Selection of fast and slow growing bacteria from fecal microbiota using continuous culture with changing dilution rate

Abstract

Background: Nutrient and energy metabolism in human colon depends on bacterial growth rate that is determined by the colonic transit rate.Objective: A novel approach, De-stat culture was used to distinguish the fast and slow growing sub-populations from fecal microbiota.Design: The enrichment and metabolism of bacteria from pooled fecal cultures of children was studied at dilution rates D = 0.2–0.0 1/h in mucin-supplemented media containing either arabinogalactan or apple pectin.Results: The study revealed clear differentiation of the fecal microbiota at higher (above 0.1 1/h) and lower (below 0.1 1/h) dilution rates, along with metabolic changes. Similarity of the fast and slow growing bacteria was observed in two different fecal pools and on both substrates, suggesting the dilution rate as the main triggering parameter for selection of bacteria. At high dilution rates, the species Collinsella aerofaciens, Dorea longicatena, Escherichia coli, Lachnoclostridium torques, and different Bacteroides (B. caccae, B. fragilis, B. ovatus, B. thetaiotaomicron, B. vulgatus) were dominant in both media variants. At low dilution rates, Akkermansia muciniphila, Eisenbergiella tayi, Negativicoccus succinivorans, and a group of Ruminococcaceae became dominant in both media and in both fecal pools. This change in bacterial population accompanied by the increased production of propionic and butyric acids as well as higher consumption of alanine and branched chain amino acids at low dilution rates.Conclusions: The study suggests that specific growth rate has important effect on the dynamics of colon microbiota. Manipulation of the proportions of fast and slow growing gut bacteria through modulation of the transit rate could be a target in human nutrition studies. The De-stat study would enable to predict changes in microbiota composition associated with the decrease or increase of the colonic transit rate.

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

“…The concentrations of the BCFA methylbutyrate, isovalerate, and isobutyrate increased ( Figure 6), which indicates that protein fermentation was favored at faster TT. These findings are in accordance with previous results and strengthen the hypothesis that protein fermentation is favored with faster TT [46,47]. Functional changes in the pathway abundances of low abundant SIHUMIx bacteria were not detected.…”

“…In our study, the production of BCFAs was correlated with the most abundant member of SIHUMIx B. thetaiotaomicron. However, only the production of propionate has been described to date [46][. At approximately 65%, B. thetaiotaomicron is the most abundant member of SIHUMIx.…”

Lean and obese microbiota: differences in in vitro fermentation of food-by-products

“…The effects were more prominent for the obese microbiota (Figure 5B), which at the end of the experiment led to higher abundances of Bacteroides than in the lean microbiota (Figure 7). Despite that growth of Bacteroides has been shown to be affected by dilution rate, pH and other factors (Adamberg and Adamberg, 2018;Adamberg et al, 2020), we show here a positive association between Bacteroides and the presence of xylose (rho=0.79; q-value=7.09×10 -06 ) and the presence of fucose (rho=0.63; q-value=0.003), both sugars present in PFPs (Supplementary Table S1). Xylose and fucose are sugars present in nonstarch polysaccharides, such as hemicellulose and pectin.…”

Different Bacteroides Species Colonise Human and Chicken Intestinal Tract

“…Differences between human- and chicken-adapted isolates were observed also during in vitro growth. The fact that some species overgrew the others was not unexpected since B. ovatus was already reported as belonging among rapidly multiplying species from human microbiota [ 36 ]. Rather unexpected was that all human-adapted species outgrew all the chicken-adapted species.…”