{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T14:08:37Z","timestamp":1790431717087,"version":"4.1.0"},"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2021,1,6]],"date-time":"2021-01-06T00:00:00Z","timestamp":1609891200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Kasetsart University Research and Development Institute (KURDI) at Kasetsart University"},{"name":"Department of Zoology, Faculty of Science, Kasetsart University"},{"name":"Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University"},{"name":"Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University"},{"name":"International Affairs Division (IAD), Kasetsart University"},{"DOI":"10.13039\/501100004192","name":"National Science and Technology Development Agency","doi-asserted-by":"crossref","award":["P-17-50648"],"award-info":[{"award-number":["P-17-50648"]}],"id":[{"id":"10.13039\/501100004192","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Ratchadapisek Research Funds","award":["CU-GR(S)_61_38_30_03"],"award-info":[{"award-number":["CU-GR(S)_61_38_30_03"]}]},{"DOI":"10.13039\/501100002873","name":"Chulalongkorn University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002873","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Deutsche Forschungsgemeinschaft (DFG) CRC\/Transregio 124 \u201cPathogenic fungi and their human host: Networks of interaction\u201d, subprojects B5 and INF"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008487","type":"journal-article","created":{"date-parts":[[2021,1,6]],"date-time":"2021-01-06T19:32:22Z","timestamp":1609961542000},"page":"e1008487","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut 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Vogtmann","year":"2016","journal-title":"PloS one"},{"issue":"11","key":"pcbi.1008487.ref007","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1038\/s41592-018-0176-y","article-title":"Species-level functional profiling of metagenomes and metatranscriptomes","volume":"15","author":"EA Franzosa","year":"2018","journal-title":"Nature methods"},{"issue":"1","key":"pcbi.1008487.ref008","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1038\/s41467-019-08844-4","article-title":"Microbial abundance, activity and population genomic profiling with mOTUs2","volume":"10","author":"A Milanese","year":"2019","journal-title":"Nature communications"},{"issue":"9","key":"pcbi.1008487.ref009","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"MG Langille","year":"2013","journal-title":"Nature 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American Academy of Dermatology Guidelines","volume":"4","author":"LF Eichenfield","year":"2017","journal-title":"Alergologia Polska-Polish Journal of Allergology"},{"issue":"8","key":"pcbi.1008487.ref041","doi-asserted-by":"crossref","first-page":"e1000465","DOI":"10.1371\/journal.pcbi.1000465","article-title":"A parsimony approach to biological pathway reconstruction\/inference for genomes and metagenomes","volume":"5","author":"Y Ye","year":"2009","journal-title":"PLoS computational biology"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008487","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,6]],"date-time":"2021-01-06T19:34:51Z","timestamp":1609961691000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1008487"}},"subtitle":[],"editor":[{"given":"Sergei 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