Comparative genomic analysis revealed that dietary habits affected the adaptation of Bifidobacterium bifidum to the intestinal tract in different geographic populations
Open accessAbstract
Recent research on the genome of Bifidobacterium bifidum has mainly focused on the isolation sources (intestinal tract niche) recently, but reports on the isolation region are limited. This study analyzed the differences in the genome of B. bifidum isolated from different geographical populations by comparative genomic analysis. Results at the genome level indicated that the GC content of American isolates was significantly higher than that of Chinese and Russian isolates. The phylogenetic tree, based on 919 core genes showed that B. bifidum might be related to the geographical characteristics of isolation region. Furthermore, functional annotation analysis demonstrated that copy numbers of carbohydrate-active enzymes (CAZys) involved in the degradation of polysaccharide from plant and host sources in B. bifidum were high, and 18 CAZys showed significant differences across different geographical populations, indicating that B. bifidum had adapted to the human intestinal environment, especially in the groups with diets rich in fiber. Dietary habits were one of the main reasons for the differences of B. bifidum across different geographical populations. Additionally, B. bifidum exhibited high diversity, evident in glycoside hydrolases, the CRISPR-Cas system, and prophages. This study provides a genetic basis for further research and development of B. bifidum.
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Previous comparative genomics studies of B. bifidum, limited to smaller datasets of cultured isolates from Westernized populations, consistently reported an open pangenome structure.
“Previous comparative genomics studies of this species, limited to smaller datasets of cultured isolates from Westernized populations, consistently reported an open pangenome structure [29-32] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [32]
Section 3.3 reports an open pangenome in this paper's analysis of 110 B. bifidum genomes. But the Discussion says earlier studies reported a closed pangenome, not consistently an open one; the Introduction and section 3.1 also describe genomes from China, the USA, Russia, and unknown origins, rather than a dataset limited to cultured isolates from Westernized populations. Page numbers were not provided in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe genomic diversity of B. bifidum has not yet been comprehensively surveyed, and current reference collections capture only a fraction of the global B. bifidum pangenome.
“Despite its relevance in early life, the species' genomic diversity has not yet been comprehensively surveyed, and current reference collections capture only a fraction of the global B. bifidum pangenome.”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [32]
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Fu, P., Qi, H., & Liu, W. (2025) · Foods · doi:10.3390/foods14152747 · 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
- Authors
- Li, M., Yu, J., Li, W., Wu, Q., Sun, J., & Sun, Z.
- Affiliations
- Inner Mongolia Agricultural University (CN)
- Corresponding author
- Sun, Zhihong
- Venue
- Food Science and Human Wellness
- Publisher
- Tsinghua University Press
- Published
- 2024-09
- Volume
- 13
- Issue
- 5
- Pages
- 3006-3017
- ISSN
- 2097-0765 (ISSN-L)
- 2213-4530
- OpenAlex
- W4388247830
- Cited by
- 5
- References
- 59
- Citations by year
- 2026: 4 · 2025: 1
- FWCI
- 0.44
- Type
- journal article
- Language
- en
- Open access
- diamond
- dx.doi.org
- Licence
- cc-by-nc-nd
- Locations
- Food Science and Human Wellness (publishedVersion, cc-by-nc-nd)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Natural Science Foundation of China (32325040)
- Natural Science Foundation of Inner Mongolia (2020ZD12)
- 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 bifidum, dietary habits, intestinal adaptation, genome-wide comparison, GC content, carbohydrate-active enzymes, polysaccharide degradation, dietary fiber, glycoside hydrolases, CRISPR-Cas, prophages, core genes, gut microbiota
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