Abstract
Knowledge of the intra-individual spatial and regional distribution of intestinal microbial populations is essential to understand gut host-microbial interactions. In this study, we performed a compositional analysis of luminal and mucosal samples from the small and large intestine of four organ donors by 16S rRNA amplicon sequencing and high-throughput quantitative polymerase chain reaction. Since the human microbiota is subject to selection pressure at lower taxonomic levels, we isolated over 400 bacterial strains and investigated strain-level variation of 11 Lactobacillus rhamnosus from different intestinal regions. Results substantiate reported inter-individual variability as well as intra-individual differences along the gastrointestinal tract. Although the luminal and mucosal-associated communities were similar within individuals, relative abundance reflected the donors' demographic and potential pathologies. The total bacterial load of all donors increased from small intestine to colon, while Bifidobacterium was in greater abundance in the small intestine. Comparative genomic analysis of L. rhamnosus showed the strains segregated into two distinct clusters and identified no features specific to location. Analysis revealed genetic differences for exopolysaccharide production, carbohydrate utilization, pilus formation and vitamin K biosynthesis between clusters. This study contributes to the understanding of niche-specific microbial communities, encouraging subsequent studies to better understand microbial signatures at lower taxonomic levels.
Highlights
Host-associated microorganisms play significant roles in systemic disease prevention and maintenance of overall good gut health
Intestinal segments from four organ donors were procured from Carolina Donor Services, an organization that supports and provides organs and tissues for transplantation, between 2017 and 2018
Lumen and mucosa from sections of the duodenum, jejunum, ileum, ascending, transverse and descending colons were analysed by 16S rRNA amplicon sequencing and high-throughput quantitative PCR
Summary
Host-associated microorganisms play significant roles in systemic disease prevention and maintenance of overall good gut health. Sampling of the human gastrointestinal (GI) tract presents logistical and practical challenges (Human Microbiome Project, 2012), limited studies have analysed the microbial populations associated with specific regions of the intestine Such studies have typically been carried out using biopsies (Stearns et al, 2011; Zmora et al, 2018) or inferred from animal models, which may not be directly comparable to humans (Yasuda et al, 2015). As the small intestine is the primary site for nutrient absorption and assimilation, bacteria residing here must compete with the host for simple dietary nutrients (Zmora et al, 2018). These attributes ensure lower colonization rates compared to the large intestine
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