we observed significant genus-level metabolic diversification linked to bacterial life strategies. Within each genus, metabolic consistency varied significantly, being low in Firmicutes genera and higher in Bacteroides. Differentiation of fermentable substrate degradation potential contributed to metagenomic functional repertoire variation between individuals, with different enterotypes showing distinct saccharolytic/proteolytic/lipolytic profiles. Finally, we found that module-derived functional redundancy was reduced in the low-richness Bacteroides enterotype, potentially indicating a decreased resilience to perturbation, in line with its frequent association to dysbiosis. These results provide insights into the complex structure of gut microbiome-encoded metabolic properties and emphasize the importance of functional and ecological assessment of gut microbiome variation in clinical studies.

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Species-function relationships shape ecological properties of the human gut microbiome.

Affiliations

Authors

Authors

Authors

ORCIDs linked to this article

Abstract

Full text links

References

Ecological and evolutionary forces shaping microbial diversity in the human intestine.

The first 1000 cultured species of the human gastrointestinal microbiota.

Functional interactions between the gut microbiota and host metabolism.

Structure, function and diversity of the healthy human microbiome.

Microbial interactions: from networks to models.

Richness of human gut microbiome correlates with metabolic markers.

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

The control and consequences of bacterial fermentation in the human colon.

Hughes, R., Magee, E. A. & Bingham, S. Protein degradation in the large intestine: relevance to colorectal cancer. Curr. Issues Intest. Microbiol. 1, 51–58 (2000).

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Smart citations by scite.ai
Explore citation contexts and check if this article has been supported or disputed.
https://scite.ai/reports/10.1038/nmicrobiol.2016.88

Article citations

Causal relationship between the gut microbiota, immune cells, and coronary heart disease: a mediated Mendelian randomization analysis.

High-tannin food enhances spatial memory and scatter-hoarding in rodents via the microbiota-gut-brain axis.

Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities.

Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health.

Enteropathway: the metabolic pathway database for the human gut microbiota.

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Search life-sciences literature (44,833,495 articles, preprints and more)

Species-function relationships shape ecological properties of the human gut microbiome.

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Hughes, R., Magee, E. A. & Bingham, S. Protein degradation in the large intestine: relevance to colorectal cancer. Curr. Issues Intest. Microbiol. 1, 51–58 (2000).

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