Regional variation and adaptive evolution in Bifidobacterium pseudocatenulatum: Insights into genomic and functional diversity in human gut
Abstract
Bifidobacterium pseudocatenulatum is a prevalent gut microbe in humans of all ages and plays a crucial role in host health. However, its adaptive evolutionary characteristics remain poorly understood. This study analyzed the genome of 247 B. pseudocatenulatum isolates from Chinese, Vietnamese, Japanese and other region populations using population genomics and functional genomics. Our findings revealed high genetic heterogeneity and regional clustering within B. pseudocatenulatum isolates. Significant differences were observed in genome characteristics, phylogeny, and functional genes. Specifically, Chinese and Vietnamese isolates exhibited a higher abundance of genes involved in the metabolism of plant-derived carbohydrates (GH13, GH43, and GH5 enzyme families), aligning with the predominantly vegetable-, wheat- and fruit-based diets of these populations. Additionally, we found widespread transmission of antibiotic resistance genes (tetO and tetW) through mobile genetic elements, such as genomic islands (GIs), resulting in substantial intra-regional differences. Our findings highlight distinct adaptive evolution in B. pseudocatenulatum driven by gene specialization, possibly in response to regional variations in diet and lifestyle. This study sheds light on bifidobacteria colonization mechanisms in the host gut. IMPORTANCE: Gut microbiota, as a key link in the gut-brain axis, helps to maintain the health of the organism, among which, Bifidobacterium pseudocatenulatum (B. pseudocatenulatum) is an important constituent member of the gut microbiota, which plays an important role in maintaining the balance of gut microbiota. The probiotic properties of B. pseudocatenulatum have been widely elaborated, and in order to excavate its evolutionary features at the genomic level, here we focused on the genetic background and evolutionary mechanism of the B. pseudocatenulatum genomes isolated from the intestinal tracts of different populations. Ultimately, based on the phylogenetic tree, we found that B. pseudocatenulatum has high genetic diversity and regional clustering phenomenon, in which plant-derived carbohydrate metabolism genes (GH13, GH43, GH5) showed significant regional differences, and this genetic differentiation drove the adaptive evolution, which likely shaped by diet and lifestyle.
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Previous studies of B. bifidum and other HBS have focused more on descriptive aspects.
“adds to the results of previous studies, which have focused more on descriptive aspects in B. bifidum [29,104] and other HBS [105-107]”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [106]
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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
- Wu, Q., Li, W., Kwok, L.-Y., Lv, H., Sun, J., & Sun, Z.
- Affiliations
- Inner Mongolia Agricultural University (CN)
- Corresponding author
- Sun, Jiaqi
- Sun, Zhihong
- Venue
- Food Research International
- Publisher
- Elsevier BV
- Published
- 2024-09
- Volume
- 192
- Pages
- 114840
- ISSN
- 0963-9969 (ISSN-L)
- OpenAlex
- W4401198635
- Cited by
- 9
- References
- 60
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 1
- FWCI
- 1.22
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- Locations
- Food Research International (publishedVersion)
- PubMed (publishedVersion)
- 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 pseudocatenulatum, gut microbiota, adaptive evolution, population genomics, regional genetic variation, antibiotic resistance genes, genomic islands, mobile genetic elements, diet and gut microbiota, probiotics
- MeSH terms
- Gastrointestinal Microbiome, Bifidobacterium pseudocatenulatum, Diet, Humans, Phylogeny, Genetic Variation, Genome, Bacterial, Genomics
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