Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy
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Aim: The human gut Bifidobacterium community has been studied in detail in infants and following dietary interventions in adults. However, the variability of the distribution of Bifidobacterium species and intra-species functions have been little studied, particularly beyond infancy. Here, we explore the ecology of Bifidobacterium communities in a large public dataset of human gut metagenomes, mostly corresponding to adults. Methods: We selected 9.515 unique gut metagenomes from curatedMetagenomicData. Samples were partitioned by applying Dirichlet’s multinomial mixture to Bifidobacterium species. A functional analysis was performed on > 2.000 human-associated Bifidobacterium metagenome-assembled genomes (MAGs) paired with participant gut microbiome and health features. Results: We identified several Bifidobacterium-based partitions in the human gut microbiome differing in terms of the presence and abundance of Bifidobacterium species. The partitions enriched in both B. longum and B. adolescentis were associated with gut microbiome diversity and a higher abundance of butyrate producers and were more prevalent in healthy individuals. B. bifidum MAGs harboring a set of genes potentially related to phages were more prevalent in partitions associated with a lower gut microbiome diversity and were genetically more closely related. Conclusion: This study expands our knowledge of the ecology and variability of the Bifidobacterium community, particularly in adults, and its specific association with the gut microbiota and health. Its findings may guide the rational selection of Bifidobacterium strains for gut microbiome complementation according to the individual’s endogenous Bifidobacterium community. Our results also suggest that gut microbiome stratification for particular genera may be relevant for studies of variations of species and associations with the gut microbiome and health.
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B. bifidum is characteristic of the bifidobacterial communities residing in the infant gut and contributes to early microbial colonization, alongside B. breve.
“B. bifidum is characteristic of the bifidobacterial communities residing in the infant gut and contributes to early microbial colonization, alongside Bifidobacterium breve [6-10] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [9]
The Introduction (page unavailable) says B. bifidum and B. breve are typically abundant and prevalent in infant gut microbiota. The Results (page unavailable) also report higher B. breve prevalence in children under three. These passages support their presence in the infant gut, but do not establish that B. bifidum contributes to early microbial colonization. (LLM, conf=0.84)
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Ebel, E. R., Kulkarni, A. S., Mongad, D., Olm, M. R., Sarangthem, I., Mir, B. A., Ozarkar, S., Sonnenburg, E. D., Shouche, Y. S., Sonnenburg, J. L., et al. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2694242 · Cited by 3 · see citing works
Selleri, E., Longhi, G., Tarracchini, C., Carolis, E. D., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Ventura, M., & Lugli, G. A. (2026) · Microbiome Research Reports · doi:10.20517/mrr.2026.19
Identifying the non-Bifidobacterial hallmarks of a Bifidobacterium-receptive gut microbiomePreprint
Goswami, S., Ansari, A., Saraf, C., O’Toole, P. W., Shanahan, F., Ahuja, V., & Ghosh, T. S. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.09.675069
Mannila, E., Gómez-Gallego, C., Muluh, G., Nuotio, P., Koistinen, V., Erawijantari, P. P., Salminen, S., Lahti, L., Kolehmainen, M., & Linderborg, K. M. (2026) · Journal of Nutrition · doi:10.1016/j.tjnut.2026.101690
Leschonski, K. P., Pang, Y., Faria, R. A., Geppel, A., Hansen, L. B. S., Kabel, M. A., Olsen, P., Krogh, K. B. R. M., & Laursen, M. F. (2026) · Gut Microbiology · doi:10.1016/j.gutmic.2026.100021
- Authors
- Ladeira, R., Tap, J., & Derrien, M.
- Affiliations
- Danone (France) (FR)
- AgroParisTech (FR)
- Corresponding author
- Tap, Julien
- Derrien, Muriel
- Venue
- Microbiome Research Reports
- Publisher
- OAE Publishing Inc.
- Published
- 2023
- Volume
- 2
- Issue
- 2
- Pages
- 9
- ISSN
- 2771-5965 (ISSN-L)
- PMC
- PMC10688807
- OpenAlex
- W4362460788
- Cited by
- 19
- References
- 65
- Citations by year
- 2026: 9 · 2025: 5 · 2024: 5
- FWCI
- 1.69
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by
- Locations
- Microbiome Research Reports (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- Lirias (submittedVersion, cc-by)
- Funders
- Danone
- Danone Nutricia Research
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Keywords
- Bifidobacterium, gut microbiota, metagenome-assembled genomes, Bifidobacterium longum, Bifidobacterium adolescentis, Bifidobacterium bifidum, butyrate production, gut microbiota diversity, phage genes, human health, adults
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