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A Bayesian framework for identifying consistent patterns of microbial abundance between body sites

Author

Listed:
  • Meier Richard

    (Department of Biostatistics and Data Science, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA)

  • Thompson Jeffrey A.

    (Department of Biostatistics and Data Science, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA)

  • Chung Mei

    (Department of Public Health and Community Medicine, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA)

  • Zhao Naisi

    (Department of Public Health and Community Medicine, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA)

  • Kelsey Karl T.

    (Department of Epidemiology, Department of Pathology and Laboratory Medicine, Brown University, 70 Ship Street, Providence, RI 02912, USA)

  • Michaud Dominique S.

    (Department of Public Health and Community Medicine, Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA 02111, USA)

  • Koestler Devin C.

    (Department of Biostatistics and Data Science, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS 66160, USA)

Abstract

Recent studies have found that the microbiome in both gut and mouth are associated with diseases of the gut, including cancer. If resident microbes could be found to exhibit consistent patterns between the mouth and gut, disease status could potentially be assessed non-invasively through profiling of oral samples. Currently, there exists no generally applicable method to test for such associations. Here we present a Bayesian framework to identify microbes that exhibit consistent patterns between body sites, with respect to a phenotypic variable. For a given operational taxonomic unit (OTU), a Bayesian regression model is used to obtain Markov-Chain Monte Carlo estimates of abundance among strata, calculate a correlation statistic, and conduct a formal test based on its posterior distribution. Extensive simulation studies demonstrate overall viability of the approach, and provide information on what factors affect its performance. Applying our method to a dataset containing oral and gut microbiome samples from 77 pancreatic cancer patients revealed several OTUs exhibiting consistent patterns between gut and mouth with respect to disease subtype. Our method is well powered for modest sample sizes and moderate strength of association and can be flexibly extended to other research settings using any currently established Bayesian analysis programs.

Suggested Citation

  • Meier Richard & Thompson Jeffrey A. & Chung Mei & Zhao Naisi & Kelsey Karl T. & Michaud Dominique S. & Koestler Devin C., 2019. "A Bayesian framework for identifying consistent patterns of microbial abundance between body sites," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 18(6), pages 1-15, December.
    • Handle: RePEc:bpj:sagmbi:v:18:y:2019:i:6:p:15:n:4
    DOI: 10.1515/sagmb-2019-0027
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    References listed on IDEAS

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    1. Haitao Chai & Hongmei Jiang & Lu Lin & Lei Liu, 2018. "A marginalized two-part Beta regression model for microbiome compositional data," PLOS Computational Biology, Public Library of Science, vol. 14(7), pages 1-16, July.
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