In:
PLOS Computational Biology, Public Library of Science (PLoS), Vol. 17, No. 1 ( 2021-1-6), p. e1008487-
Abstract:
Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.
Type of Medium:
Online Resource
ISSN:
1553-7358
DOI:
10.1371/journal.pcbi.1008487
DOI:
10.1371/journal.pcbi.1008487.g001
DOI:
10.1371/journal.pcbi.1008487.g002
DOI:
10.1371/journal.pcbi.1008487.g003
DOI:
10.1371/journal.pcbi.1008487.g004
DOI:
10.1371/journal.pcbi.1008487.g005
DOI:
10.1371/journal.pcbi.1008487.t001
DOI:
10.1371/journal.pcbi.1008487.t002
DOI:
10.1371/journal.pcbi.1008487.s001
DOI:
10.1371/journal.pcbi.1008487.s002
DOI:
10.1371/journal.pcbi.1008487.s003
DOI:
10.1371/journal.pcbi.1008487.s004
DOI:
10.1371/journal.pcbi.1008487.s005
DOI:
10.1371/journal.pcbi.1008487.s006
DOI:
10.1371/journal.pcbi.1008487.s007
DOI:
10.1371/journal.pcbi.1008487.s008
DOI:
10.1371/journal.pcbi.1008487.s009
DOI:
10.1371/journal.pcbi.1008487.s010
DOI:
10.1371/journal.pcbi.1008487.r001
DOI:
10.1371/journal.pcbi.1008487.r002
DOI:
10.1371/journal.pcbi.1008487.r003
DOI:
10.1371/journal.pcbi.1008487.r004
Language:
English
Publisher:
Public Library of Science (PLoS)
Publication Date:
2021
detail.hit.zdb_id:
2193340-6
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