The Simplified Human Intestinal Microbiota (SIHUMIx) Shows High Structural and Functional Resistance against Changing Transit Times in In Vitro Bioreactors

Abstract

Many functions in host-microbiota interactions are potentially influenced by intestinal transit times, but little is known about the effects of altered transition times on the composition and functionality of gut microbiota. To analyze these effects, we cultivated the model community SIHUMIx in bioreactors in order to determine the effects of varying transit times (TT) on the community structure and function. After five days of continuous cultivation, we investigated the influence of different medium TT of 12 h, 24 h, and 48 h. For profiling the microbial community, we applied flow cytometric fingerprinting and revealed changes in the community structure of SIHUMIx during the change of TT, which were not associated with changes in species abundances. For pinpointing metabolic alterations, we applied metaproteomics and metabolomics and found, along with shortening the TT, a slight decrease in glycan biosynthesis, carbohydrate, and amino acid metabolism and, furthermore, a reduction in butyrate, methyl butyrate, isobutyrate, valerate, and isovalerate concentrations. Specifically, B. thetaiotaomicron was identified to be affected in terms of butyrate metabolism. However, communities could recover to the original state afterward. This study shows that SIHUMIx showed high structural stability when TT changed-even four-fold. Resistance values remained high, which suggests that TTs did not interfere with the structure of the community to a certain degree.

Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx

“…This led us to the conclusion that the microbes showed a temporal response to the treatment. SIHUMIx responded to the treatment, but reaches a constant state as reported previously [ 24 ]. This may still indicate that microbes are affected, but can cope with chemicals occurring in the gut.…”

“…The same threshold was set for the protein FDR (<1%). Protein grouping was performed as described [ 24 ]. GhostKOALA was used to assign KO numbers from Kyoto Encyclopedia of Genes and Genomes (KEGG) to identified functions of identified protein sequences [ 32 , 33 ].…”

“…SIHUMIx comprises of eight species representing a majority of metabolic activities typically found in the human intestine. The cultivation in vitro is highly reproducible and reaches a constant state giving a starting point for stress exposure studies [ 24 ]. In this study, we investigated how the exposure of 45 µM BPS in DMSO modulates (i) overall growth, (ii) membrane fatty acid composition, (iii) taxonomic composition, and (iv) functional changes of SIHUMIx.…”

Quantification of glyphosate and aminomethylphosphonic acid from microbiome reactor fluids

“…In a model community, SIHUMIx takes five days to stabilize the community, and this can also be observed in the metabolic profile. Once the community is stable small perturbations like the transit time only slightly affect the community . However, the more complex community arising from pig colon content is expected to be even more stable against external influences.…”

The Activation of Mucosal-Associated Invariant T (MAIT) Cells Is Affected by Microbial Diversity and Riboflavin Utilization in vitro

“…For complex microbiota protein coding sequences of all "bacteria" were downloaded from UniProt (13.05.2017; http://www.uniprot.org/) resulting in 15,214,675 protein coding sequences. Protein identification was performed as descried (Schäpe et al, 2019). In brief, the false discovery rates (FDR) 1 http://www.uniprot.org/ were determined with the node Percolator (Käll et al, 2007) embedded in Proteome Discoverer (v 2.2) and we set the FDR threshold at peptide and protein level at 5%.…”