Moms and Microbiomes: Making the Breast(feeding) Decision


Parents want to know the best ways to protect and maintain their child’s health. Most parents have strong opinions about the best way to ensure their child stays healthy. The decision to breastfeed or use formula is just one example of a highly controversial parenting choice in recent years. Another very contested issue is the maternal diet during pregnancy, which has been found to have lasting impacts on the child’s health.

Picture of me as a baby in a diaper, pushing the seat of a swing over my head.
Figure 1: Myself as a baby, pushing a swing. Photo by my mother, Kristine Bristow.

A new topic that has become increasingly important in the consideration of childhood health is the microbiome. The microbiome is the entire community of microscopically small organisms that live on and in your body, including the surfaces they live in and on. Imbalances or other changes in the microbiome impact the health of the host, and they are especially influential in childhood health, as Saavedra et al. (1995) showed when they found that feeding infants formula supplemented with bacteria thought to be beneficial resulted in fewer incidences of diarrhea . The infant microbiome can particularly impact child health, as Marko Kalliomäki et. al (2001) illustrated when they found that changes in the gut microbiomes of infants preceded a significant number of those infants developing allergies .

However, the microbiome is just one of the many factors in infant health. The LISA Study group found that maternal diet during pregnancy also influences child health by influencing the development of allergies (Stefanie Sausenthaler et al, 2007). Additionally, breastfeeding has been shown to promote helpful bacteria like Bifidobacterium, Lactobacillus, and Clostridium in the intestinal microbiome of infants (P. L. Stark and A. Lee, 1982). In light of all these early-life health factors, Jessica Savage et al (2018), the authors of this study, investigated connections between maternal and infant diet and the infant gut microbiome.

Central Question and Goals

What are the associations between the child gut microbiome and diet during pregnancy and infancy? The authors examined specific facets of child diet, such as breastfeeding versus formula, solid food introduction, and maternal diet during pregnancy to make these connections.


The authors sourced samples from 323 infants whose mothers participated in another trial which was investigating Vitamin D as a possible treatment to prevent the child from developing one of the parents’ allergies and/or asthma. They gathered information about the participants’ diets and sequenced the DNA from their stool samples, identifying the microbes in each sample. Using this DNA, the authors investigated four specific genera (groups of species) of microbes associated with early diet and health effects: Bacteroides, Lactobacillus, Bifidobacterium, and Clostridium.

They found that the most significant association between maternal diet during pregnancy and the microbiome was the positive association between Lactobacillus species and a high vegetable intake/low processed meat and fried food intake. Clostridium species were found to be significantly associated with solid food introduction into the child’s diet.

Consistent with previous studies (P. L. Stark and A. Lee, 1982; H.Yoshioka et al, 1983), the strongest associations were found between infant feeding type (breastfed vs. formula) and the microbiome. Breastfed infants had higher numbers of positive microbes like Bifidobacterium, Lactobacillus, and Clostridium. The authors also found that the breastfed infant microbiome had lower diversity than the formula fed one.

The authors did not find any significant associations between the maternal diet during pregnancy and the gut microbiome during infancy, perhaps suggesting that the diet of the infant after birth is more determinate of the microbiome than maternal diet during pregnancy is.

The lack of ethnic diversity in previous studies of this kind spurred the authors to specifically analyze the results in light of ethnicity. They found that when differences in the microbiome were sorted by ethnicity, the differences could not be explained by diet. This suggests that the ethnicity of the child somehow affects the relationship between the microbiome and the diet, but the authors noted that this needed to be replicated in order to to draw conclusions about the effects of genetics on the microbiome’s response to the diet. Other studies were also limited by small numbers of participants, or by the use of techniques that depended on being able to grow the microbes in a lab setting. Those techniques severely limit studies because only a small proportion of microbes can be grown in a lab.(Eric J. Stewart, 2012)

My Questions and Thoughts

Why did the breastfed infants show lower diversity than the formula fed infants?

Could this study’s results have been influenced by the parents’ status as allergy and/or asthma patients? Since other studies have shown connections between the microbiome and allergies (Marko Kalliomäki et al, 2001), I would be very interested to see this study replicated in a larger group (perhaps 150 mothers/infants for each treatment group, from 3 or 4 larger, more ethnically diverse cities across the US) and without the potential impact of the allergic/asthmatic parents.

Further Readings

An obvious next step that this study inspires is that of a probiotic formula containing the helpful microbes that formula- fed children have been seen to lack. Most of the probiotic formulas and studies on probiotic-supplemented formula included one or both Bifidobacterium and Lactobacillus genuses, but I could not find any that included Clostridium. I believe this could be due to the public’s concern about the species Clostridium botulinum, which releases toxins and causes botulism, but I couldn’t find any explanation. For more information on the observed effects of probiotic formula, see Long-term consumption of infant formulas containing live probiotic bacteria: tolerance and safety

For further reading on how the microbiome colonizes and develops with the infant’s gut, see The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.


  • Kalliomäki, Marko, et al. “Distinct Patterns of Neonatal Gut Microflora in Infants in Whom Atopy Was and Was Not Developing.” Journal of Allergy and Clinical Immunology, vol. 107, no. 1, 2001, pp. 129–134., doi:10.1067/mai.2001.111237.
  • Sausenthaler, Stefanie, et al. “Maternal Diet during Pregnancy in Relation to Eczema and Allergic Sensitization in the Offspring at 2 y of Age.” The American Journal of Clinical Nutrition, vol. 85, no. 2, Jan. 2007, pp. 530–537., doi:10.1093/ajcn/85.2.530.
  • Saavedra, J M, et al. “Feeding of Bifidobacterium Bifidum and Streptococcus Thermophilus to Infants in Hospital for Prevention of Diarrhoea and Shedding of Rotavirus.” The Journal of Pediatrics, vol. 126, no. 5, 1995, pp. 841–842., doi:10.1016/s0022-3476(95)70426-4.
  • Savage, Jessica H., et al. “Diet during Pregnancy and Infancy and the Infant Intestinal Microbiome.” The Journal of Pediatrics, 2018, doi:10.1016/j.jpeds.2018.07.066.
  • Stark, P. L., and A. Lee. “The Microbial Ecology of the Large Bowel of Breastfed and Formula-Fed Infants During the First Year of Life.” Journal of Medical Microbiology, vol. 15, no. 2, Jan. 1982, pp. 189–203., doi:10.1099/00222615-15-2-189.
  • Stewart, Eric J. “Growing Unculturable Bacteria.” Journal of Bacteriology, vol. 194, no. 16, Jan. 2012, pp. 4151–4160., doi:10.1128/jb.00345-12.
  • Yoshioka , H., et al. “Development and Differences of Intestinal Flora in the Neonatal Period in Breast-Fed and Bottle-Fed Infants.” Pediatrics, vol. 72, no. 3, pp. 317–321.



One Reply to “Moms and Microbiomes: Making the Breast(feeding) Decision”

  1. I wonder if freezing expressed breastmilk and also thawing affects the breastmilk and how it supports the microbiome in an infants gut. Thank you for the great article! You’ve got me thinking about more research topics!

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