Comparative Genomic Analysis of Bifidobacterium bifidum Strains Isolated from Different Niches
Open accessAbstract
The potential probiotic benefits of Bifidobacterium bifidum have received increasing attention recently. We used comparative genomic analysis to explore the differences in the genome and the physiological characteristics of B. bifidum isolated from the fecal samples of Chinese adults and infants. The relationships between genotypes and phenotypes were analyzed to assess the effects of isolation sources on the genetic variation of B. bifidum. The phylogenetic tree results indicated that the phylogeny of B. bifidum may be related to the geographical features of its isolation source. B. bifidum was found to have an open pan-genome and a conserved core genome. The genetic diversity of B. bifidum is mainly reflected in carbohydrate metabolism- and immune/competition-related factors, such as the glycoside hydrolase gene family, bacteriocin operons, antibiotic resistance genes, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. Additionally, the type III A CRISPR-Cas system was discovered in B. bifidum for the first time. B. bifidum strains exhibited niche-specific characteristics, and the results of this study provide an improved understanding of the genetics of this species.
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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 [30]
The Introduction says there was only one earlier comparative genomics study of B. bifidum and that its 15-strain analysis proposed a closed pan-genome—the opposite of the claim that previous studies consistently reported an open one. This paper's own 140-genome analysis finds an open pan-genome (Results, §3.2), although its Discussion also describes previous studies as finding one. (LLM, conf=0.85)
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Experimental — accuracy not yet measuredA larger survey of 140 strains isolated from Chinese adult and infant feces confirmed an open pangenome and traced most intraspecific diversity to carbohydrate metabolism and defense-related functions, indicating the type III-A CRISPR-Cas locus as characteristic of this taxon, with phylogenetic clustering tracking both geographic origin and host age.
“A larger survey of 140 strains isolated from Chinese adult and infant feces later confirmed an open pangenome and traced most of the observed intraspecific diversity to carbohydrate metabolism and defense-related functions, including glycoside hydrolase content, bacteriocin operons, antibiotic-resistance genes, and CRISPR-Cas systems, indicating the type III-A CRISPR-Cas locus as characteristic of”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [30]
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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 [30]
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Cites
MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018) · Molecular Biology and Evolution · doi:10.1093/molbev/msy096 · Cited by 37,683 · see citing works
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works
The carbohydrate-active enzymes database (CAZy) in 2013
Lombard, V., Ramulu, H. G., Drula, É., Coutinho, P. M., & Henrissat, B. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1178 · Cited by 6,355 · see citing works
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707 · see citing works
CARD 2020: Antibiotic Resistome Surveillance with the Comprehensive Antibiotic Resistance Database
Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A.-L. V., Cheng, A. A., Liu, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz935 · Cited by 3,202 · see citing works
Identifying bacterial genes and endosymbiont DNA with Glimmer
Delcher, A. L., Bratke, K. A., Powers, E. C., & Salzberg, S. L. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm009 · Cited by 3,141 · see citing works
Gruber, A. R., Lorenz, R., Bernhart, S. H., Neuböck, R., & Hofacker, I. L. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn188 · Cited by 2,717 · see citing works
Temporal development of the gut microbiome in early childhood from the TEDDY study
Stewart, C. J., Ajami, N. J., O’Brien, J. L., Hutchinson, D. S., Smith, D. P., Wong, M. C., Ross, M. C., Lloyd, R. E., Doddapaneni, H., Metcalf, G., et al. (2018) · Nature · doi:10.1038/s41586-018-0617-x · Cited by 1,996 · see citing works
Couvin, D., Bernheim, A. G., Toffano‐Nioche, C., Touchon, M., Michálik, J., Néron, B., Rocha, E. P. C., Vergnaud, G., Gautheret, D., & Pourcel, C. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky425 · Cited by 1,582 · see citing works
BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins
van Heel, A. J., de Jong, A., Song, C., Viel, J. H., Kok, J., & Kuipers, O. P. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky383 · Cited by 1,134 · see citing works
Evolview v3: a webserver for visualization, annotation, and management of phylogenetic trees
Subramanian, B., Gao, S., Lercher, M. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz357 · Cited by 1,021 · see citing works
HemI: A Toolkit for Illustrating Heatmaps
Deng, W., Wang, Y., Liu, Z., Cheng, H., & Xue, Y. (2014) · PLoS ONE · doi:10.1371/journal.pone.0111988 · Cited by 993 · see citing works
SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Huang, W., He, G., Gu, S., Li, S., et al. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu077 · Cited by 979 · see citing works
Bacteriocin Production: a Probiotic Trait?
Dobson, A., Cotter, P. D., Ross, R. P., & Hill, C. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.05576-11 · Cited by 690 · see citing works
MAFFT: Iterative Refinement and Additional Methods
Katoh, K., & Standley, D. M. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-646-7_8 · Cited by 520 · see citing works
PGAP: pan-genomes analysis pipeline
Zhao, Y., Wu, J., Yang, J., Sun, S., Xiao, J., & Yu, J. M. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr655 · Cited by 518 · see citing works
Ciufo, S. A., Kannan, S., Sharma, S., Badretdin, A. J., Clark, K., Turner, S. D., Brover, S., Schoch, C. L., Kimchi, A., & DiCuccio, M. N. (2018) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.002809 · Cited by 513 · see citing works
Xu, M., Guo, L., Gu, S., Wang, O., Zhang, R., Peters, B. A., Fan, G., Liu, X., Xu, X., Deng, L., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa094 · Cited by 485 · see citing works
Abby, S. S., Néron, B., Ménager, H., Touchon, M., & Rocha, E. P. C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0110726 · Cited by 399 · see citing works
Turroni, F., Bottacini, F., Foroni, E., Mulder, I., Kim, J.-H., Zomer, A., Sánchez, B., Bidossi, A., Ferrarini, A., Giubellini, V., et al. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011100107 · Cited by 364 · see citing works
Verma, R., Lee, C., Jeun, E.-J., Yi, J., Kim, K. S., Ghosh, A., Byun, S., Lee, C.-G., Kang, H.-J., Kim, G.-C., et al. (2018) · Science Immunology · doi:10.1126/sciimmunol.aat6975 · Cited by 242 · see citing works
PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes
Arndt, D., Marcu, A., Liang, Y., & Wishart, D. S. (2017) · Briefings in Bioinformatics · doi:10.1093/bib/bbx121 · Cited by 234 · see citing works
Yıldırım, Z., Winters, D. K., & Johnson, M. G. (1999) · Journal of Applied Microbiology · doi:10.1046/j.1365-2672.1999.00629.x · Cited by 160 · see citing works
Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers
Duranti, S., Gaiani, F., Mancabelli, L., Milani, C., Grandi, A., Bolchi, A., Santoni, A., Lugli, G. A., Ferrario, C., Mangifesta, M., et al. (2016) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiw191 · Cited by 159 · see citing works
Bifidobacterium bifidum reduces apoptosis in the intestinal epithelium in necrotizing enterocolitis
Khailova, L. S., Patrick, S. K. M., Arganbright, K. M., Halpern, M. D., Kinouchi, T., & Dvořák, B. (2010) · American Journal of Physiology-Gastrointestinal and Liver Physiology · doi:10.1152/ajpgi.00131.2010 · Cited by 157 · see citing works
Bifidobacterium bifidum: A Key Member of the Early Human Gut Microbiota
Turroni, F., Duranti, S., Milani, C., Lugli, G. A., van Sinderen, D., & Ventura, M. (2019) · Microorganisms · doi:10.3390/microorganisms7110544 · Cited by 140 · see citing works
Bifidobacterium bifidum as an example of a specialized human gut commensal
Turroni, F., Duranti, S., Bottacini, F., Guglielmetti, S., van Sinderen, D., & Ventura, M. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00437 · Cited by 120 · see citing works
Duranti, S., Milani, C., Lugli, G. A., Mancabelli, L., Turroni, F., Ferrario, C., Mangifesta, M., Viappiani, A., Sánchez, B., Margollés, A., et al. (2016) · Scientific Reports · doi:10.1038/srep23971 · Cited by 116 · see citing works
Pei, Z., Sadiq, F. A., Han, X. J., Zhao, J., Zhang, H., Ross, R. P., Lu, W., & Chen, W. (2021) · mSystems · doi:10.1128/msystems.01211-20 · Cited by 108 · see citing works
Self-citationvan Heel, A. J., Kloosterman, T. G., Montalbán‐López, M., Deng, J., Plat, A., Baudu, B., Hendriks, D., Moll, G. N., & Kuipers, O. P. (2016) · ACS Synthetic Biology · doi:10.1021/acssynbio.6b00033 · Cited by 86 · see citing works
Insights from genomes of representatives of the human gut commensal B ifidobacterium bifidum
Duranti, S., Milani, C., Lugli, G. A., Turroni, F., Mancabelli, L., Sánchez, B., Ferrario, C., Viappiani, A., Mangifesta, M., Mancino, W., et al. (2014) · Environmental Microbiology · doi:10.1111/1462-2920.12743 · Cited by 83 · see citing works
Turroni, F., Milani, C., van Sinderen, D., & Ventura, M. (2011) · Gut Microbes · doi:10.4161/gmic.2.3.16105 · Cited by 77 · see citing works
Delétoile, A., Passet, V., Aires, J., Chambaud, I., Butel, M., Smokvina, T., & Brisse, S. (2010) · Research in Microbiology · doi:10.1016/j.resmic.2009.12.006 · Cited by 74 · see citing works
Wang, Q., Wang, K., Wu, W., Lv, L., Bian, X., Yang, L., Wang, Q., Li, Y., Ye, J., Fang, D., et al. (2020) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-020-10621-z · Cited by 74 · see citing works
Zanotti, I., Turroni, F., Piemontese, A., Mancabelli, L., Milani, C., Viappiani, A., Prevedini, G., Sánchez, B., Margollés, A., Elviri, L., et al. (2015) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-6564-7 · Cited by 72 · see citing works
Characterization and Exploitation of CRISPR Loci in Bifidobacterium longum
Hidalgo-Cantabrana, C., Crawley, A. B., Sánchez, B., & Barrangou, R. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01851 · Cited by 70 · see citing works
Schwenninger, S. M., Stierli, M. P., Teuber, M., et al. (2000) · Systematic and Applied Microbiology · doi:10.1016/s0723-2020(00)80002-8 · Cited by 53 · see citing works
Bottacini, F., Morrissey, R., Roberts, R. J., James, K., van Breen, J., Egan, M., Lambert, J. M., van Limpt, K., Knol, J., Motherway, M. O., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1289 · Cited by 48 · see citing works
Wang, F., Xu, T. C., Zhang, Y., Zheng, T., He, Y., He, F., & Jiang, Y. (2020) · FEMS Microbiology Letters · doi:10.1093/femsle/fnaa048 · Cited by 41 · see citing works
Complete Genome Sequence of Bifidobacterium bifidum S17
Zhurina, D. S., Zomer, A., Gleinser, M., Brancaccio, V. F., Auchter, M., Waidmann, M. S., Westermann, C., van Sinderen, D., & Riedel, C. U. (2010) · Journal of Bacteriology · doi:10.1128/jb.01180-10 · Cited by 36 · see citing works
Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum
Albert, K., Rani, A., & Sela, D. A. (2019) · Microorganisms · doi:10.3390/microorganisms8010007 · Cited by 30 · see citing works
Mode of action and structure–activity relationship studies of geobacillin I
Garg, N., Oman, T. J., Wang, T. A., et al. (2013) · The Journal of Antibiotics · doi:10.1038/ja.2013.112 · Cited by 29 · see citing works
Complete Genome Sequence of the Probiotic Bacterium Bifidobacterium bifidum Strain BGN4
Yu, D., Jeong, H., Lee, D. H., Kwon, S.-K., Song, J., Kim, B. K., Park, M.-S., Ji, G. E., Oh, T.-K., & Kim, J. F. (2012) · Journal of Bacteriology · doi:10.1128/jb.00988-12 · Cited by 19 · see citing works
Lugli, G. A., Mancino, W., Milani, C., Duranti, S., Mancabelli, L., Napoli, S., Mangifesta, M., Viappiani, A., Anzalone, R., Longhi, G., et al. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.02806-18 · Cited by 16 · see citing works
Yamamoto, K. (2012) · Bioscience Biotechnology and Biochemistry · doi:10.1271/bbb.120401 · Cited by 14 · see citing works
Yadav, M. K., Singh, B., & Tiwari, S. K. (2018) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-018-9445-4 · Cited by 13 · see citing works
Substrate tolerance of the biosynthetic enzymes of glycosylated lanthipeptide NAI-112
Sheng, W., Xu, B., Chen, S., et al. (2020) · Organic & Biomolecular Chemistry · doi:10.1039/d0ob01215g · Cited by 13 · see citing works
Strain-Specific Identification ofBifidobacterium bifidumOLB6378 by PCR
Toshimitsu, T., Nakamura, M., Ikegami, S., Terahara, M., & Itou, H. (2013) · Bioscience Biotechnology and Biochemistry · doi:10.1271/bbb.120803 · Cited by 9 · see citing works
Genome Sequence of the Immunomodulatory Strain Bifidobacterium bifidum LMG 13195
Gueimonde, M., Ventura, M., Margollés, A., et al. (2012) · Journal of Bacteriology · doi:10.1128/jb.01953-12 · Cited by 4 · see citing works
Andryuschenko, S. V., Ev, I., Nb, P., et al. (2018) · Microbiology Resource Announcements · doi:10.1128/mra.01271-18 · Cited by 1 · see citing works
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Self-citationLi, M., Yu, J., Li, W., Wu, Q., Sun, J., & Sun, Z. (2024) · Food Science and Human Wellness · doi:10.26599/fshw.2022.9250243 · Cited by 5 · 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
- Lu, W., Pei, Z., Zang, M., Lee, Y.-K., Zhao, J., Chen, W., Wang, H., & Zhang, H.
- Affiliations
- Jiangnan University (CN)
- National University of Singapore (SG)
- Corresponding author
- Wang, Hongchao
- Zhang, Hao
- Venue
- Genes
- Publisher
- MDPI AG
- Published
- 2021-09-25
- Volume
- 12
- Issue
- 10
- Pages
- 1504
- ISSN
- 2073-4425 (ISSN-L)
- PMC
- PMC8535415
- OpenAlex
- W3203125872
- Cited by
- 17
- References
- 50
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 2 · 2023: 4 · 2022: 2
- FWCI
- 1.20
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genes (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- National University of Singapore (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- Bifidobacterium bifidum, comparative genomics, pan-genome, core genome, genetic diversity, probiotics, gut microbiota, antibiotic resistance genes, CRISPR-Cas, phylogeny
- MeSH terms
- Bifidobacterium bifidum, Adult, Feces, Genes, Bacterial, Humans, Infant
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