Investigating the human jejunal microbiota

Abstract

Descriptions of the small intestinal microbiota are deficient and conflicting. We aimed to get a reliable description of the jejunal bacterial microbiota by investigating samples from two separate jejunal segments collected from the luminal mucosa during surgery. Sixty patients with morbid obesity selected for elective gastric bypass surgery were included in this survey. Samples collected by rubbing a swab against the mucosa of proximal and mid jejunal segments were characterized both quantitatively and qualitatively using a combination of microbial culture, a universal quantitative PCR and 16S deep sequencing. Within the inherent limitations of partial 16S sequencing, bacteria were assigned to the species level. By microbial culture, 53 patients (88.3%) had an estimated bacterial density of < 1600 cfu/ml in both segments whereof 31 (51.7%) were culture negative in both segments corresponding to a bacterial density below 160 cfu/ml. By quantitative PCR, 46 patients (76.7%) had less than 104 bacterial genomes/ml in both segments. The most abundant and frequently identified species by 16S deep sequencing were associated with the oral cavity, most often from the Streptococcus mitis group, the Streptococcus sanguinis group, Granulicatella adiacens/para-adiacens, the Schaalia odontolytica complex and Gemella haemolysans/taiwanensis. In general, few bacterial species were identified per sample and there was a low consistency both between the two investigated segments in each patient and between patients. The jejunal mucosa of fasting obese patients contains relatively few microorganisms and a core microbiota could not be established. The identified microbes are likely representatives of a transient microbiota and there is a high degree of overlap between the most frequently identified species in the jejunum and the recently described ileum core microbiota.

Separation of the effects of small intestinal microbiome-diet interactions on human gut hormone secretion

“…To test if CAMIO permits growth of small intestinal microbes, we selected human microbes ( Table 1 ) that are largely predicted to be prevalent, abundant, or of interest to the function of the human small intestine (Leite et al, 2019; Seekatz et al, 2019; Sundin et al, 2017; Villmones et al, 2022; Wang et al, 2005). We therefore utilized a six-member community comprised of human-derived Prevotella histicola, Lacticaseibacillus casei, Limosilactobacillus reuteri, Streptococcus mitis, Streptococcus salivarius , and Veillonella atypica ( Table 1 ).…”

Identification of d-arabinan-degrading enzymes in mycobacteria

“…6 ). We reasoned that the abundance of Mycobacteriales in environmental niches in addition to the availability of d- arabinofuranose polymers in organisms such as P. aeruginosa PA7 and corynebacteria meant that the capacity to degrade this carbohydrate was likely to be encoded in the human gut microbiota 30 , 42 , allowing identification by metabolic methods with arabinogalactan as sole carbon source.

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Mining the human gut microbiome identifies mycobacterial d-arabinan degrading enzymes

“…To achieve this, we took the unintuitive step of challenging bacteria that do not contain arabinogalactan to use it as a sole carbon source. We reasoned that the abundance of Actinomycetota in environmental niches in addition to the availability of D-arabinofuranose polymers in organisms such as P. aeruginosa PA7 and Corynebacteria meant that the capacity to degrade this carbohydrate was likely to be encoded in the human gut microbiota 40, 41 .…”

“…We have mined the human gut microbiome and leveraged evolutionary conservation to identify these enzymes in mycobacteria, along with new exo- d -arabinofuranosidases and exo- d -galactofuranosidases ( Figure 7 ). We reasoned that the abundance of Mycobacteriales in environmental niches in addition to the availability of d -arabinofuranose polymers in organisms such as P. aeruginosa PA7 and corynebacteria meant that the capacity to degrade this carbohydrate was likely to be encoded in the human gut microbiota 42,43 , allowing identification by metabolic methods with arabinogalactan as sole carbon source.…”