Bifidobacterium bifidum and the infant gut microbiota: an intriguing case of microbe‐host co‐evolution
Abstract
Summary: Bifidobacterium bifidum is reported to be among the first colonizers of the newborn's gastrointestinal tract due to its ability to metabolize human milk oligosaccharides (HMOs). In order to investigate biological features that allow this bifidobacterial species to colonize a newborn, bifidobacterial internally transcribed spacer profiling of stool samples of 50 mother‐infant dyads, as well as corresponding breastmilk samples, was performed. Hierarchical clustering based on bifidobacterial population profiles found in infant faecal samples revealed the presence of four bifidobacterial clusters or the so‐called bifidotypes. Bifidobacterium bifidum was shown to be a key member among bifidotypes, in which its presence correlate with several different bifidobacterial species retrieved in infant faecal samples. For this reason, we investigated cross‐feeding behaviour facilitated by B. bifidum on a bioreactor model using human milk as growth substrate. Transcriptional profiles of this strain were evaluated when grown on nine specific glycans typically constituting HMOs. Remarkably, these analyses suggest extensive co‐evolution with the host and other bifidobacterial species in terms of resource provision and sharing, respectively, activities that appear to support a bifidobacteria‐dominant microbiome.
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B. bifidum is a relevant member of the human gut microbiota from early life, where it plays a pivotal role in maintaining host homeostasis by modulating immune responses, inhibiting pathogenic organisms, and supporting the structural integrity of the intestinal barrier.
“This species is a relevant member of the human gut microbiota from early life, where it plays a pivotal role in maintaining host homeostasis by modulating immune responses, inhibiting pathogenic organisms, and supporting the structural integrity of the intestinal barrier [2-5] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [2]
Cites
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696 · see citing works
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063 · see citing works
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works
Jacomy, M., Venturini, T., Heymann, S., & Bastian, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0098679 · Cited by 2,909 · see citing works
A framework for human microbiome research
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11209 · Cited by 2,650 · see citing works
Milani, C., Duranti, S., Bottacini, F., Casey, E., Turroni, F., Mahony, J., Belzer, C., Delgado Palacio, S., Arboleya Montes, S., Mancabelli, L., et al. (2017) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00036-17 · Cited by 1,950 · see citing works
Self-citationBifidobacteria and Their Role as Members of the Human Gut Microbiota
O’Callaghan, A. A., & van Sinderen, D. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00925 · Cited by 1,108 · see citing works
Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens
Ng, K. M., Ferreyra, J. A., Higginbottom, S. K., Lynch, J. B., Kashyap, P. C., Gopinath, S., Naidu, N., Choudhury, B., Weimer, B. C., Monack, D. M., et al. (2013) · Nature · doi:10.1038/nature12503 · Cited by 1,035 · see citing works
Carbohydrate metabolism in Bifidobacteria
Pokusaeva, K., Fitzgerald, G. F., & van Sinderen, D. (2011) · Genes & Nutrition · doi:10.1007/s12263-010-0206-6 · Cited by 855 · see citing works
Development of intestinal microbiota in infants and its impact on health
Matamoros, S., Guen, C. G., Vacon, F. L., Potel, G., & de la Cochetière, M.-F. (2013) · Trends in Microbiology · doi:10.1016/j.tim.2012.12.001 · Cited by 533 · see citing works
Moossavi, S., Sepehri, S., Robertson, B., Bode, L., Goruk, S. D., Field, C. J., Lix, L. M., de Souza, R. J., Becker, A. B., Mandhane, P. J., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.01.011 · Cited by 513 · see citing works
Physiology of Consumption of Human Milk Oligosaccharides by Infant Gut-associated Bifidobacteria
Asakuma, S., Hatakeyama, E., Urashima, T., Yoshida, E., Katayama, T., Yamamoto, K., Kumagai, H., Ashida, H., Hirose, J., & Kitaoka, M. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.248138 · Cited by 442 · see citing works
Microbial nutrient niches in the gut
Pereira, F. C., & Berry, D. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13659 · Cited by 365 · 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
Self-citationBifidobacteria and Their Molecular Communication with the Immune System
Ruíz, L., Delgado, S., Ruas‐Madiedo, P., Sánchez, B., & Margollés, A. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.02345 · Cited by 329 · see citing works
Duranti, S., Lugli, G. A., Mancabelli, L., Armanini, F., Turroni, F., James, K., Ferretti, P., Gorfer, V., Ferrario, C., Milani, C., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0282-6 · Cited by 327 · see citing works
Self-citationBifidobacterium and Lactobacillus DNA in the human placenta
Satokari, R. M., Grönroos, T., Laitinen, K., Salminen, S., & Isolauri, E. (2008) · Letters in Applied Microbiology · doi:10.1111/j.1472-765x.2008.02475.x · Cited by 304 · see citing works
Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut
Milani, C., Lugli, G. A., Duranti, S., Turroni, F., Mancabelli, L., Ferrario, C., Mangifesta, M., Hevia, A., Viappiani, A., Scholz, M., et al. (2015) · Scientific Reports · doi:10.1038/srep15782 · Cited by 284 · see citing works
Self-citationGlycan Utilization and Cross-Feeding Activities by Bifidobacteria
Turroni, F., Milani, C., Duranti, S., Mahony, J., van Sinderen, D., & Ventura, M. (2018) · Trends in Microbiology · doi:10.1016/j.tim.2017.10.001 · Cited by 263 · see citing works
Self-citationExploring Vertical Transmission of Bifidobacteria from Mother to Child
Milani, C., Mancabelli, L., Lugli, G. A., Duranti, S., Turroni, F., Ferrario, C., Mangifesta, M., Viappiani, A., Ferretti, P., Gorfer, V., et al. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.02037-15 · Cited by 259 · see citing works
Self-citationTurroni, F., Serafini, F., Foroni, E., Duranti, S., Motherway, M. O., Taverniti, V., Mangifesta, M., Milani, C., Viappiani, A., Roversi, T., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1303897110 · Cited by 246 · see citing works
Self-citationGerman, J. B., Freeman, S. L., Lebrilla, C. B., & Mills, D. A. (2008) · Nestlé Nutrition Workshop series. Pediatric program/Nestlé Nutrition Workshop series. Paediatric program · doi:10.1159/000146322 · Cited by 238 · see citing works
Mucin Degradation by Bifidobacterium Strains Isolated from the Human Intestinal Microbiota
Ruas‐Madiedo, P., Gueimonde, M., Fernández-García, M., Reyes‐Gavilán, C. G. D. L., & Margollés, A. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.02509-07 · Cited by 222 · see citing works
Vatanen, T., Plichta, D. R., Somani, J., Münch, P. C., Arthur, T. D., Hall, A. B., Rudolf, S., Oakeley, E. J., Ke, X., Young, R. A., et al. (2018) · Nature Microbiology · doi:10.1038/s41564-018-0321-5 · Cited by 216 · see citing works
Turroni, F., Milani, C., Duranti, S., Mancabelli, L., Mangifesta, M., Viappiani, A., Lugli, G. A., Ferrario, C., Gioiosa, L., Ferrarini, A., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2015.236 · Cited by 207 · see citing works
Self-citationEgan, M., Motherway, M. O., Kilcoyne, M., Kane, M., Joshi, L., Ventura, M., & van Sinderen, D. (2014) · BMC Microbiology · doi:10.1186/s12866-014-0282-7 · Cited by 192 · see citing works
Self-citationMetabolism of Sialic Acid by Bifidobacterium breve UCC2003
Egan, M., Motherway, M. O., Ventura, M., & van Sinderen, D. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.01114-14 · Cited by 148 · see citing works
Self-citationOmics of bifidobacteria: research and insights into their health-promoting activities
Bottacini, F., van Sinderen, D., & Ventura, M. (2017) · Biochemical Journal · doi:10.1042/bcj20160756 · Cited by 126 · see citing works
Self-citationBifidobacterium 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
Self-citationUnveiling bifidobacterial biogeography across the mammalian branch of the tree of life
Milani, C., Mangifesta, M., Mancabelli, L., Lugli, G. A., James, K., Duranti, S., Turroni, F., Ferrario, C., Ossiprandi, M. C., van Sinderen, D., et al. (2017) · The ISME Journal · doi:10.1038/ismej.2017.138 · Cited by 119 · see citing works
Self-citationBifidobacterial Enzymes Involved in the Metabolism of Human Milk Oligosaccharides
Kitaoka, M. (2012) · Advances in Nutrition · doi:10.3945/an.111.001420 · Cited by 118 · see citing works
Inferring Metabolic Mechanisms of Interaction within a Defined Gut Microbiota
Medlock, G. L., Carey, M. A., McDuffie, D. G., Mundy, M. B., Giallourou, N., Swann, J. R., Kolling, G. L., & Papin, J. A. (2018) · Cell Systems · doi:10.1016/j.cels.2018.08.003 · Cited by 117 · see citing works
Glycan cross-feeding activities between bifidobacteria under in vitro conditions
Turroni, F., Özcan, E., Milani, C., Mancabelli, L., Viappiani, A., van Sinderen, D., Sela, D. A., & Ventura, M. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.01030 · Cited by 98 · see citing works
Self-citationMilani, C., Lugli, G. A., Turroni, F., Mancabelli, L., Duranti, S., Viappiani, A., Mangifesta, M., Segata, N., van Sinderen, D., & Ventura, M. (2014) · FEMS Microbiology Ecology · doi:10.1111/1574-6941.12410 · Cited by 88 · see citing works
Self-citationInsights 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
Self-citationAnalysis of Predicted Carbohydrate Transport Systems Encoded by Bifidobacterium bifidum PRL2010
Turroni, F., Strati, F., Foroni, E., Serafini, F., Duranti, S., van Sinderen, D., & Ventura, M. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.00629-12 · Cited by 81 · see citing works
Self-citationTurroni, F., Milani, C., van Sinderen, D., & Ventura, M. (2011) · Gut Microbes · doi:10.4161/gmic.2.3.16105 · Cited by 77 · see citing works
Self-citationSerafini, F., Strati, F., Ruas‐Madiedo, P., Turroni, F., Foroni, E., Duranti, S., Milano, F., Perotti, A., Viappiani, A., Guglielmetti, S., et al. (2013) · Anaerobe · doi:10.1016/j.anaerobe.2013.03.003 · Cited by 76 · see citing works
Self-citationNishiyama, K., Aki, N., Uribayashi, K., Yamamoto, Y., Mukai, T., & Okada, N. (2018) · Anaerobe · doi:10.1016/j.anaerobe.2018.05.007 · Cited by 75 · see citing works
Study of the adhesion of bifidobacterium bifidum MIMBb75 to human intestinal cell lines
Guglielmetti, S., Tamagnini, I., Minuzzo, M., Arioli, S., Parini, C., Comelli, E., & Mora, D. (2009) · Current Microbiology · doi:10.1007/s00284-009-9415-x · Cited by 56 · see citing works
Proteinaceous Molecules Mediating Bifidobacterium-Host Interactions
Ruíz, L., Delgado, S., Ruas‐Madiedo, P., Margollés, A., & Sánchez, B. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01193 · Cited by 53 · see citing works
Lugli, G. A., Mangifesta, M., Duranti, S., Anzalone, R., Milani, C., Mancabelli, L., Alessandri, G., Turroni, F., Ossiprandi, M. C., van Sinderen, D., et al. (2018) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2018.01.002 · Cited by 36 · see citing works
Self-citationDuranti, S., Lugli, G. A., Napoli, S., Anzalone, R., Milani, C., Mancabelli, L., Alessandri, G., Turroni, F., Ossiprandi, M. C., van Sinderen, D., et al. (2019) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.003306 · Cited by 34 · see citing works
Self-citationBifidobacterium vansinderenii sp. nov., isolated from faeces of emperor tamarin (Saguinus imperator)
Duranti, S., Mangifesta, M., Lugli, G. A., Turroni, F., Anzalone, R., Milani, C., Mancabelli, L., Ossiprandi, M. C., & Ventura, M. (2017) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.002243 · Cited by 29 · see citing works
Self-citationGuglielmetti, S., Balzaretti, S., Taverniti, V., Miriani, M., Milani, C., Scarafoni, A., Corona, S., Ciranna, A., Arioli, S., Santala, V. P., et al. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.01413-14 · Cited by 17 · see citing works
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- Authors
- Duranti, S., Lugli, G. A., Milani, C., James, K., Mancabelli, L., Turroni, F., Alessandri, G., Mangifesta, M., Mancino, W., Ossiprandi, M. C., Iori, A., Rota, C., Gargano, G., Bernasconi, S., Di Pierro, F., van Sinderen, D., & Ventura, M.
- Affiliations
- University of Parma (IT)
- National University of Ireland (IE)
- GenProbio srl Parma Italy
- Santa Maria Nuova Hospital (IT)
- Research Department Velleja Research Milan Italy
- APC Microbiome Institute and School of Microbiology, Bioscience Institute National University of Ireland Cork Ireland
- Corresponding author
- Ventura, Marco
- ORCID
- Venue
- Environmental Microbiology
- Publisher
- Wiley
- Published
- 2019-06-20
- Volume
- 21
- Issue
- 10
- Pages
- 3683-3695
- ISSN
- 1462-2912 (ISSN-L)
- 1462-2920
- OpenAlex
- W2949547122
- Cited by
- 72
- References
- 46
- Citations by year
- 2026: 3 · 2025: 7 · 2024: 15 · 2023: 5 · 2022: 7 · 2021: 13 · 2020: 17 · 2019: 5
- FWCI
- 7.99
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Environmental Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Fondazione Cariparma (TeachInParma Project)
- MIUR (N/A)
- Science Foundation Ireland (15/JP‐HDHL/3280)
- Topics
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- 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
- Keywords
- Bifidobacterium bifidum, infant gut microbiota, human milk oligosaccharides, cross-feeding, mother-infant dyads, host-microbe coevolution, gene expression profiling, bioreactor model, glycans, breast milk
- MeSH terms
- Gastrointestinal Microbiome, Bifidobacterium bifidum, Biological Coevolution, Adolescent, Adult, Feces, Female, Humans, Infant, Newborn, Milk, Human, Oligosaccharides, Polysaccharides, Bioreactors, Young Adult
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