Exploring the functional composition of the human microbiome using a hand-curated microbial trait database

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dc.contributor.authorWeissman, Jake L.
dc.contributor.authorDogra, Sonia
dc.contributor.authorJavadi, Keyan
dc.contributor.authorBolten, Samantha
dc.contributor.authorFlint, Rachel
dc.contributor.authorDavati, Cyrus
dc.contributor.authorBeattie, Jess
dc.contributor.authorDixit, Keshav
dc.contributor.authorPeesay, Tejasvi
dc.contributor.authorAwan, Shehar
dc.contributor.authorThielen, Peter
dc.contributor.authorBreitwieser, Florian
dc.contributor.authorJohnson, Philip L. F.
dc.contributor.authorKarig, David
dc.contributor.authorFagan, William F.
dc.contributor.authorBewick, Sharon
dc.date.accessioned2021-09-07T19:09:46Z
dc.date.available2021-09-07T19:09:46Z
dc.date.issued2021-06-07
dc.description.abstractEven when microbial communities vary wildly in their taxonomic composition, their functional composition is often surprisingly stable. This suggests that a functional perspective could provide much deeper insight into the principles governing microbiome assembly. Much work to date analyzing the functional composition of microbial communities, however, relies heavily on inference from genomic features. Unfortunately, output from these methods can be hard to interpret and often suffers from relatively high error rates. We built and analyzed a domain-specific microbial trait database from known microbe-trait pairs recorded in the literature to better understand the functional composition of the human microbiome. Using a combination of phylogentically conscious machine learning tools and a network science approach, we were able to link particular traits to areas of the human body, discover traits that determine the range of body areas a microbe can inhabit, and uncover drivers of metabolic breadth. Domain-specific trait databases are an effective compromise between noisy methods to infer complex traits from genomic data and exhaustive, expensive attempts at database curation from the literature that do not focus on any one subset of taxa. They provide an accurate account of microbial traits and, by limiting the number of taxa considered, are feasible to build within a reasonable time-frame. We present a database specific for the human microbiome, in the hopes that this will prove useful for research into the functional composition of human-associated microbial communities.en_US
dc.description.urihttps://doi.org/10.1186/s12859-021-04216-2
dc.identifierhttps://doi.org/10.13016/8aem-buv0
dc.identifier.citationWeissman, J.L., Dogra, S., Javadi, K. et al. Exploring the functional composition of the human microbiome using a hand-curated microbial trait database. BMC Bioinformatics 22, 306 (2021).en_US
dc.identifier.urihttp://hdl.handle.net/1903/27676
dc.language.isoen_USen_US
dc.publisherSpringer Natureen_US
dc.relation.isAvailableAtCollege of Computer, Mathematical & Physical Sciencesen_us
dc.relation.isAvailableAtDigital Repository at the University of Marylanden_us
dc.relation.isAvailableAtBiologyen_us
dc.relation.isAvailableAtUniversity of Maryland (College Park, MD)en_us
dc.subjectTrait databaseen_US
dc.subjectFunctional communityen_US
dc.subjectRandom foresten_US
dc.subjectPhylogenetic correctionen_US
dc.titleExploring the functional composition of the human microbiome using a hand-curated microbial trait databaseen_US
dc.typeArticleen_US

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