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

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.

Comparisons of oral, intestinal, and pancreatic bacterial microbiomes in patients with pancreatic cancer and other gastrointestinal diseases

“…An ASV was defined to exhibit a consistent PASTA pattern, if either one of the three possible quantities was associated between oral and pancreatic tissues or intestinal site samples: (1) The probability of absence ( p ), which denotes the probability of observing a relative abundance of zero, (2) The non-zero mean relative abundance (ω), which denotes mean relative abundance among those samples in which ASV is present; and (3) The mean relative abundance across all samples (μ). Further information about the data model, approach, and performance of the PASTA test has been published in detail [ 28 ] and briefly summarized in Supplemental Material 2.…”

Oral, intestinal, and pancreatic microbiomes are correlated and exhibit co-abundance in patients with pancreatic cancer and other gastrointestinal diseases

“…This probability can be understood as a rejection threshold, where a value of less than or equal to 0.05 was considered statistically significant (i.e., strong evidence of association) and a value of less than 0.1 was considered as marginally significant (i.e., moderate evidence of association). Further information about the data model, approach, and performance of the PASTA test have been published in detail 44 .…”