Establishment of a Stable Human Small Intestinal and Colonic Microbiota in an In Vitro Cultivar: Form vs. Function and Response to Oxygen

Authors: Firrman, Jenni; FRIEDMAN, ELLIOT - University Of Pennsylvania; STRANGE, WILLIAM - University Of Pennsylvania; LEE, JUNG-JIN - Children'S Hospital - Philadelphia, Pennsylvania; BITTINGER, KYLE - Children'S Hospital - Philadelphia, Pennsylvania; Liu, Linshu; WU, GARY - University Of Pennsylvania

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/15/2020
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Background: Despite a large amount of information regarding the composition of the human fecal microbiota, there is very limited information about the communities that inhabit the small intestine. Due to the difficulties in accessing the human small intestine to perform longitudinal studies, we sought to develop an in vitro model of the human small intestinal microbiota using a cultivar system to compare its steady state composition and metabolite production with an established fecal community. Methods: Chemostatic bioreactors (pH=7.4; fed three times per day with SHIME feed (ProDigest), pancreatin, and oxbile; continuously mixed; sparged with 1 L gas/min) were used to model the small intestinal and fecal communities in vitro. Two reactors, one inoculated with a fecal sample from a healthy donor and one with an ileostomy sample from a healthy donor (non-IBD), were sparged with nitrogen for two weeks; subsequently, reactors were sparged with 5% oxygen (a level roughly equivalent to tissue oxygenation) for two weeks. The third reactor, inoculated with the same fecal sample, was sparged with 5% oxygen for the first two weeks then subsequently with nitrogen for two weeks. Bacterial communities were analyzed by 16S tagged sequencing and metabolomics was performed by UPLC. Results. The alpha diversity in the small intestinal reactor was lower than in the fecal reactors, and was not significantly altered by the addition of oxygen. Beta diversity showed maximal separation between the small intestinal and fecal communities along PC1 explaining 77% of the variance, where the composition of the steady state communities was remarkably similar to that of their respective innocula. The small intestinal reactor had a higher proportion of Clostridia than the fecal reactors but lacked Bacteroidetes and Actinobacteria, both of which were present in the fecal reactors. The addition of oxygen to the small intestinal community made its composition more similar to the inoculum, leading to an outgrowth of Klebsiella, Ruminococcus, and Veillonella spp. By contrast, the addition of oxygen had little effect on the composition of the fecal community. The production of both secondary bile acids and SCFA levels were significantly higher in the fecal community. Conclusions: It is possible to establish a stable small intestinal bacterial community in vitro using a cultivar that is similar to composition of an ileostomy inoculum, but maximally distinct from a fecal community established using the same culture conditions. The functionality of the small intestinal community demonstrates the predicted metabolic functionality in vivo, specifically regarding bile acid and SCFA production. The use of in vitro cultivar technologies may be helpful in creating models of the human small intestinal microbiota to examine the effect of diet and other perturbations on its composition and function.