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Comparison of Sewage and Animal Fecal Microbiomes by using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups
Fisher, J., A. Eren, H. Green, O. Shanks, H. Morrison, J. Vineis, M. Sogin, AND S. McLellan. Comparison of Sewage and Animal Fecal Microbiomes by using Oligotyping Reveals Potential Human Fecal Indicators in Multiple Taxonomic Groups. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. American Society for Microbiology, Washington, DC, 81(20):7023-7033, (2015).
To inform the public.
Most DNA-based microbial source tracking (MST) approaches target host-associated organisms within the order Bacteroidales, but human and other animal gut microbiota contain an array of other taxonomic groups that might serve as indicators for sources of fecal pollution. High throughput sequencing of sewage and animal fecal samples produced detailed community profiles that revealed host-related patterns among highly similar sequences within all ten taxonomic groups examined. Oligotyping, which can detect subtle differences between rRNA gene sequences from ecologically relevant taxonomic subgroups, was used to examine the fine scale population structure and distribution patterns within the dominant gut phyla Bacteroidetes and Firmicutes. Oligotypes within each individual taxon clearly resolved the human fecal portion of sewage from animal fecal samples and often resolved different animals from each other. Multiple oligotypes from each taxon were exclusively or preferentially found in humans and might serve as targets for development of novel alternative indicators. While our strategy has practical applications for identification of genetic markers for MST, the implications of these findings extend to delineating relationships between bacteria and their hosts. These patterns of reproducible, fine scale population structure within fecal taxa can provide the basis for deeper exploration of host specialization within the gut microbiome.