Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling

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.

Novel Insights into the Molecular Mechanisms Underlying Robustness and Stability in Probiotic Bifidobacteria

“…Most of the 20 free proteinogenic amino acids supplied in the CDM ( 18 ) were continuously consumed by both strains throughout growth, with most of them being nearly depleted when the strains reached their stationary phase ( Fig. 2A ).…”

“…BB-12 is an exceptionally stress tolerant and stable strain ( 7 , 8 ), whereas Bifidobacterium longum strains are generally known to be more sensitive to stressors ( 7 , 8 ). The 2 strains were cultivated in lab-scale pH-controlled fermentations in a recently developed chemically defined medium (CDM) ( 18 ), and compared in terms of their growth, substrate consumption, metabolite production, cell envelope characteristics, and short-term survivability. In addition, global and differential gene expression analyses were applied to obtain a detailed picture of their phenotypes, and identify potential transcriptional signatures associated with robustness and stability.…”

Teasing out Missing Reactions in Genome-scale Metabolic Networks through Graph Convolutional Networks

“…3j). This is not surprising as the poor performance of draft GEMs is mostly due to poor annotation of transporter genes [45][46][47] . Notably, the acetic acid transport reaction is not unique.…”

“…3j). This is not surprising as the poor performance of draft GEMs is mostly due to poor annotation of transporter genes [39][40][41] . Beside false negatives, CHESHIRE can also identify false-positive predictions.…”

Dynamic genome-based metabolic modeling of the predominant cellulolytic rumen bacteriumFibrobacter succinogenesS85

“…Genome-scale metabolic models are widely used for microbial defined growth medium identification (30,82), metabolic functional characterization (29,83) or design of novel treatment against pathogens (84). Regarding gut communities, they have been mainly applied to human gut bacteria in order to decipher the microbial interactions in the human intestinal microbiome (28,30,(85)(86)(87).…”