Abstract
Although bifidobacteria are widely used as probiotics, their metabolism and physiology remain to be explored in depth. In this work, strain-specific genome-scale metabolic models were developed for two industrially and clinically relevant bifidobacteria, Bifidobacterium animalis subsp. lactis BB-12® and B. longum subsp. longum BB-46, and subjected to iterative cycles of manual curation and experimental validation. A constraint-based modeling framework was used to probe the metabolic landscape of the strains and identify their essential nutritional requirements. Both strains showed an absolute requirement for pantethine as a precursor for coenzyme A biosynthesis. Menaquinone-4 was found to be essential only for BB-46 growth, whereas nicotinic acid was only required by BB-12®. The model-generated insights were used to formulate a chemically defined medium that supports the growth of both strains to the same extent as a complex culture medium. Carbohydrate utilization profiles predicted by the models were experimentally validated. Furthermore, model predictions were quantitatively validated in the newly formulated medium in lab-scale batch fermentations. The models and the formulated medium represent valuable tools to further explore the metabolism and physiology of the two species, investigate the mechanisms underlying their health-promoting effects and guide the optimization of their industrial production processes.
Highlights
Bifidobacteria are Gram-positive, obligate anaerobic prokaryotes that commonly inhabit the gastrointestinal tract of humans and animals
The presence of bifidobacteria is associated with a healthy gastrointestinal tract and a strong immune function of the host
The hybrid assembly of B. longum BB-46 genome resulted in a single 2.385.558-bp circular chromosome with an average G + C content of 60.33%
Summary
Bifidobacteria are Gram-positive, obligate anaerobic prokaryotes that commonly inhabit the gastrointestinal tract of humans and animals. Health-promoting effects of bifidobacteria include the production of antimicrobial agents and vitamins[1], the inhibition of adhesion of pathogens and toxins to epithelial cells, and the stimulation of the host’s immune response[2,3] Based on their beneficial impact on health, several Bifidobacterium strains, such as Bifidobacterium animalis subsp. As bifidobacteria are rather fastidious microorganisms, most previous studies used either complex undefined media[10,12,19,20] or semi-defined media supplemented with complex additives, such as (hydrolyzed) casein or the permeate of dialyzed complex medium[21,22], to sustain growth While such media allow for high growth rates and high final biomass concentrations, they are not suitable for detailed physiological studies since complex medium components with undefined composition may hide the effect of a metabolite and hamper the quantification of product yields and growth energetics. The models were quantitatively validated in the newly developed medium in lab-scale batch fermentations
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