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Microbiomics is a growing scientific field focusing on the quantification, characterization, and functional determination of complex microbial communities. Microbiomics utilizes microbiology, molecular biology, and bioinformatics analysis to study the composition of microorganisms and the inner workings of microbial populations in a distinct habitat and to assess microbe - derived genomic signatures, proteins, and metabolites. The current review examines microbiome research literature and extracts critical evidence highlighting current and potential benefits and applications of microbiome investigations in medicine, agriculture, and biotechnology. It focuses on how metatranscriptomic and metabolomic techniques have identified key molecules and mechanisms that have expanded our understanding of how microbial communities function in their natural ecosystem. Additional microbiomics research will continue to uncover essential microbial molecules and pathways of societal significance.
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Exploring the functional composition of the human microbiome using a hand-curated microbial trait database
Abstract Background Even 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. Results 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. Conclusions 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.
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- Award ID(s):
- 1632976
- PAR ID:
- 10287439
- Date Published:
- Journal Name:
- BMC Bioinformatics
- Volume:
- 22
- Issue:
- 1
- ISSN:
- 1471-2105
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1186/s12859-021-04216-2
