Microbiome study of initial gut microbiota from newborn infants to children reveals that diet determines its compositional development
Open accessAbstract
The gastrointestinal tract (GIT) of newborn infants is rapidly colonized by members of a variety of bacterial genera after birth [1,2].It has been generally reported that the gut microbiota performs important functions for the human host, including protecting the infant's intestinal health by immune stimulation [3] and preventing infantile diarrhea [4].Previous studies have suggested that the phylum Actinobacteria including Bifidobacterium is generally dominant in breast milk-fed infants, whereas the phylum Proteobacteria including Escherichia coli is dominant in formula-fed infants [5,6], suggesting that human breast milk may influence the composition of gut microbiota in infants.However, little research into the formation and development of initial gut microbiota in infants has been conducted yet.In addition, the compositional conversion and progression from initial infantile gut microbiota to an adult-like one in children remain inadequately understood.Therefore, it is necessary to elucidate initial formation of gut microbiota in infants and the developmental mechanism of progression to one that is adult-like.To characterize the composition and change of gut microbiota, fecal samples were obtained from newborn Korean infants who underwent a natural delivery and children up to five years old with an approval number ) from the Kyung Hee University Institutional Review Board (IRB).The total fecal DNA of each sample was extracted and purified following a previous protocol [7].The 16S rRNA genes were PCR-amplified using a 926F/1505R primer set for GS-FLX+ pyrosequencing [7] or a 341F and 805R primer set for Illumina MiSeq sequencing (Illumina, USA) [8].The PCR products were sequenced using one of these next-generation sequencing methods.These 16S rRNA sequencing reads were analyzed using the SILVA 16S v128 database [9] for bacterial taxonomic assignments and the Microbial Genomics Module of the CLC Genomics Workbench software (Qiagen, Germany), following the default workflow and parameters for bacterial composition analysis.For compositional analysis of initial gut microbiota in newborn infants, meconium and fecal samples were collected from two breast milk-fed (BM1) and seven formula milk-fed (FM1) infants (Table 1).Most of the To understand the formation of initial gut microbiota, three initial fecal samples were collected from two groups of two breast milk-fed (BM1) and seven formula milk-fed (FM1) infants, and the compositional changes in gut microbiota were determined using metagenomics.Compositional change analysis during week one showed that Bifidobacterium increased from the first to the third fecal samples in the BM1 group (1.3% to 35.1%), while Klebsiella and Serratia were detected in the third fecal sample of the FM1 group (4.4% and 34.2%, respectively), suggesting the beneficial effect of breast milk intake.To further understand the compositional changes during progression from infancy to childhood (i.e., from three weeks to five years of age), additional fecal samples were collected from four groups of two breast milk-fed infants (BM2), one formula milk-fed toddler (FM2), three weaning food-fed toddlers (WF), and three solid food-fed children (SF).Subsequent compositional change analysis and principal coordinates analysis (PCoA) revealed that the composition of the gut microbiota changed from an infant-like composition to an adult-like one in conjunction with dietary changes.Interestingly, overall gut microbiota composition analyses during the period of progression from infancy to childhood suggested increasing complexity of gut microbiota as well as emergence of a new species of bacteria capable of digesting complex carbohydrates in WF and SF groups, substantiating that diet type is a key factor in determining the composition of gut microbiota.Consequently, this study may be useful as a guide to understanding the development of initial gut microbiota based on diet.
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Following birth, colonization of the infant gut is majorly determined by the early feeding mode, with distinguishable microbial compositions between breast- and formula-fed infants.
“Following birth, colonization of the infant gut is majorly determined by the early feeding mode, with distinguishable microbial compositions between breast-and formula-fed infants (254, 255).”
From Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health (2021) · cites this paper as [254]
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Cites
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055 · see citing works
Human gut microbiome viewed across age and geography
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., et al. (2012) · Nature · doi:10.1038/nature11053 · Cited by 7,815 · see citing works
Gut flora in health and disease
Guarner, F., & Malagelada, J. (2003) · The Lancet · doi:10.1016/s0140-6736(03)12489-0 · Cited by 3,395 · see citing works
Role of the normal gut microbiota
Jandhyala, S. M. (2015) · World Journal of Gastroenterology · doi:10.3748/wjg.v21.i29.8787 · Cited by 3,001 · see citing works
Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea
Herlemann, D. P. R., Labrenz, M., Jürgens, K., Bertilsson, S., Waniek, J. J., & Andersson, A. F. (2011) · The ISME Journal · doi:10.1038/ismej.2011.41 · Cited by 2,885 · see citing works
Succession of microbial consortia in the developing infant gut microbiome
Koenig, J. E., Spor, A., Scalfone, N., Fricker, A. D., Stombaugh, J., Knight, R., Angenent, L. T., & Ley, R. E. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000081107 · Cited by 2,540 · see citing works
Factors influencing the composition of the intestinal microbiota in early infancy
Penders, J., Thijs, C., Vink, C., Stelma, F. F., Snijders, B., Kummeling, I., van den Brandt, P. A., & Stobberingh, E. E. (2006) · PEDIATRICS · doi:10.1542/peds.2005-2824 · Cited by 2,232 · see citing works
Immune adaptations that maintain homeostasis with the intestinal microbiota
Hooper, L. V., & Macpherson, A. J. (2010) · Nature reviews. Immunology · doi:10.1038/nri2710 · Cited by 1,455 · see citing works
The microbiology of butyrate formation in the human colon
Pryde, S. E., Duncan, S. H., Hold, G. L., Stewart, C. S., & Flint, H. J. (2002) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2002.tb11467.x · Cited by 1,320 · see citing works
THE COLONIC EPITHELIUM IN ULCERATIVE COLITIS: AN ENERGY-DEFICIENCY DISEASE?
Roediger, W. E. W. (1980) · The Lancet · doi:10.1016/s0140-6736(80)91934-0 · Cited by 727 · see citing works
Yoshioka, H., Iseki, K.-I., & Fujita, K. (1983) · PEDIATRICS · doi:10.1542/peds.72.3.317 · Cited by 516 · see citing works
Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides
Sela, D. A., & Mills, D. A. (2010) · Trends in Microbiology · doi:10.1016/j.tim.2010.03.008 · Cited by 468 · see citing works
Human milk oligosaccharide consumption by intestinal microbiota
Marcobal, A. M., & Sonnenburg, J. L. (2012) · Clinical Microbiology and Infection · doi:10.1111/j.1469-0691.2012.03863.x · Cited by 311 · see citing works
The Intestinal Microflora During the First Weeks of Life
Bezirtzoglou, E. (1997) · Anaerobe · doi:10.1006/anae.1997.0102 · Cited by 145 · see citing works
Oligosaccharides in 4 Different Milk Groups, Bifidobacteria, and Ruminococcus obeum
Coppa, G. V., Gabrielli, O., Zampini, L., Galeazzi, T., Ficcadenti, A., Padella, L., Santoro, L., Soldi, S., Carlucci, A., Bertino, E., et al. (2011) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1097/mpg.0b013e3182073103 · Cited by 107 · see citing works
Fan, W., Huo, G., Li, X., Yang, L., & Duan, C. (2014) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.1309.09029 · Cited by 85 · see citing works
Ku, H.-J., & Lee, J.-H. (2014) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.1403.03032 · Cited by 21 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Diet and the Microbiota–Gut–Brain Axis: Sowing the Seeds of Good Mental Health
Berding, K., Vlckova, K., Marx, W., Schellekens, H., Stanton, C., Clarke, G., Jacka, F., Dinan, T. G., & Cryan, J. F. (2021) · Advances in Nutrition · doi:10.1093/advances/nmaa181 · Cited by 451 · see citing works
Ling, Z., Liu, X., Cheng, Y., Yan, X., & Wu, S. (2020) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2020.1867054 · Cited by 366 · see citing works
Microbial Colonization From the Fetus to Early Childhood—A Comprehensive Review
Senn, V., Bassler, D., Choudhury, R. A., Scholkmann, F., Righini‐Grunder, F., Vuille-dit-Bille, R. N., & Restin, T. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.573735 · Cited by 97 · see citing works
Interactions between dietary fibre and the gut microbiota
Thomson, C. L., García, A. L., & Edwards, C. A. (2021) · Proceedings of The Nutrition Society · doi:10.1017/s0029665121002834 · Cited by 73 · see citing works
Role of pattern recognition receptors and the microbiota in neurological disorders
Keogh, C. E., Rude, K. M., & Gareau, M. G. (2021) · The Journal of Physiology · doi:10.1113/jp279771 · Cited by 41 · see citing works
Golshany, H., Helmy, S. A., Morsy, N. F. S., Kamal, A., Yu, Q., & Fan, L. (2024) · International Journal of Food Sciences and Nutrition · doi:10.1080/09637486.2024.2437472 · Cited by 39 · see citing works
Zoghi, S., Heravi, F. S., Nikniaz, Z., Shirmohamadi, M., Moaddab, S. Y., & Leylabadlo, H. E. (2023) · Engineering in Life Sciences · doi:10.1002/elsc.202300070 · Cited by 28 · see citing works
Breast milk IgG engages the mouse neonatal immune system to instruct responses to gut antigens
Shenoy, M. K., Rico, D. M., Lorant, A. K., Touré, H., Gordon, S., Milburn, L. J., Schwensen, J. S., Cabán, M., & Koch, M. A. (2025) · Science · doi:10.1126/science.ado5294 · Cited by 24 · see citing works
Elgarten, C. W., Li, Y., Getz, K., Hemmer, M., Huang, Y.-S. V., Hall, M., Wang, T., Kitko, C. L., Jagasia, M., Nishihori, T., et al. (2020) · Transplantation and Cellular Therapy · doi:10.1016/j.jtct.2020.10.012 · Cited by 24 · see citing works
Infant gut microbiome reprogramming following introduction of solid foods (weaning)
Ding, M., Ross, R. P., Dempsey, E. M., Li, B., & Stanton, C. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2571428 · Cited by 22 · see citing works
Intestinal permeability, food antigens and the microbiome: a multifaceted perspective
Valitutti, F., Mennini, M., Monacelli, G., Fagiolari, G., Piccirillo, M., Nardo, G. D., & Cara, G. D. (2025) · Frontiers in Allergy · doi:10.3389/falgy.2024.1505834 · Cited by 22 · see citing works
A Triple Threat? The Role of Diet, Nutrition, and the Microbiota in T1D Pathogenesis
Hamilton‐Williams, E. E., Lorca, G. L., Norris, J. M., & Dunne, J. L. (2021) · Frontiers in Nutrition · doi:10.3389/fnut.2021.600756 · Cited by 20 · see citing works
Herrera‐Quintana, L., Vázquez‐Lorente, H., Hinojosa-Nogueira, D., & Plaza‐Díaz, J. (2024) · Children · doi:10.3390/children11081030 · Cited by 13 · see citing works
Complementary Feeding and Infant Gut Microbiota: A Narrative Review
Noles, D. L., Matzeller, K. L., Frank, D. N., Krebs, N. F., & Tang, M. (2025) · Nutrients · doi:10.3390/nu17050743 · Cited by 13 · see citing works
The Effects of Helicobacter pylori Infection on Gastric Microbiota in Children With Duodenal Ulcer
Zheng, W., Zhu, Z., Ying, J., Long, G., Chen, B., Peng, K., Li, F., Zhao, H., & Jiang, M. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.853184 · Cited by 13 · see citing works
Associations Between Gut Microbes and Social Behavior in Healthy 2-Year-Old Children
Delgadillo, D. R., Pressman, S. D., Christian, L. M., Galley, J. D., & Bailey, M. T. (2022) · Psychosomatic Medicine · doi:10.1097/psy.0000000000001103 · Cited by 12 · see citing works
Pandrea, I., Brooks, K., Desai, R. P., Tare, M., Brenchley, J. M., & Apetrei, C. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.899559 · Cited by 11 · see citing works
Rediscovering the nutrition of whole foods: the emerging role of gut microbiota
Song, X., Zhang, X., Ma, C., Hu, X., & Chen, F. (2022) · Current Opinion in Food Science · doi:10.1016/j.cofs.2022.100908 · Cited by 11 · see citing works
Structural characteristics of gut microbiota in longevity from Changshou town, Hubei, China
Ai, X., Liu, Y., Shi, J., Xie, X., Li, L., Duan, R., Lv, Y., Xiong, K., Miao, Y., & Zhang, Y. (2024) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-024-13140-3 · Cited by 8 · see citing works
Coeliac disease and microbiota: is it time for personalised biotics intervention? A scoping review
Valitutti, F., Cavalli, E., Leter, B., Leonard, M. M., Alessio, F., & Cucchiara, S. (2025) · BMJ Nutrition Prevention & Health · doi:10.1136/bmjnph-2024-001100 · Cited by 6 · see citing works
Does preeclampsia impact the gut microbiota of preterm offspring during early infancy?
Chen, Y., Yi, Z.-T., Yu, H., Wu, X., Wang, J., Nie, C., Li, H., Li, S., Yan, Q., He, T., et al. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-025-06120-2 · Cited by 5 · see citing works
Bar‐Yoseph, H., Krekhno, Z., Cirstea, M. S., Holani, R., Moon, K., Foster, L. J., Wieck, M. M., Piper, H. G., & Finlay, B. B. (2023) · Journal of Nutrition · doi:10.1016/j.tjnut.2023.12.020 · Cited by 3 · see citing works
How do we define normal bowel frequency from newborn to teens?: A Bayesian meta‐analysis
Munasinghe, S., Manathunga, S. S., Hathagoda, W., Kuruppu, C., Ranasinghe, P. D., Devanarayana, N. M., Baaleman, D. F., Benninga, M. A., & Rajindrajith, S. (2024) · Journal of Pediatric Gastroenterology and Nutrition · doi:10.1002/jpn3.12432 · Cited by 2 · see citing works
Yin, L., Zhao, J., Zhou, Z., Zhang, J., Qu, X., Shi, J., & Yin, F. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-025-07296-3 · Cited by 1 · see citing works
Breastmilk IgG engages the neonatal immune system to instruct host-microbiota mutualismPreprint
Shenoy, M. K., Rico, D. M., Gordon, S., Milburn, L. J., Schwensen, J. S., Cabán, M., & Koch, M. A. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.23.609293
Gut microbiota and the biosocial co-constitution of children's development: A scoping review
Iftikhar, S., Millei, Z., Ferreira, J. M., & Olsen, E. (2026) · Contemporary Issues in Early Childhood · doi:10.1177/14639491261484003
- Authors
- Ku, H.-J., Kim, Y.-T., & Lee, J.-H.
- Affiliations
- Kyung Hee University (KR)
- Corresponding author
- Lee, Ju-Hoon
- Venue
- Journal of Microbiology and Biotechnology
- Published
- 2020-07-28
- Volume
- 30
- Issue
- 7
- Pages
- 1067-1071
- ISSN
- 1017-7825 (ISSN-L)
- 1738-8872
- PMC
- PMC9728344
- OpenAlex
- W3016256720
- Cited by
- 26
- References
- 17
- Citations by year
- 2026: 1 · 2025: 7 · 2024: 5 · 2023: 2 · 2022: 4 · 2021: 3 · 2020: 4
- FWCI
- 1.05
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Journal of Microbiology and Biotechnology (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Ministry of Agriculture, Food and Rural Affairs
- 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
- gut microbiota development, breastfeeding, bottle feeding, infant nutrition, meconium, Bifidobacterium, Escherichia coli, actinobacteria, Proteobacteria, microbial community composition, fecal microbiota, Korean infants, 16S rRNA gene sequencing, pyrosequencing, metagenomics
- MeSH terms
- Gastrointestinal Microbiome, Breast Feeding, Child, Preschool, Diet, Feces, Female, Humans, Infant, Infant, Newborn, Klebsiella, Male, Milk, Human, Serratia
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