Restriction lift date: 2027-09-30
Unlocking carbohydrate metabolism in bifidobacteria
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Date
2026-02-06
Authors
Friess, Lisa
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Publisher
University College Cork
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Abstract
Bifidobacteria are common gut commensals and can be isolated from the gut contents of birds, insects and mammals, including humans. They are often associated with positive health effects exerted on their human host and are therefore commercially exploited as probiotics. While being in high relative abundance during infancy, bifidobacterial relative abundance decreases when transitioning from infancy to adolescence and into adulthood, with a further decrease observed in the elderly population. Similarly, the species composition of bifidobacteria present in the human gut changes with age, with certain infant-associated species being less prevalent in adults and vice versa for adult related species. This shift is often associated with a change in the diet of their host and their ability to utilise available carbohydrates. During infancy the bifidobacterial (sub)species present are often associated with their ability to utilise human milk oligosaccharides, while species commonly found in adults are able to utilise complex plant-derived glycans. One bifidobacterial (sub)species that is frequently isolated from both infant and adult faecal samples is Bifidobacterium longum subsp. longum. Members of this subspecies have been studied in connection with their ability to metabolise plant-based carbohydrates that are part of the adult diet. Such plant-based carbohydrates are abundant in dietary fibre, are indigestible by humans and may therefore represent effective prebiotics. It has been shown that an increase of a specific plant-derived glycan, for example arabinoxylan, may increase their relative abundance, although little is known as to the metabolic activities that would explain this increase in molecular detail.
In Chapter II of this thesis, the ability of B. longum subsp. longum to utilise arabinoxylan together with multiple other plant-derived carbohydrates was analysed. Combining transcriptomic data and molecular techniques two extracellular α-arabinofuranosidases were identified as key enzymes required for growth of this species on cereal-derived, ‘simple’ arabinoxylan. These two enzymes are able to hydrolyse the bonds between xylan backbone and the arabinose-sidechain, thus allowing extracellular release of these saccharidic substitutions.
Chapter III focuses on the uptake and metabolism of (extracellularly released) arabinose by previously mentioned α-arabinofuranosidases. Together with two other pentose sugars, xylose and ribose, a common ABC-transporter system and pentose-specific metabolic clusters were identified. Growth assays using the three sugars and comparative analysis showed that arabinose and xylose utilisation is a universal trait of the species, while only strains encoding a specific ribokinase are able to utilise ribose as their sole carbohydrate source.
Chapter IV investigates the utilisation of xylooligosaccharides (XOS) by B. longum subsp. longum. Transcriptomic analysis revealed a novel locus involved in XOS uptake and degradation. This cluster is partially conserved in this species and homologues can also be found in other adult-associated bifidobacterial species, including B. adolescentis and B. pseudocatenulatum. Further genetic manipulation revealed the importance of (i) an ABC-type carbohydrate uptake system encoded within the cluster for import of XOS into the cell, and (ii) one of three glycosyl hydrolases (GHs) encoded within this cluster, this GH representing the key enzyme for degradation of unbranched short-chain XOS.
Chapter V describes the presence of two adjacent gene clusters in the genome of B. longum subsp. longum NCIMB 8809 that are predicted to be involved in the metabolism of as yet unknown plant-derived oligosaccharides. The four GH 43 enzymes encoded by the pgg gene cluster, as well as a GH51 and a GH27 specified by the pgx gene cluster were analysed for their ability to hydrolyse a variety of different arabino-(xylo)oligosaccharides. While the assessed enzymes show in some cases overlapping hydrolytic activity, their distinct transcriptional regulation and conservation across different bifidobacterial species, indicates that they are two independent carbohydrate utilisation clusters. Although their precise glycan substrates remain unknown, it is possible that the enzymes encoded by the pgg and pgx clusters metabolise similar sidechains attached to different plant cell wall polysaccharides.
This thesis provides a substantial amount of new scientific information regarding the enzymatic degradation, uptake and metabolism of plant-derived poly/oligosaccharides, specifically on arabinoxylan and its individual compounds by B. longum subsp. longum. Understanding the molecular mechanisms behind bifidobacterial utilisation of these saccharidic compounds is expected to facilitate the rational development of novel functional foods and better targeted prebiotics to improve and support human health.
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Keywords
Bifidobacteria , Bifidobacterium longum , Carbohydrate metabolism , Plant glycan , Prebiotics , Gut microbiota , Dietary fibre , Probiotics
Citation
Friess, L. 2026. Unlocking carbohydrate metabolism in bifidobacteria. PhD Thesis, University College Cork.