This study demonstrates that several Bifidobacterium species residing in the gut of gummivorous primates, such as marmosets, possess previously uncharacterised pathways for the efficient utilisation of type-II arabinogalactan (AG), the major polysaccharide component of tree gums.
Abstract
Bifidobacteria inhabiting the primate gut exhibit host-dependent genetic diversification, particularly in their gene repertoire related to carbohydrate metabolism, suggesting adaptation to host diets. However, these diverse genetic traits remain poorly associated with specific dietary components. Here, through enzymatic and genetic analyses, we demonstrate that several Bifidobacterium species residing in the gut of gummivorous primates, such as marmosets, possess previously uncharacterised pathways for the efficient utilisation of type-II arabinogalactan (AG), the major polysaccharide component of tree gums. The assimilation pathways comprises two key components: a bifunctional β-1,3-galactanase that cleaves the AG backbone via both endo- and exo-mode actions and an ATP-binding cassette transporter that internalises the released arabinogalactan oligosaccharides (AGOs) into cells. Data mining of deposited metagenomic datasets suggested that the endo/exo-β-1,3-galactanase and the AGO transporter contribute to cross-feeding interactions within Bifidobacterium communities in the gut of gummivorous primates. Our study not only highlights molecular strategies employed by certain Bifidobacterium species to adapt to the dietary habits of a host but may also inform probiotic intervention strategies for the health and welfare of these primates in captive settings.
ABSTRACT Bifidobacteria are common members of the human gut microbiota and are associated with host health. Bifidobacterium longum subsp. longum (B. longum) is prevalent across host ages and can utilise diverse plant-derived glycans, including xylooligosaccharides (XOS), that are indigestible by humans. Here, we show that XOS utilisation is strain specific among members of B. longum. In B. longum NCIMB 8809, growth on XOS induced transcription of genes encoding three glycoside hydrolases (XouA, XouB, and XouC), together with adjacent genes (xouDEF) predicted to encode an ABC-type carbohydrate uptake system. Biochemical analyses demonstrated that XouA and XouC are β-xylosidases, whereas XouB is an α-arabinofuranosidase. Genetic disruption and complementation experiments showed that XouA and the XouDEF uptake system are required for growth on XOS. Together, these findings identify the genetic and enzymatic basis of XOS utilisation in B. longum and highlight how strain-level variation in carbohydrate metabolism may inform the design of targeted prebiotic and synbiotic strategies to promote gut health.
Lisa Friess, F. McAuliffe, Paul D. Cotter et al.· Gut microbes· 0 citations
This study reconstructed the first comprehensive pangenome of B. bifidum using 1,351 high-quality genomes, including metagenome-assembled genomes to identify species-specific genetic and functional features and identified significant gain-of-function events.
Emanuele Selleri, G. Longhi, C. Tarracchini et al.· Microbiome Research Reports· 0 citations
A global genomic atlas of >7,000 MAGs/genomes from infants, domesticated animals, non-human primates, and ancient humans helps explain subspecies differentiation in the gut microbiota of Western and non-Western infants and provides a framework for community-mediated interventions in early life.
Wei Guo, Wen Zhang, Lili Yang et al.· bioRxiv· 0 citations
The gut microbiota orchestrates host health by influencing nutrition, immunity, and behavior. Bifidobacterium species are early colonizers maintaining gut homeostasis in honeybees. Despite these critical roles, strain-level dynamics and driving forces behind microbial competition during social transmission remain poorly understood. Here, we established six field-mimicking colonies to track Bifidobacterium communities across successive generations of newly emerged workers. Social transmission markedly reshaped community structure, generating distinct trajectories among phylotypes. OTU10 consistently dominated, reaching a median relative abundance of 77%, whereas OTU61 and OTU43146 were progressively outcompeted or lost. Comparative genomics of five representative species identified 69 carbohydrate-active enzyme families, with GH43 glycosyl hydrolases driving genomic divergence. Bifidobacterium polysaccharolyticum encoded an expanded CAZyme repertoire, supporting rapid growth on glucose and arabinan and indicating an r-selected strategy. In vitro and in vivo competition assays demonstrated that nutrient availability and priority effects act as key ecological filters. Pollen favored Bifidobacterium apousia, whereas sucrose-only diets promoted B. polysaccharolyticum. Moreover, early colonizers excluded later arrivals to some extent, highlighting priority effects. Together, these findings reveal how pollen polysaccharides and transmission bottlenecks interact to structure the strain-level landscape of the social microbiome.
Yiyuan Li, Fangyuan Ye, Jiaqiang Wu et al.· Integrative Zoology· 0 citations
As a paradigmatic next-generation probiotic, Faecalibacterium species play a major role in butyrate generation, intestinal barrier integrity, and immune homeostasis. However, its clinical translation is severely hindered by profound physiological fragility-namely, extreme oxygen sensitivity and inherent metabolic bottlenecks, such as its strict dependence on exogenous acetate for butyrate synthesis-which collectively impede in vitro cultivation, in vivo colonisation, and scalable production. To circumvent these constraints, leveraging the gut microbiota's "cross-feeding" network has emerged as a highly promising ecological strategy, with prebiotics serving as precise molecular tools to orchestrate these interactions. This review systematically delineates the biological characteristics and metabolic constraints of Faecalibacterium, comprehensively dissecting its cross-feeding mechanisms with pivotal commensals (e.g., Bifidobacterium and Akkermansia muciniphila) across metabolic complementarity, ecological niche synergy, and multi-species networks. Building on this ecological framework, we highlight how traditional prebiotics (oligosaccharides and polysaccharides) and novel non-conventional substrates (e.g., riboflavin and specific glycoconjugates) can be strategically utilised to drive these networks for the targeted enrichment of Faecalibacterium. Bridging ecological interventions with formulation engineering, this paper further critically evaluates advanced delivery technologies designed to safeguard live cell viability. Emphasis is placed on dual-modality protection strategies: physical spatial isolation (via microencapsulation and cryoprotectant optimisation) and biochemical microenvironmental remodelling (via antioxidant excipients). Ultimately, by integrating microecological interaction theory with cutting-edge formulation engineering, this review provides a comprehensive roadmap for the rational design, development, and industrial-scale production of Faecalibacterium-based biotherapeutics, functional foods, and medical nutrition.
Xilong Deng, Xiaoya Sheng, Chenbin Yang et al.· Microbiology Research· 0 citations
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