Michaud, D. S. | bioRxiv Science

bioRxiv2019

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

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.

microbiology↗

bioRxiv2017

The Microbiomes of Pancreatic Tissue in Pancreatic Cancer and Non-Cancer Subjects

ObjectiveTo determine whether bacteria are present in the pancreas of pancreatic cancer and non-cancer subjects and examine whether bacterial profiles vary by site and disease phenotype.\n\nDesign77 patients requiring surgery for pancreatic diseases, or diseases of the foregut, at the Rhode Island Hospital (RIH) were recruited into this study between 2014 and 2016. In addition, 36 whole pancreas were obtained from the National Disease Research Interchange (NDRI) from subjects who were of similar age as the RIH patients and had not died of cancer. The primary exposure of interest was the measurement of the relative abundance of bacterial taxa in all tissue specimens using 16S rRNA gene sequencing.\n\nResultsNumber of bacterial reads per sample varied substantially across sample type and patients, but all demonstrated the presence of diverse gastrointestinal bacteria, including bacterial taxa typically identified in the oral cavity. Bacterial profiles were noted to be more similar within individuals across sites in the pancreas, than between individuals by site, suggesting that the pancreas as a whole has its own microbiome. Comparing the mean relative abundance of bacterial taxa in pancreatic cancer patients to those without cancer revealed differences in bacterial taxa previously linked to periodontal disease, including Porphyromonas.\n\nConclusionsBacterial taxa known to inhabit the oral cavity, as well as the intestine, were identified in pancreatic tissue of cancer and non-cancer subjects. Whether any of these bacteria play a causal role in pancreatic carcinogenesis, or are simply opportunistic in nature, needs to be further examined.

epidemiology↗