- Ideally, baby gut maturation is low in the early days and steadily increases until it reaches adult-like maturity around 3-5 years of age.
- Breastfeeding exclusivity and duration sets the pace of baby gut development.
- Formula-feeding and early introduction of solids may accelerate baby gut maturation.
- Early microbiome maturation may be linked with increased BMI, eczema, and asthma.
Baby Gut Microbiome Development: Preparing Yourself
Summary
In the same way that your baby hits motor milestones with turning over, sitting, and walking - the baby gut microbiome goes through its own stages of development. While there’s a rough trajectory that we like to see with gut microbiome development, what takes shape is something that’s unique to each baby.
Factors like breastmilk, formula, how your baby is born, and medication can have a big impact.
What is seeding?
Starting from birth, your baby’s gut picks up, selects for, and feeds a collection of microbes. This is known as seeding and selection.
The microbes your baby picks up change over time [1]. During the first years of life, these changes follow a defined pattern known as gut microbiome maturation [2]. Typically, the gut microbiome reaches full, adult-like maturity by the time your child is 3-5 years old [2], [3].
But first, what is seeding? And how does selection take place?
We can define seeding as the event when microbes colonize the baby’s entire body, from their skin and mouth to their digestive tract. A wide variety of microbes have the ability to seed your baby’s gut [4].
These microbes mostly come from you - during birth and breastfeeding - and the environment [5], [6].
Selection happens when factors like the temperature, oxygen availability, and pH of the gut allow some microbes to thrive while others pass through or die off. Certain types of bacteria will take up residence in the gut when conditions are right. After conditions change, they will fade out while other types of bacteria grow.
Tip: Make sure your baby’s gut doesn’t mature too quickly
As you might imagine, the gut microbiome plays a big role in gut development.
The first year or so of life is when your baby’s gut develops into a digestive and immune system organ [7], [8]. It’s when the gut learns to deal with whatever enters it: helpful nutrients, particles from the environment, friendly and unfriendly microbes.
Ideally, the timing between gut development and microbiome maturity lines up. But without a well-composed cast of microbes in place at the right times, baby gut development could go off course [9].
Emerging evidence suggests that overly-rapid or out-of-sync maturation may increase future risk of developing:
- Increased body mass index (BMI) or obesity [9]–[11]
- Infections [12]
- Type 1 diabetes [13], [14]
- Asthma [15]
- Atopic dermatitis, or eczema [16]
The key to protecting and nurturing your baby’s microbiome is to keep it from maturing too quickly [3].
How breastfeeding sets the pace of baby gut development
After birth, breastmilk can be the next source of protective microbes seeding your baby’s gut [17], [18]. With many compounds that nourish friendly bacteria, it’s also a means of selection.
Certain friendly bacteria called Bifidobacterium are key players in your baby’s gut development. This is because they:
- Fend off unfriendly bacteria [12], [19], [20]
- Help your baby’s immune and metabolic systems develop [19], [21]–[23]
- Provide nutrients that your baby needs [24]
An important source of Bifidobacterium is a baby’s birthing mother [25], [26]. If the mom’s gut has Bifidobacterium, they can transfer to her baby during delivery [27].
If breastfeeding, then breastmilk becomes a major source of Bifidobacterium.
Once Bifidobacterium are established, an ongoing supply of breastmilk sustains them. They thrive on human milk oligosaccharides (HMOs), which are the sugars found in breastmilk.
Feeding on HMOs gives beneficial Bifidobacterium a competitive edge over other microbes. When these Bifidobacterium flourish, they produce enough acid to make your baby’s gut inhospitable to unfriendly bacteria [12], [20].
In breastfed babies, Bifidobacterium outcompete other microbes and assume a dominant role [2], [13], [28]. Because of this, the overall diversity - or variety of bacteria in the gut - is low, which is ideal for young babies.
As long as your baby is breastfed, there’s a good chance that Bifidobacterium will remain high during their first 6 months [13]. This is important because low levels of Bifidobacterium in babies are linked to chronic diseases, including autoimmunity, asthma, and obesity [29]–[31].
It’s important to note that not all moms have Bifidobacterium. Microbiome testing before birth helps to make sure that a mom has these bacteria to pass along to her baby. If no Bifidobacterium are found, this might be an ideal time to supplement with probiotics.
How formula feeding sets the pace of baby gut development
The gut microbiome of formula-fed babies is different from that of breastfed babies [32]. On average, this may include :
- Different types of bacteria [13]
- Lower levels of Bifidobacterium [13]
- Greater diversity [2], [13], [32]
- A more mature microbiome [32]
In short, formula feeding may speed up baby gut microbiome maturation [32].
The unique combination of the probiotic and prebiotic components of human breastmilk can provide breastfed babies with a stable and relatively uniform gut microbiome compared with formula-fed babies. Some formulas contain prebiotics like HMOs that help to feed beneficial bacteria.
Breastmilk remains the ideal source of nutrition for babies.
If it’s available to you, continue to breastfeed even if feeding your baby formula. This is because it’s been found that breastmilk seems to suppress baby gut microbiome maturation in formula-fed babies [13].
There are only a few studies on the effects of mixed formula and breastfeeding on the baby’s gut microbiome. That means we don’t know what the threshold is. We don’t know how much breastmilk it takes to hold off the maturing influence of formula.
If you choose to supplement breastmilk with formula, we suggest:
- Tip the breastmilk/formula balance as far in favor of breastmilk as you can
- Wait as long as you can to introduce formula; holding off until a baby is 4-6 months old may reduce the risk of obesity later in childhood
Microbiome maturation speeds up when a baby stops breastfeeding
Complete weaning - or no longer giving your baby breastmilk - drives the maturation of a baby’s gut microbiome [2]. While breastfeeding, Bifidobacterium tend to dominate the baby’s gut, even with the introduction of solid food [17].
Like breastmilk, solid food helps to shape which microbes flourish and which do not. If you continue breastfeeding, then introducing solids will only bring on a slight increase in maturation [13].
But when a baby or toddler weans and stops breastfeeding, their gut microbiome matures rapidly, moving towards a diverse, adult-like composition [32]. These bacteria act together to break down all the different foods your child eats [13].
After weaning, your baby’s gut microbiome will continue to change through early childhood before stabilizing at around 3-5 years [3], [28], [33].
It’s worth keeping in mind that food isn’t the only factor shaping your baby’s gut microbiome. Between weaning and full maturity, other environmental factors come into play. This includes:
- Close contact with caretakers [6]
- Geographical location [32]
- Air quality [32]
- Pet and animal exposure [34], [35]
- Daycare [32], [36]
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References
[1] J. E. Koenig et al., “Succession of microbial consortia in the developing infant gut microbiome,” Proc National Acad Sci, vol. 108, no. Supplement 1, pp. 4578–4585, 2011, doi: 10.1073/pnas.1000081107.
[2] F. Bäckhed et al., “Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life,” Cell Host Microbe, vol. 17, no. 5, pp. 690–703, 2015, doi: 10.1016/j.chom.2015.04.004.
[3] J. Roswall et al., “Developmental trajectory of the healthy human gut microbiota during the first 5 years of life,” Cell Host Microbe, vol. 29, no. 5, pp. 765-776.e3, 2021, doi: 10.1016/j.chom.2021.02.021.
[4] C. Milani et al., “The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota,” Microbiol Mol Biol R, vol. 81, no. 4, pp. e00036-17, 2017, doi: 10.1128/mmbr.00036-17.
[5] K. Korpela et al., “Selective maternal seeding and environment shape the human gut microbiome,” Genome Res, vol. 28, no. 4, pp. 561–568, 2018, doi: 10.1101/gr.233940.117.
[6] P. Ferretti et al., “Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome,” Cell Host Microbe, vol. 24, no. 1, pp. 133-145.e5, 2018, doi: 10.1016/j.chom.2018.06.005.
[7] T. Gensollen, S. S. Iyer, D. L. Kasper, and R. S. Blumberg, “How colonization by microbiota in early life shapes the immune system,” Science, vol. 352, no. 6285, pp. 539–544, 2016, doi: 10.1126/science.aad9378.
[8] H. Renz, P. G. Holt, M. Inouye, A. C. Logan, S. L. Prescott, and P. D. Sly, “An exposome perspective: Early-life events and immune development in a changing world,” J Allergy Clin Immun, vol. 140, no. 1, pp. 24–40, 2017, doi: 10.1016/j.jaci.2017.05.015.
[9] S. Tamburini, N. Shen, H. C. Wu, and J. C. Clemente, “The microbiome in early life: implications for health outcomes,” Nat Med, vol. 22, no. 7, pp. 713–722, 2016, doi: 10.1038/nm.4142.
[10] M. K. Differding et al., “Potential interaction between timing of infant complementary feeding and breastfeeding duration in determination of early childhood gut microbiota composition and BMI,” Pediatr Obes, vol. 15, no. 8, p. e12642, 2020, doi: 10.1111/ijpo.12642.
[11] L. P. M. Pluymen, A. H. Wijga, U. Gehring, G. H. Koppelman, H. A. Smit, and L. van Rossem, “Early introduction of complementary foods and childhood overweight in breastfed and formula-fed infants in the Netherlands: the PIAMA birth cohort study,” Eur J Nutr, vol. 57, no. 5, pp. 1985–1993, 2018, doi: 10.1007/s00394-018-1639-8.
[12] S. Fukuda et al., “Bifidobacteria can protect from enteropathogenic infection through production of acetate,” Nature, vol. 469, no. 7331, pp. 543–547, 2011, doi: 10.1038/nature09646.
[13] C. J. Stewart et al., “Temporal development of the gut microbiome in early childhood from the TEDDY study,” Nature, vol. 562, no. 7728, pp. 583–588, 2018, doi: 10.1038/s41586-018-0617-x.
[14] T. Vatanen et al., “The human gut microbiome in early-onset type 1 diabetes from the TEDDY study,” Nature, vol. 562, no. 7728, pp. 589–594, 2018, doi: 10.1038/s41586-018-0620-2.
[15] J. Stokholm et al., “Delivery mode and gut microbial changes correlate with an increased risk of childhood asthma,” Sci Transl Med, vol. 12, no. 569, p. eaax9929, 2020, doi: 10.1126/scitranslmed.aax9929.
[16] G. Galazzo et al., “Development of the Microbiota and Associations With Birth Mode, Diet, and Atopic Disorders in a Longitudinal Analysis of Stool Samples, Collected From Infancy Through Early Childhood,” Gastroenterology, vol. 158, no. 6, pp. 1584–1596, 2020, doi: 10.1053/j.gastro.2020.01.024.
[17] P. S. Pannaraj et al., “Association Between Breast Milk Bacterial Communities and Establishment and Development of the Infant Gut Microbiome,” Jama Pediatr, vol. 171, no. 7, p. 647, 2017, doi: 10.1001/jamapediatrics.2017.0378.
[18] R. Cabrera-Rubio, M. C. Collado, K. Laitinen, S. Salminen, E. Isolauri, and A. Mira, “The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery,” Am J Clin Nutrition, vol. 96, no. 3, pp. 544–551, 2012, doi: 10.3945/ajcn.112.037382.
[19] I. O’Neill, Z. Schofield, and L. J. Hall, “Exploring the role of the microbiota member Bifidobacterium in modulating immune-linked diseases,” Emerg Top Life Sci, vol. 1, no. 4, pp. 333–349, 2017, doi: 10.1042/etls20170058.
[20] S. A. Frese et al., “Persistence of Supplemented Bifidobacterium longum subsp. infantis EVC001 in Breastfed Infants,” Msphere, vol. 2, no. 6, pp. e00501-17, 2017, doi: 10.1128/msphere.00501-17.
[21] B. M. Henrick et al., “Bifidobacteria-mediated immune system imprinting early in life,” Cell, 2021, doi: 10.1016/j.cell.2021.05.030.
[22] B. M. Henrick et al., “Colonization by B. infantis EVC001 modulates enteric inflammation in exclusively breastfed infants,” Pediatr Res, vol. 86, no. 6, pp. 749–757, 2019, doi: 10.1038/s41390-019-0533-2.
[23] J. E. Spreckels and A. Zhernakova, “Milk and bugs educate infant immune systems,” Immunity, vol. 54, no. 8, pp. 1633–1635, 2021, doi: 10.1016/j.immuni.2021.07.013.
[24] C. M. Dieterich, J. P. Felice, E. O’Sullivan, and K. M. Rasmussen, “Breastfeeding and Health Outcomes for the Mother-Infant Dyad,” Pediatr Clin N Am, vol. 60, no. 1, pp. 31–48, 2013, doi: 10.1016/j.pcl.2012.09.010.
[25] M. Yassour et al., “Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life,” Cell Host Microbe, vol. 24, no. 1, pp. 146-154.e4, 2018, doi: 10.1016/j.chom.2018.06.007.
[26] M. F. Laursen, M. I. Bahl, and T. R. Licht, “Settlers of our inner surface – factors shaping the gut microbiota from birth to toddlerhood,” Fems Microbiol Rev, p. fuab001, 2021, doi: 10.1093/femsre/fuab001.
[27] Y. Shao et al., “Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,” Nature, vol. 574, no. 7776, pp. 117–121, 2019, doi: 10.1038/s41586-019-1560-1.
[28] T. Yatsunenko et al., “Human gut microbiome viewed across age and geography,” Nature, vol. 486, no. 7402, pp. 222–227, 2012, doi: 10.1038/nature11053.
[29] K. E. Fujimura et al., “Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation,” Nat Med, vol. 22, no. 10, pp. 1187–1191, 2016, doi: 10.1038/nm.4176.
[30] J. Stokholm et al., “Maturation of the gut microbiome and risk of asthma in childhood,” Nat Commun, vol. 9, no. 1, p. 141, 2018, doi: 10.1038/s41467-017-02573-2.
[31] T. Vatanen et al., “Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans,” Cell, vol. 165, no. 4, pp. 842–853, 2016, doi: 10.1016/j.cell.2016.04.007.
[32] R. E. Moore and S. D. Townsend, “Temporal development of the infant gut microbiome,” Open Biol, vol. 9, no. 9, p. 190128, 2019, doi: 10.1098/rsob.190128.
[33] S. Subramanian et al., “Persistent gut microbiota immaturity in malnourished Bangladeshi children,” Nature, vol. 510, no. 7505, pp. 417–421, 2014, doi: 10.1038/nature13421.
[34] M. B. Azad et al., “Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of household pets and siblings on microbiota composition and diversity,” Allergy Asthma Clin Immunol Official J Can Soc Allergy Clin Immunol, vol. 9, no. 1, pp. 15–15, 2013, doi: 10.1186/1710-1492-9-15.
[35] M. Nermes, A. Endo, J. Aarnio, S. Salminen, and E. Isolauri, “Furry pets modulate gut microbiota composition in infants at risk for allergic disease,” J Allergy Clin Immun, vol. 136, no. 6, pp. 1688-1690.e1, 2015, doi: 10.1016/j.jaci.2015.07.029.
[36] M. I. Roslund et al., “Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children,” Sci Adv, vol. 6, no. 42, p. eaba2578, 2020, doi: 10.1126/sciadv.aba2578.