Quantitative physiology and proteome adaptations of Bifidobacterium breve NRBB57 at near-zero growth rates

In natural environments, nutrients are usually scarce causing microorganisms to grow slow while staying metabolically active. These natural conditions can be simulated using retentostat cultivations. The present study describes the physiological and proteome adaptations of the probiotic Bifidobacterium breve NRBB57 from high (0.4 h-1) to near-zero growth rates. Lactose-limited retentostat cultivations were carried out for 21 days in which the bacterial growth rate progressively reduced to 0.00092 h-1, leading to a 3.4-fold reduction of the maintenance energy requirement. Lactose was mainly converted into acetate, formate and ethanol at high growth rates while in the retentostat lactate production increased. Interestingly, the consumption of several amino acids (serine, aspartic acid and glutamine/arginine) and glycerol increased over time in the retentostat. Morphological changes and viable but non-culturable cells were also observed in the retentostat. Proteomes were compared for all growth rates, revealing a down-regulation of ribosomal proteins at near-zero growth rates and an up-regulation of proteins involved in the catabolism of alternative energy sources. Finally, we observed induction of the stringent response and stress defense systems. Retentostat cultivations were proven useful to study the physiology of B. breve, mimicking the nutrient scarcity of its complex habitat, the human gut.