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Diversity of Bifidobacteria within the Infant Gut Microbiota
Open accessAbstract
BACKGROUND: The human gastrointestinal tract (GIT) represents one of the most densely populated microbial ecosystems studied to date. Although this microbial consortium has been recognized to have a crucial impact on human health, its precise composition is still subject to intense investigation. Among the GIT microbiota, bifidobacteria represent an important commensal group, being among the first microbial colonizers of the gut. However, the prevalence and diversity of members of the genus Bifidobacterium in the infant intestinal microbiota has not yet been fully characterized, while some inconsistencies exist in literature regarding the abundance of this genus. METHODS/PRINCIPAL FINDINGS: In the current report, we assessed the complexity of the infant intestinal bifidobacterial population by analysis of pyrosequencing data of PCR amplicons derived from two hypervariable regions of the 16 S rRNA gene. Eleven faecal samples were collected from healthy infants of different geographical origins (Italy, Spain or Ireland), feeding type (breast milk or formula) and mode of delivery (vaginal or caesarean delivery), while in four cases, faecal samples of corresponding mothers were also analyzed. CONCLUSIONS: In contrast to several previously published culture-independent studies, our analysis revealed a predominance of bifidobacteria in the infant gut as well as a profile of co-occurrence of bifidobacterial species in the infant's intestine.
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“PS infants showed an earlier and more robust colonisation of infant-associated Bifidobacterium species, particularly B. breve and B. longum subsp. infantis, compared to NPS infants51–53.”
From Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. (2025) · cites this paper as [52]
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“In fact, diet is, together with genetics and environmental factors, one of the main contributors to the diversity of human intestinal microbiota((37)).”
Gioia, D. D., Aloisio, I., Mazzola, G., & Biavati, B. (2013) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-013-5405-9 · Cited by 215
“Turroni et al. (2012) delineated that the low counts obtained by these investigations were most likely due to technical biases, in particular related to DNA extraction protocols and/or the PCR primers used.”
BackgroundTurroni, 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 210
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“…(Actinobacteria) appear between days 2 and 5 after birth and reach a maximum of up to 99% of all bacteria within one week becoming the predominant bacterial component of the infant fecal microbiota (Kurokawa et al., 2007; Mitsuoka and Kaneuchi, 1977; Turroni et al., 2012; Yatsunenko et al., 2012).”
BackgroundBifidobacteria and the infant gut: an example of co-evolution and natural selection
Turroni, F., Milani, C., Duranti, S., Ferrario, C., Lugli, G. A., Mancabelli, L., van Sinderen, D., & Ventura, M. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2672-0 · Cited by 214
Self-citationHost–microbe interactions that facilitate gut colonization by commensal bifidobacteria
Ventura, M., Turroni, F., Motherway, M. O., MacSharry, J. A., & van Sinderen, D. (2012) · Trends in Microbiology · doi:10.1016/j.tim.2012.07.002 · Cited by 197
Self-citationGut microbiome and breast-feeding: Implications for early immune development
Davis, E. C., Dunne-Castagna, V. P., Sela, D. A., Hilliard, M. A., Lindberg, S. K., Mantis, N. J., Seppo, A., & Järvinen, K. M. (2022) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2022.07.014 · Cited by 245
Gastrointestinal function development and microbiota
Mauro, A. D., Neu, J., Riezzo, G., Raimondi, F., Martinelli, D., Francavilla, R., & Indrio, F. (2013) · The Italian Journal of Pediatrics/Italian journal of pediatrics · doi:10.1186/1824-7288-39-15 · Cited by 204
Egan, 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 193
“breve strains have been identified in the adult human bifidobacterial population, although the relative abundance is lower than in infants [5,64].”
BackgroundInfluentialSelf-citationGarrido, D. A., Ruiz‐Moyano, S., Lemay, D. G., Sela, D. A., German, J. B., & Mills, D. A. (2015) · Scientific Reports · doi:10.1038/srep13517 · Cited by 189
Garrido, D. A., Ruiz‐Moyano, S., Kirmiz, N., Davis, J. C. C., Totten, S. M., Lemay, D. G., Ugalde, J. A., German, J. B., Lebrilla, C. B., & Mills, D. A. (2016) · Scientific Reports · doi:10.1038/srep35045 · Cited by 191
Priming for Life: Early Life Nutrition and the Microbiota-Gut-Brain Axis
Ratsika, A., Codagnone, M. G., O’Mahony, S. M., Stanton, C., & Cryan, J. F. (2021) · Nutrients · doi:10.3390/nu13020423 · Cited by 194
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“47 The genus Bifidobacterium has a fructose-6-phosphate phos-phoketolase pathway used for carbohydrate fermentation.”
BackgroundLaforest‐Lapointe, I., & Arrieta, M. (2017) · Frontiers in Immunology · doi:10.3389/fimmu.2017.00788 · Cited by 195
“Bifidobacterium species and subspecies are dominant members of the infant gut microbiome (56) and are strong modulators of the immune response (57).”
BackgroundThe Impact of the Milk Glycobiome on the Neonate Gut Microbiota
Pacheco, A. R., Barile, D., Underwood, M. A., & Mills, D. A. (2014) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-022114-111112 · Cited by 187
“It is well established now that bifidobacteria dominate the intestinal microbial population of infants (72, 74, 75), reaching∼75%of the gut microbial population (51).”
BackgroundBifidobacteria—Insight into clinical outcomes and mechanisms of its probiotic action
Sarkar, A., & Mandal, S. (2016) · Microbiological Research · doi:10.1016/j.micres.2016.07.001 · Cited by 190
“Bifidobacterial flora in neonatal gut is established within the first few days after delivery and constitutes upto almost 80% of the microfloral composition during infancy (Turroni et al. 2012).”
Diversity, ecology and intestinal function of bifidobacteria
Bottacini, F., Ventura, M., van Sinderen, D., & Motherway, M. O. (2014) · Microbial Cell Factories · doi:10.1186/1475-2859-13-s1-s4 · Cited by 184
“7%, respectively [105], while it was noted that these two Bifidobacterium species were apparently absent in a study that analysed the Bifidobacterium composition of the adult gut microbiota [106].”
BackgroundSelf-citationAbility of bifidobacteria to metabolize chitin-glucan and its impact on the gut microbiota
Alessandri, G., Milani, C., Duranti, S., Mancabelli, L., Ranjanoro, T., Modica, S., Carnevali, L., Statello, R., Bottacini, F., Turroni, F., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-42257-z · Cited by 183
Self-citationBojović, K., Ignjatović, Đ., Bajić, S. S., Milutinović, D. V., Tomić, M., Golić, N., & Tolinački, M. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00223 · Cited by 172
“It is important to emphasize that Bifidobacteria are among the first microbial colonizers of the gut immediately after birth (Turroni et al., 2012), a dominant bacterial genus in the infant gut microbiota (Harmsen et al.”
BackgroundDavis, E. C., Wang, M., & Donovan, S. M. (2017) · Gut Microbes · doi:10.1080/19490976.2016.1278104 · Cited by 169
Association between the gut microbiota and diet: Fetal life, early childhood, and further life
Kashtanova, D. A., Popenko, A., Ткачева, О. Н., Tyakht, A., Alexeev, D. G., & Boytsov, S. A. (2016) · Nutrition · doi:10.1016/j.nut.2015.12.037 · Cited by 176
The infant gut microbiome as a microbial organ influencing host well-being
Turroni, F., Milani, C., Duranti, S., Lugli, G. A., Bernasconi, S., Margollés, A., Pierro, F. D., van Sinderen, D., & Ventura, M. (2020) · The Italian Journal of Pediatrics/Italian journal of pediatrics · doi:10.1186/s13052-020-0781-0 · Cited by 176
“bifidum is among the first colonizers of the human gut, reaching high numbers in the infant gut, but also detected at very low levels in adults [11].”
BackgroundSelf-citationFeeding the microbiota: Transducer of nutrient signals for the host
Shanahan, F., van Sinderen, D., O’Toole, P. W., & Stanton, C. (2017) · Gut · doi:10.1136/gutjnl-2017-313872 · Cited by 157
Self-citationElucidating 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
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Correlation between lactoferrin and beneficial microbiota in breast milk and infant’s feces
Mastromarino, P., Capobianco, D., Campagna, G., Laforgia, N., Drimaco, P., Dileone, A., & Baldassarre, M. E. (2014) · BioMetals · doi:10.1007/s10534-014-9762-3 · Cited by 157
“1 %, respectively (Turroni et al. 2012).”
Yan, S., Yang, B. K., Zhao, J., Zhao, J., Stanton, C., Ross, R. P., Zhang, H., & Chen, W. (2019) · Food & Function · doi:10.1039/c9fo00014c · Cited by 157
Validating bifidobacterial species and subspecies identity in commercial probiotic products
Lewis, Z. T., Shani, G., Masarweh, C. F., Popovic, M., Frese, S. A., Sela, D. A., Underwood, M. A., & Mills, D. A. (2016) · Pediatric Research · doi:10.1038/pr.2015.244 · Cited by 154
“Bifidobacterium-containing products are often used in a NICU setting due to their status as generally recognized as safe (GRAS) microorganisms, their ubiquity in the gut of healthy breast-fed infants, and their observed health effects (17,18).”
BackgroundA Review of the Source and Function of Microbiota in Breast Milk
Stuebe, A. M., Seed, P. C., & LaTuga, M. S. (2014) · Seminars in Reproductive Medicine · doi:10.1055/s-0033-1361824 · Cited by 166
“14,20,21 In terms of viruses, human immunode fi ciency virus (HIV) in breast milk appears to be distinct based on phylogenetic classi fi cation from HIV found in the peripheral blood of infected mothers.”
BackgroundJames, K., Motherway, M. O., Bottacini, F., & van Sinderen, D. (2016) · Scientific Reports · doi:10.1038/srep38560 · Cited by 153
Metabolism 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 151
“breve strains are numerically prevalent in the gut microbiota of healthy, breast-fed infants (16), although the ability of members of this bifidobacterial species to utilize human milk and hostderived carbohydrates is relatively unexplored (see below).”
BackgroundSelf-citationBomhof, M. R., Saha, D. C., Reid, D. T., Paul, H. A., & Reimer, R. A. (2013) · Obesity · doi:10.1002/oby.20632 · Cited by 150
“infantis and other bifidobacteria are some of the first organisms to colonize the gut after childbirth and are recognized as an important commensal group of bacteria (32).”
BackgroundDevelopment of Gut Microbiota in the First 1000 Days after Birth and Potential Interventions
Pantazi, A. C., Bălașa, A. L., Mihai, C. M., Chisnoiu, T., Lupu, V. V., Kassim, M. A. K., Mihai, L., Frecuș, C. E., Chirila, S. I., Lupu, A., et al. (2023) · Nutrients · doi:10.3390/nu15163647 · Cited by 166
Human Milk Microbiota and Oligosaccharides: A Glimpse into Benefits, Diversity, and Correlations
Moubareck, C. A. (2021) · Nutrients · doi:10.3390/nu13041123 · Cited by 155
“It is essential here to note the distinction between gut microbiota of breastfed and formula-fed infants: It is well known today that Bifidobacterium is the predominant intestinal genus in both feeding modes [151], with species variations.”
BackgroundAlessandri, G., van Sinderen, D., & Ventura, M. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.03.006 · Cited by 152
“revealed the presence of putative novel members of the genus Bifidobacterium [36,41,67].”
BackgroundSelf-citationBifidobacterium 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
“infantis, are more typically found in the fecal samples from breast-fed infants [7].”
BackgroundSelf-citationThe Microbiota of the Human Mammary Ecosystem
Fernández, L., Pannaraj, P. S., Rautava, S., & Rodríguez, J. M. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.586667 · Cited by 149
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“The diversity of bifidobacteria population in 11 newborn fecal samples has recently been investigated using pyrosequencing (Turroni et al. 2012).”
Gut Microbiota as a Target for Preventive and Therapeutic Intervention against Food Allergy
Aitoro, R., Paparo, L., Amoroso, A., Costanzo, M. D., Cosenza, L., Granata, V., Scala, C. D., Nocerino, R., Trinchese, G., Montella, M. O., et al. (2017) · Nutrients · doi:10.3390/nu9070672 · Cited by 138
The Interaction of the Gut Microbiota with the Mucus Barrier in Health and Disease in Human
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“Among other bacterial species that have special relevance for the mucins is the anaerobe Bifidobacteria, which are abundant in early life, especially in breast fed infants [65,66].”
BackgroundRole of Bifidobacteria on Infant Health
Saturio, S., Nogacka, A. M., Alvarado-Jasso, G. M., Salazar, N., Reyes‐Gavilán, C. G. D. L., Gueimonde, M., & Arboleya, S. (2021) · Microorganisms · doi:10.3390/microorganisms9122415 · Cited by 148
“bifidum, are the most commonly found, although the Bifidobacterium species composition will be affected by different perinatal factors [32,40].”
BackgroundSelf-citationPaediatric oral biopharmaceutics: Key considerations and current challenges
Batchelor, H. K., Fotaki, N., & Klein, S. (2013) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2013.10.006 · Cited by 141
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Comparative genomics of the Bifidobacterium brevetaxon
Bottacini, F., Motherway, M. O., Kuczynski, J., O’Connell, K. J., Serafini, F., Duranti, S., Milani, C., Turroni, F., Lugli, G. A., Zomer, A., et al. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-170 · Cited by 130
“longum occurs immediately after birth, with a correlation being observed between strains present in mother and progeny, thus suggesting that such bifidobacteria are transmitted from mother to child during vaginal delivery and/or breast feeding [5,6].”
BackgroundSelf-citationExploring the role of the microbiota member Bifidobacterium in modulating immune-linked diseases
O’Neill, I. J., Schofield, Z., & Hall, L. J. (2017) · Emerging Topics in Life Sciences · doi:10.1042/etls20170058 · Cited by 131
Cionci, N. B., Baffoni, L., Gaggìa, F., & Gioia, D. D. (2018) · Nutrients · doi:10.3390/nu10111723 · Cited by 138
“Among the different species belonging to the Bifidobacterium genus, Bifidobacterium breve, is the dominant one in breast-fed newborns [53] and one of the most used in infants.”
Background
Metadata
- Authors
- Turroni, F., Peano, C., Pass, D. A., Foroni, E., Severgnini, M., Claesson, M. J., Kerr, C., Hourihane, J., Murray, D., Fuligni, F., Gueimonde, M., Margolles, A., De Bellis, G., O’Toole, P. W., van Sinderen, D., Marchesi, J. R., & Ventura, M.
- Affiliations
- University of Parma (IT)
- National Research Council (IT)
- Cardiff University (GB)
- University College Cork (IE)
- Consejo Superior de Investigaciones Científicas (ES)
- Corresponding author
- Ventura, Marco
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-05-11
- Volume
- 7
- Issue
- 5
- Pages
- e36957
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3350489
- OpenAlex
- W2048550695
- Cited by
- 647
- References
- 54
- Citations by year
- 2026: 17 · 2025: 32 · 2024: 45 · 2023: 36 · 2022: 49 · 2021: 57 · 2020: 71 · 2019: 29 · 2018: 46 · 2017: 56 · 2016: 52 · 2015: 50 · 2014: 48 · 2013: 41 · 2012: 17
- FWCI
- 20.04
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Royal Society
- Irish Research Council for Science, Engineering and Technology
- Science Foundation Ireland (02/CE/B124, 07/CE/B1368)
- Ministero dell’Istruzione, dell’Università e della Ricerca
- Natural Environment Research Council (NBAF010005)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- Bifidobacterium, infant gut microbiota, bacterial diversity, 16S rRNA gene, fecal microbiota, breastfeeding, bottle feeding, mode of delivery, vaginal delivery, cesarean section, maternal microbiota, species co-occurrence, gut commensal bacteria
- MeSH terms
- Base Sequence, Bifidobacterium, Feces, Female, Genes, Bacterial, Humans, Infant, Phylogeny, Pregnancy, RNA, Bacterial, RNA, Ribosomal, 16S, Genetic Variation, DNA Primers, Gastrointestinal Tract, Metagenome
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