Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts

Kujawska, Magdalena, Seki, David, Chalklen, Lisa, Malsom, Jennifer, Kiu, Raymond, Goatcher, Sara, Christoforou, Ioulios, Mitra, Suparna, Crouch, Lucy and Hall, Lindsay J. (2025) Host-specific microbiome and genomic signatures in Bifidobacterium reveal co-evolutionary and functional adaptations across diverse animal hosts. Cell Host and Microbe, 33 (9). 1502-1517.e13. ISSN 1931-3128

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Abstract

Animals harbor divergent microbiota, including various Bifidobacterium species, yet their evolutionary relationships and functional adaptations remain understudied. Using samples from insects, reptiles, birds, and mammals, we integrated taxonomic, genomic, and predicted functional annotations to uncover how Bifidobacterium adapts to host-specific environments. Host phylogeny is a major determinant of gut microbial composition. Distinct microbiota in mammalian and avian hosts reflect evolutionary adaptations to dietary niches, such as carnivory, and ecological pressures. At a strain-resolved level, Bifidobacterium and their hosts exhibit strong co-phylogenetic associations, driven by vertical transmission and dietary selection. Functional analyses highlight striking host-specific adaptations in Bifidobacterium, particularly in carbohydrate metabolism and oxidative stress responses. In mammals, Bifidobacterium strains are enriched in glycoside hydrolases tailored to complex carbohydrate-rich diets, including multi-domain GH13_28 α-amylases associated with degradation of resistant starch. Together, these findings deepen our understanding of host-microbe co-evolution and the critical role of microbiota in shaping animal health and adaptation.

Item Type:	Article
Additional Information:	Data and code availability: 16S rRNA amplicon sequencing data analyzed in this study have been deposited to the NCBI SRA: PRJNA1200941. The draft genomes of 96 Bifidobacterium isolates sequenced here have been deposited to the NCBI Genomes :PRJNA1200594. The code and associated files have been deposited to Figshare: https://doi.org/10.6084/m9.figshare.29635103. The study does not make use of unpublished data or software. Any additional information required to reanalyze the data reported in this work paper is available from the lead contact upon request. Acknowledgments: We would like to thank the zoo staff at Banham Zoo (UK), Africa Alive! (UK), and Pafos Zoo (Cyprus) for their assistance in collecting samples for this study. This work was funded by Wellcome Trust Investigator Awards 100/974/C/13/Z and 220540/Z/20/A, a BBSRC Norwich Research Park Bioscience Doctoral Training grant no. BB/M011216/1 (supervisor, L.J.H.; student, M.K.), an Institute Strategic Programme Gut Microbes and Health grant no. BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356, and a BBSRC Institute Strategic Programme Food Microbiome and Health BB/X011054/1 and its constituent project BBS/E/QU/230001B to L.J.H.
Uncontrolled Keywords:	animal host,bifidobacterium,carbohydrate metabolism,co-evolution,genomics,parasitology,microbiology,virology ,/dk/atira/pure/subjectarea/asjc/2400/2405
Faculty \ School:	Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups:	Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health
Related URLs:	http://www.scopus.com/inward/record.url?...
Depositing User:	LivePure Connector
Date Deposited:	18 Sep 2025 08:31
Last Modified:	22 Sep 2025 09:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/100432
DOI:	10.1016/j.chom.2025.08.008

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