Journal
NATURE MICROBIOLOGY
Volume 1, Issue 8, Pages -Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NMICROBIOL.2016.88
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Funding
- FP7 METACARDIS [HEALTH-F4-2012- 305312]
- IWT-SBO [100016]
- Marie Curie Actions FP7 People COFUND [267139]
- Fund for Scientific Research-Flanders (FWO-V)
- FWO-V
- Agency for Innovation by Science and Technology (IWT)
- Grants-in-Aid for Scientific Research [26242088] Funding Source: KAKEN
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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 saccharolyticproteolytic 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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