Abstract
Bifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. However, little is known about the key metabolic differences between different strains of these bifidobacteria, and consequently, their suitability for their varied commercial applications. In this context, the present study applies a constraint-based modelling approach to differentiate between 36 important bifidobacterial strains, enhancing their genome-scale metabolic models obtained from the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. By studying various growth and metabolic capabilities in these enhanced genome-scale models across 30 different nutrient environments, we classified the bifidobacteria into three specific groups. We also studied the ability of the different strains to produce short-chain fatty acids, finding that acetate production is niche- and strain-specific, unlike lactate. Further, we captured the role of critical enzymes from the bifid shunt pathway, which was found to be essential for a subset of bifidobacterial strains. Our findings underline the significance of analysing metabolic capabilities as a powerful approach to explore distinct properties of the gut microbiome. Overall, our study presents several insights into the nutritional lifestyles of bifidobacteria and could potentially be leveraged to design species/strain-specific probiotics or prebiotics.
Highlights
Bifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract
Bifidobacteria cluster into two groups based on carbohydrate utilisation
Among the strains studied, B. adolescentis ATCC 15703 could utilise 28 of the 30 carbon sources used in this study, making the strain nutritionally versatile, followed by B. dentium ATCC 27678 and B. kashiwanohense DSM 21854 belonging to B. adolescentis group[25]
Summary
Bifidobacteria, the initial colonisers of breastfed infant guts, are considered as the key commensals that promote a healthy gastrointestinal tract. Bifidobacteria are gram-positive, anaerobic, and saccharolytic, and have been reported to inhabit the intestinal tract of mammals and insects, the human oral cavity and sewage[7] This genus encompasses a broad range of enzyme-coding genes associated with the uptake and catabolism of complex and non-digestible carbohydrates, ranging from human milk oligosaccharides to plant fibre[8]. Bifidobacteria degrade the hexose sugars glucose and fructose through a unique pathway named “bifid shunt”, which is centred on the key enzyme fructose-6-phosphate phosphoketolase[9] The metabolites from this ATP-generating pathway mainly produce short-chain fatty acids (SCFAs) that antagonise pathogenic bacteria and form a barrier against infection[10]. An understanding of the metabolism of this genus in its entirety and the adaptation of distinct strains to a variety of nutrient environments is definitely necessary
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