Gut and Tissue Microbiome Biogeography and Its Response to Environmental Perturbation

Abstract

The symbiotic relationship between the host and its microbiome, which is composed of trillions of bacteria, archaea, viruses, and fungi, is essential for the host to maintain health. In the past two decades, the intestinal microbiota has become one of the most intensely studied microbial ecosystems on the planet; however, there are few studies on much of the microbiota’s distribution, the factors shaping its composition both within and outside of the gastrointestinal (GI) tract, and the microbial communities’ response to environmental factors, such as fluoride. To understand the extent of intra-intestinal microbiota composition, its representation in the stool and factors dictating site-specificity of microbial taxa within the gut, we systematically collected stool and paired lumenal and mucosal intestinal samples from ten sites distal to the jejunum from the model organism Macaca mulatta (rhesus macaque) and assayed the samples with 16S rRNA amplicon sequencing. We found that stool composition was highly correlated with the microbial composition at the colonic lumen and mucosa, as well as enrichment of oxygen-tolerant bacteria in the mucosa, suggesting that stool is a good representation of distal gut lumenal bacterial communities and that oxygen may be a strong factor in shaping the gut microbial composition. We then tested the hypothesis that environmental factors, such as fluoride, may affect the oral and gut microbial communities, as fluoride is widely prevalent in drinking water and dental products and may have unexpected effects on health. We modeled human fluoride exposure in mice by administering fluoride daily over a 12-week period. We then assayed oral and stool samples for 16S amplicons and performed shotgun metagenomic sequencing to assess the effect of fluoride on oral and gut microbiome composition and function. We found that fluoride depletes bacterial taxa belonging to acidogenic bacterial genera (such as Parabacteroides, Bacteroides, and Bilophila) in the oral community. However, fluoride treatment did not induce a significant shift in the composition of the gut microbial community in our mouse model. Although the consequences of fluoride-induced shifts in the oral microbial community on health need further study, fluoride may not affect an established gut microbiome – at least not at the levels added to drinking water and dental products. Finally, we developed a method to distinguish microbial sequencing reads from those that are introduced during sample processing as contaminants, and tested the hypothesis that microbial DNA may be detectable in low-biomass tissue samples such as intra-abdominal adipose tissues as a result of gut bacterial translocation. For this study, we collected intra-abdominal (mesenteric and omental) and peripheral (subcutaneous) adipose tissues and lymph nodes, along with paired intestinal contents (small and large intestinal contents) from mice, rhesus macaques, and humans and assayed these materials with 16S rRNA gene sequencing. By taking into account the abundance, prevalence and host-uniqueness (for each taxon) data as an input, we were able to distinguish microbial sequencing reads from those that are likely of contamination. Our data show that the majority of bacterial reads identified in human adipose tissues to be contaminants. There were, however, some bacterial sequencing reads identified in fat tissues in macaques and mice resembling those bacterial taxa from the gut. Although the macaque and mice data could possibly support the notion of gut bacterial translocation, the discrepancy with the human data, as well as having significant proportion of sequencing reads in adipose tissues made up of contaminant reads, further studies are needed to clarify whether the bacterial reads commonly found in fat and gut of macaques indeed occurred in vivo or post-mortem.