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  Meta-SourceTracker: Application of Bayesian source tracking to shotgun metagenomics

McGhee, J. J., Rawson, N., Bailey, B. A., Fernandez-Guerra, A., Sisk-Hackworth, L., & Kelley​, S. T. (2020). Meta-SourceTracker: Application of Bayesian source tracking to shotgun metagenomics. PeerJ.

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 Creators:
McGhee, Jordan J. , Author
Rawson, Nick , Author
Bailey, Barbara A. , Author
Fernandez-Guerra, Antonio1, Author           
Sisk-Hackworth , Laura , Author
Kelley​, Scott T. , Author
Affiliations:
1Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481697              

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 Abstract: Background

Microbial source tracking methods are used to determine the origin of contaminating bacteria and other microorganisms, particularly in contaminated water systems. The Bayesian SourceTracker approach uses deep-sequencing marker gene libraries (16S ribosomal RNA) to determine the proportional contributions of bacteria from many potential source environments to a given sink environment simultaneously. Since its development, SourceTracker has been applied to an extensive diversity of studies, from beach contamination to human behavior.
Methods

Here, we demonstrate a novel application of SourceTracker to work with metagenomic datasets and tested this approach using sink samples from a study of coastal marine environments. Source environment metagenomes were obtained from metagenomics studies of gut, freshwater, marine, sand and soil environments. As part of this effort, we implemented features for determining the stability of source proportion estimates, including precision visualizations for performance optimization, and performed domain-specific source-tracking analyses (i.e., Bacteria, Archaea, Eukaryota and viruses). We also applied SourceTracker to metagenomic libraries generated from samples collected from the International Space Station (ISS).
Results

SourceTracker proved highly effective at predicting the composition of known sources using shotgun metagenomic libraries. In addition, we showed that different taxonomic domains sometimes presented highly divergent pictures of environmental source origins for both the coastal marine and ISS samples. These findings indicated that applying SourceTracker to separate domains may provide a deeper understanding of the microbial origins of complex, mixed-source environments, and further suggested that certain domains may be preferable for tracking specific sources of contamination.

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Language(s): eng - English
 Dates: 2019-07-232020-03-24
 Publication Status: Issued
 Pages: 18
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Title: PeerJ
  Other : PeerJ
Source Genre: Journal
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Publ. Info: London [u.a.] : PeerJ Inc.
Pages: - Volume / Issue: - Sequence Number: - Start / End Page: - Identifier: ISSN: 2167-8359
CoNE: https://pure.mpg.de/cone/journals/resource/2167-8359