The human jejunum has an endogenous microbiota that differs from those in the oral cavity and colon

Abstract

BackgroundThe upper half of the human small intestine, known as the jejunum, is the primary site for absorption of nutrient-derived carbohydrates, amino acids, small peptides, and vitamins. In contrast to the colon, which contains 1011–1012 colony forming units of bacteria per ml (CFU/ml), the normal jejunum generally ranges from 103 to 105 CFU per ml. Because invasive procedures are required to access the jejunum, much less is known about its bacterial microbiota. Bacteria inhabiting the jejunal lumen have been investigated by classical culture techniques, but not by culture-independent metagenomics.ResultsThe lumen of the upper jejunum was sampled during enteroscopy of 20 research subjects. Culture on aerobic and anaerobic media gave live bacterial counts ranging from 5.8 × 103 CFU/ml to 8.0 × 106 CFU/ml. DNA from the same samples was analyzed by 16S rRNA gene-specific quantitative PCR, yielding values from 1.5 × 105 to 3.1 × 107 bacterial genomes per ml. When calculated for each sample, estimated bacterial viability ranged from effectively 100% to a low of 0.3%. 16S rRNA metagenomic analysis of uncultured bacteria by Illumina MiSeq sequencing gave detailed microbial composition by phylum, genus and species. The genera Streptococcus, Prevotella, Veillonella and Fusobacterium, were especially abundant, as well as non-oral genera including Escherichia, Klebsiella, and Citrobacter. The jejunum was devoid of the genera Alistipes, Ruminococcus, Faecalibacterium, and other extreme anaerobes abundant in the colon. In patients with higher bacterial loads, there was no significant change in microbial species composition.ConclusionsThe jejunal lumen contains a distinctive bacterial population consisting primarily of facultative anaerobes and oxygen-tolerant obligate anaerobes similar to those found in the oral cavity. However, the frequent abundance of Enterobacteriaceae represents a major difference from oral microbiota. Although a few genera are shared with the colon, we found no evidence for retrograde movement of the most abundant colonic microbes to the jejunum. Some individuals had much higher bacterial loads, but this was not correlated with decreases in bacterial species diversity or other evidence of dysbiosis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12866-017-1059-6) contains supplementary material, which is available to authorized users.

Soil exposure modifies the gut microbiota and supports immune tolerance in a mouse model

“…We were able to detect OTUs from soil-dwelling bacteria in the intestine of mice in the soil group, particularly in the jejunum. This upper part of the gastrointestinal tract is partially oxygenated 44 , and could therefore offer better living conditions for environmental microbes compared to the anaerobic colon. It has previously been shown that soil microbes can colonize the gut of germ-free mice 45 .…”

Akkermansia muciniphila in the Human Gastrointestinal Tract: When, Where, and How?

“…The location of the small intestine in the human body causes difficulties in sampling, in comparison to, for example, the oral and fecal microbiota. Therefore, fewer studies have been performed describing the microbiota in the small intestine [ 101 , 111 ]. In the duodenum, the phyla Firmicutes and Actinobacteria were found to be predominant in the duodenal fluid of both obese and healthy groups ( n = 5 for each group) [ 112 ].…”

“…Interestingly, the duodenal mucosa-associated microbiota found in this study overlaps in broader levels of classification with that of the oral cavity and saliva. Further down the small intestine, the most dominant phyla in jejunal fluid were found to be Firmicutes, Proteobacteria, and Bacteroidetes [ 111 ]. Less abundant phyla (5–10%) were Actinobacteria and Fusobacteria.…”

Development of a host‐microbiome model of the small intestine

“…The synthetic community was designed as a representative commensal community of the small intestine, considering the species reported as natural inhabitants of the human small intestine (9,56). No pathogenic species were included in the community and, based on TEER and LY results, the presence of the microbial community without further stimulus was not enough to significantly lower TEER values, despite slightly increasing the paracellular transport of LY and increasing the total (apical + basal) secretion of IL-8 and CXCL16.…”