A Baby’s Gut Microbiome Scientifically Explained

Sophia Williams
6 min readNov 11, 2020


The Microbiome: What Is It?

The microbiome refers to the specific community of microscopic organisms living within a particular environment of a larger host organism, such as in humans ( 1). In humans, there are around 10 to 100 trillion microorganisms present, primarily located in the gut, generally known as the “gut microflora” ( 2). Although generally initially thought of as harmful, the microbiome is in fact incredibly important for various processes in the body.

From producing important vitamins, to regulating the immune system and helping in the digestion of food, to protecting against other, harmful, bacteria, they are essential in maintaining human health (3,4). In fact, its’ complex nature, the fact that it can be inherited from a parent, and the functioning of the microbiome in a manner similar to organs have led to the theory that the microbiome itself is another human organ ( 5).

In general, increased diversity in the microbe species in the human gut has been linked to protective function ( 6) and lower diversity has been linked to various disorders including obesity, psoriatic arthritis, type 1 and 2 diabetes and coeliac disease. ( 7,8,9,10,11)

The Infant Microbiome Begins to Develop as Early as in the Womb

The microbiome in an infant develops from the womb itself, with it’s first exposure to microbes in the amniotic fluid of the mother (12). The microbiome of an infant is less diverse at birth, and develops the most during the first three years of its’ life.

This diversity can be determined by various factors, including maternal stress, feeding patterns, exposure to antibiotics and even mode of delivery. The effect of the latter can be seen in the difference between infants born vaginally, and those born by C-section.

Infants born vaginally have a gut microbiome similar to that of the mother ( 13) with bacteria known as Lactobacillus and Prevotella dominant after birth, and larger distribution of bacteria like Bifidobacterium and Bacteroides developing after a few months. But the infants born by C-section have a different microbiota, with species such as Clostridium and Staphylococcus which can lead to important health differences. This is due to the fact that Bifidobacterium and Lactobacillus, found more in the vaginal babies, are considered to be more protective microbes ( 14), while certain species of Clostridium and Staphylococcus could evolve to become pathogenic ( 15).

It has also been shown that even short-term exposure to antibiotics, usually given during C-sections or to the mother during pregnancy, have also been shown to cause changes in the gut microflora (16,17.)

The First Year of Infancy

Most of the changes in the gut microflora occur during the first year of the development of an infant, where, though there are differences between individual babies, the diet of the newborn plays an essential role in the development of its’ microflora ( 18,19).

Research has found that most breast-fed infants show a gut microbiome dominated by a species known as Bifidobacterium, which have been shown to need Human oligosaccharides (HMOs) to pass into the infant digestive tract (20,21). HMOs are carbohydrates found only in human breast milk. In addition, there are also other beneficial bacteria present in the guts of breast-fed infants, including Lactobacillus, Bacteroides, Streptococcus, etc. (22) Formula-fed infants have been shown to have more diverse species of certain bacteria, and infants exclusively formula-fed are often colonized with more C. difficile, E. coli, B. fragilis, and Lactobacilli than those that are only breastfed ( 23).

Although earlier studies used to show a reduced presence of the Bifidobacterium in formula-fed infants, recent technological changes have shown their presence in both formula and breastfed infants ( 24). When weaning to solid foods from breast milk or from a formula-based diet, the microbiome shows a change towards a more stable form, like that of an adult ( 19):

Essentially, the first three years of the life of a baby are extremely important in shaping its’ gut microbiome and its health, the effects of which could last throughout its life (25).

  1. Berg, G., Rybakova, D., Fischer, D. et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome 8, 103 (2020). https://doi.org/10.1186/s40168-020-00875-0
  2. Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007 Oct 18;449(7164):804–10. doi: 10.1038/nature06244. PMID: 17943116; PMCID: PMC3709439.
  3. Klassen, J.L. Defining microbiome function. Nat Microbiol 3, 864–869 (2018). https://doi.org/10.1038/s41564-018-0189-4
  4. Valdes Ana M, Walter Jens, Segal Eran, Spector Tim D. Role of the gut microbiota in nutrition and health BMJ 2018; 361 :k2179
  5. Baquero F, Nombela C. The microbiome as a human organ. Clin Microbiol Infect. 2012 Jul;18 Suppl 4:2–4. doi: 10.1111/j.1469–0691.2012.03916.x. PMID: 22647038
  6. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Wang J. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65.
  7. Scher JU, Ubeda C, Artacho A, et alDecreased bacterial diversity characterizes the altered gut microbiota in patients with psoriatic arthritis, resembling dysbiosis in inflammatory bowel disease. Arthritis Rheumatol2015;67:128–39. doi:10.1002/art.38892 pmid:25319745
  8. de Goffau MC, Luopajärvi K, Knip M, et al. Fecal microbiota composition differs between children with β-cell autoimmunity and those without. Diabetes2013;62:1238–44. doi:10.2337/db12–0526 pmid:23274889
  9. Schippa S, Iebba V, Barbato M, et al. A distinctive ‘microbial signature’ in celiac pediatric patients. BMC Microbiol2010;10:175. doi:10.1186/1471–2180–10–175 pmid:20565734
  10. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature. 2009 Jan 22;457(7228):480–4. doi: 10.1038/nature07540. Epub 2008 Nov 30. PMID: 19043404; PMCID: PMC2677729.
  11. Lambeth SM, Carson T, Lowe J, Ramaraj T, Leff JW, Luo L, Bell CJ, Shah VO. Composition, Diversity and Abundance of Gut Microbiome in Prediabetes and Type 2 Diabetes. J Diabetes Obes. 2015 Dec 26;2(3):1–7. doi: 10.15436/2376–0949.15.031. PMID: 26756039; PMCID: PMC4705851
  12. Stinson LF, Boyce MC, Payne MS and Keelan JA (2019) The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth. Front. Microbiol. 10:1124. doi: 10.3389/fmicb.2019.01124
  13. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010 Jun 29;107(26):11971–5. doi: 10.1073/pnas.1002601107. Epub 2010 Jun 21
  14. Rastall RA. Bacteria in the gut: friends and foes and how to alter the balance. J Nutr. 2004 Aug;134(8 Suppl):2022S-2026S. doi: 10.1093/jn/134.8.2022S. PMID: 15284393.
  15. Adlerberth I, Wold AE. Establishment of the gut microbiota in Western infants. Acta Paediatr. 2009 Feb;98(2):229–38. doi: 10.1111/j.1651–2227.2008.01060.x. PMID: 19143664.
  16. Jakobsson HE, Jernberg C, Andersson AF, Sjölund-Karlsson M, Jansson JK, Engstrand L. Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome. PLoS One. 2010 Mar 24;5(3):e9836. doi: 10.1371/journal.pone.0009836. PMID: 20352091; PMCID: PMC2844414.
  17. Cho CE, Norman M. Cesarean section and development of the immune system in the offspring. Am J Obstet Gynecol. 2013 Apr;208(4):249–54. doi: 10.1016/j.ajog.2012.08.009. Epub 2012 Aug 10. PMID: 22939691.
  18. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007 Jul;5(7):e177. doi: 10.1371/journal.pbio.0050177. Epub 2007 Jun 26. PMID: 17594176; PMCID: PMC1896187.
  19. Stark PL, Lee A. The microbial ecology of the large bowel of breast-fed and formula-fed infants during the first year of life. J Med Microbiol. 1982 May;15(2):189–203. doi: 10.1099/00222615–15–2–189. PMID: 7143428.
  20. Bezirtzoglou E, Tsiotsias A, Welling GW. Microbiota profile in feces of breast-and formula-fed newborns by using fluorescence in situ hybridization (FISH) Anaerobe. 2011;17:478–482.
  21. Marcobal A, Sonnenburg JL. Human milk oligosaccharide consumption by intestinal microbiota. Clinical Microbiology and Infection. 2012;18:12–15.
  22. Harmsen HJM, Wildeboer-Veloo ACM, Raangs GC, Wagendorp AA, Klijn N, Bindels JG, Welling GW. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. Journal of Pediatric Gastroenterology and Nutrition. 2000;30:61–67.
  23. Penders J, Thijs C, Vink C, Stelma FF, Snijders B, Kummeling I, van den Brandt PA, Stobberingh EE. Factors influencing the composition of the intestinal microbiota in early infancy. Pediatrics. 2006 Aug;118(2):511–21. doi: 10.1542/peds.2005–2824. PMID: 16882802.
  24. Yang, I., Corwin, E. J., Brennan, P. A., Jordan, S., Murphy, J. R., & Dunlop, A. (2016). The Infant Microbiome: Implications for Infant Health and Neurocognitive Development. Nursing research, 65(1), 76–88. https://doi.org/10.1097/NNR.0000000000000133
  25. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Ley RE. Succession of microbial consortia in the developing infant gut microbiome. Proceedings of the National Academy of Sciences. 2011;108:4578–4585.

Originally published at https://organicsbestshop.com.