Prebiotics enhance persistence of fermented-food associated bacteria in in vitro cultivated fecal microbial communities

It is well established that the gastrointestinal (GI) microbiota plays a major role in human health. Dietary interventions, and consumption of fermented foods that contain live microbes, in particular, are among the approaches being investigated to modulate the GI microbiota and improve health. However, persistence of fermentation associated bacteria within the GI tract is typically limited by host factors that limit colonization and competition with autochthonous microbes. In this research, we examined if addition of prebiotics, dietary substrates that are selectively metabolized by microbes to improve health, would enhance persistence of Lactobacillaceae from fermented foods. We evaluated persistence of Lactobacillaceae over time from three live microbe-containing fermented foods -kefir, sausage, and sauerkraut - in fecal microbial communities from four healthy adults. Fecal communities were propagated in vitro and were inoculated with fermentation associated microbes from kefir, sausage, or sauerkraut at an initial concentration of 106 CFU/ml. Communities were diluted 1:100 every 24 hours into fresh medium to simulate microbial community turnover. Persistence of Lactobacillaceae from the initial fermented food inoculum was determined by quantitative PCR (qPCR), and 16S rRNA sequencing was used to assess other changes in the microbiota. Food-derived Lactobacillaceae were unable to persist in vitro, reaching undetectable levels within 96 hours. However, addition of prebiotics, including xylooligosaccharides and a mixture of galactooligosaccharides and fructooligosaccharides enhanced persistence of Lactobacillaceae at near-inoculation levels, but persistence varied by fecal donor. We also observed that addition of prebiotics increased the relative abundance of Bifidobacterium species present in the fecal samples. Collectively, our results support previous in vivo studies demonstrating the transient nature of fermentation associated bacteria in the GI tract and indicate that consumption of prebiotics may enhance persistence of fermentation associated microbes.