The cultivable microbiota of the human distal ileum

Abstract

Objectives: The existing literature on the microbiota of the ileum is inconsistent. To further characterize the microbiota, we analysed samples obtained directly from resected ileums used for urinary diversion after radical cystectomy. Methods: We included 150 patients with bladder cancer operated on from March 2016 to March 2019. Samples obtained by rubbing a swab against the ileal mucosa 25 cm from the ileocecal valve were cultivated at the local laboratory. Microbial colonies were identified by matrix-assisted laser desorption/ ionization-time of flight mass spectrometry (MALDI-TOF). Results: The microbial density of the distal ileum was low. Among our samples, 79% (95% confidence interval (CI) 71%, 84%) harboured less than 1.6 Â 10 4 cfu/mL, whereas 36% (95% CI 28%, 44%) harboured less than 1.6 Â 10 3 cfu/mL. The flora was dominated by viridans streptococci, Candida, Actinomyces, Rothia and Lactobacillus species. Colon-related bacteria i.e. strict anaerobic bacteria, Enterobacteriales and enterococci, were recovered from 14% of the samples. Constipation was associated with increased recovery of colon-related bacteria. Antibiotic treatment prior to surgical procedures did not affect culture results. Increased age was significantly associated with more substantial fungal growth and use of proton pump inhibitors seemed to increase both bacterial and fungal growth. Conclusions: The microbiota of the human distal ileum is sparse and differs significantly from the colonic microbiota both quantitatively and by composition. These findings contradict recent metagenomics studies based on samples collected by retrograde colonoscopy and emphasize the crucial importance of adequate sampling techniques.

Investigating the human jejunal microbiota

“…Despite being performed on two different patient populations, the overall spectrum of bacteria identified from the jejunal samples in the present study, bears a striking resemblance to the ileal core microbiota as defined by our recent studies on surgically collected ileal samples (Fig. 3 a,b) 27 , 29 . 16S Ct-values indicate that the bacterial concentration in ileum is at least 100 fold higher than in jejunum.…”

High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota

“…The cecal bacterial concentration can be as high as 10 11 –10 12 CFU/mL, hence it provides a base for receptor bacteria and a favorable place for bacterial conjugation and transfer. Because the small intestine is close to the stomach and the pH value is low, it is not conducive to the survival of bacteria, hence the bacterial content can be as low as 10 3 –10 4 CFU/mL, 35 and few receptor bacteria are available for conjugation and transfer. The amount of ARGs detected in different intestinal segments differs, mainly due to the intestinal structure and differences in the types and amounts of bacteria.…”

Resolving the Paradox of Colon Cancer Through the Integration of Genetics, Immunology, and the Microbiota

“…At the genus level, several genera are commonly found in the small intestine, such as Lactobacillus, Clostridium, Staphylococcus, Streptococcus, and Bacteroides (124)(125)(126)(127). Sample collection from the distal ileum has shown that Streptococcus, Granulicatella, Actinomyces, Solobacterium, Rothia, Gemella, and TM7(G-1) are the most frequently detected bacterial genera by 16S gene sequencing (127) with Streptococci, Actinomyces, Rothia and Lactobacillus species most frequently identified by culturomics and mass spectrometry (128). In contrast, the colon contains roughly 70% of all the bacteria of the human body (129).…”