Kenyan infant fecal microbiota continuous cultivation

The aim of this study was to develop a continuous fermentation model based on the PolyFermS platform to closely mimic the gut microbiota of infants living in low- and middle-income countries (LMIC) in low hygiene conditions. Fresh Kenyan infant fecal microbiota was immobilized in polymer beads and used to inoculate a bioreactor continuously fed with medium mimicking the infant diet. Fructo-oligosaccharides (FOS) supplementation (1, 4 and 8 g/L) and cultivation pH (5.8 and 6.3) were stepwise investigated. Conditions providing a close match between fecal and in vitro microbiota (pH 5.8 with 1 g/L FOS) were selected for investigating long-term stability of four Kenyan infant PolyFermS microbiota. The shared fraction of top bacterial genera between fecal and in vitro microbiota was high (74-89%) and stable during 107 days of continuous cultivation. Community diversity was maintained, and two distinct fermentation metabolite profiles, propiogenic and butyrogenic, of infant fecal microbiota established from day 8 onwards and stayed stable. We present here the first stable continuous cultivation of fecal microbiota from LMIC infants using a fresh fecal inoculum. This model is therefore an important tool to study the effect of dietary factors on the gut microbiota of LMIC infants with a high enteropathogen burden.