Quantitative sequencing clarifies the role of disruptor taxa, the oral microbiome, and strict anaerobes in the human small intestinal microbiome

Upper gastrointestinal disorders and pain are common in society and thought to have a link to the gut microbiome. However, most published studies sample from stool which drastically differs from the small intestinal microbiome and use relative abundance measures that are confounded by changes in total load. Using our digital PCR based quantitative sequencing method we evaluated the total and taxon specific microbial loads from a subset of 250 human duodenal aspirate samples and 21 paired saliva samples from the REIMAGINE cohort. Paired saliva and duodenum samples indicate high transmission of microbes between the two body sites. Additionally, our analyses revealed a subset of mainly aerobic disruptor taxa from the Enterobacteriaceae family that displace commonly found strict anaerobes in the duodenum. As the load of these disruptor taxa increased, there was a higher likelihood of having more GI symptoms. Overall, our results demonstrate the importance of absolute microbial-load analyses, that there is a clear relationship between the oral and small intestinal microbiomes, and that several taxonomic groups are linked to GI pain in the human small intestine.