Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.
Saccharibacteria (TM7)
computational biology
human microbiome
metabolic modeling
oral microbial flora
oral prokaryotes
systems biology
uncultivated bacteria
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
13 06 2019
13 06 2019
Historique:
received:
05
07
2018
accepted:
13
06
2019
pubmed:
14
6
2019
medline:
19
2
2020
entrez:
14
6
2019
Statut:
epublish
Résumé
The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several
Identifiants
pubmed: 31194675
doi: 10.7554/eLife.39733
pii: 39733
pmc: PMC6609349
doi:
pii:
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIGMS NIH HHS
ID : T32GM008764
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008764
Pays : United States
Organisme : NIDCR NIH HHS
ID : R01 DE024468
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM121950
Pays : United States
Organisme : Biological and Environmental Research
ID : DE-SC0012627
Pays : International
Organisme : Human Frontier Science Program
ID : RGP0020/2016
Pays : International
Organisme : National Science Foundation
ID : NSFOCE-BSF 1635070
Pays : International
Organisme : Defense Advanced Research Projects Agency
ID : HR0011-15-C-0091
Pays : International
Organisme : NIDCR NIH HHS
ID : R37DE016937
Pays : United States
Organisme : NIDCR NIH HHS
ID : R37 DE016937
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01GM121950
Pays : United States
Organisme : NIDCR NIH HHS
ID : R01DE024468
Pays : United States
Organisme : National Science Foundation
ID : 1457695
Pays : International
Informations de copyright
© 2019, Bernstein et al.
Déclaration de conflit d'intérêts
DB, FD, DS No competing interests declared
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