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

PeerJ

article

Jordan J. McGhee¹  Nick Rawson²  Barbara A. Bailey²  Antonio Fernandez-Guerra³  Laura Sisk-Hackworth⁵  Scott T. Kelley⁵ 

[1] Bioinformatics and Medical Informatics Program, San Diego State University;Department of Mathematics and Statistics, San Diego State University;Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine Microbiology;Current affiliation: Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen;Department of Biology, San Diego State University

关键词: Bioinformatics;    Environmental microbiology;    Software;   

DOI  :  10.7717/peerj.8783

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

BackgroundMicrobial 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.MethodsHere, 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).ResultsSourceTracker 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.

【 授权许可】

CC BY