TY - JOUR
T1 - Species-function relationships shape ecological properties of the human gut microbiome
AU - Vieira-Silva, Sara
AU - Falony, Gwen
AU - Darzi, Youssef
AU - Lima-Mendez, Gipsi
AU - Garcia Yunta, Roberto
AU - Okuda, Shujiro
AU - Vandeputte, Doris
AU - Valles-Colomer, Mireia
AU - Hildebrand, Falk
AU - Chaffron, Samuel
AU - Raes, Jeroen
N1 - Publisher Copyright:
© 2016 Macmillan Publishers Limited. All rights reserved.
PY - 2016/6/13
Y1 - 2016/6/13
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84991204326&partnerID=8YFLogxK
U2 - 10.1038/nmicrobiol.2016.88
DO - 10.1038/nmicrobiol.2016.88
M3 - Article
C2 - 27573110
AN - SCOPUS:84991204326
SN - 2058-5276
VL - 1
JO - Nature Microbiology
JF - Nature Microbiology
IS - 8
M1 - 16088
ER -