Ask the Expert: How does breastfeeding affect the microbiome?

Ask the Expert: How does breastfeeding affect the microbiome?

August 2022

In this month's Ask the Expert series, Chief Science Officer Beth DuPriest, PhD discusses changes that occur in the vaginal biome during lactation and what to expect when estrogen levels decline during the postpartum period. 

Q: How does breastfeeding effect the microbiome?

A: Breastfeeding (lactation) affects both the mother’s and baby’s microbiomes. The most discussed effects surround colonization of the infant’s gut with healthy microbes. There is plenty of research suggesting that breastfeeding helps to set up a baby for good gut and immune health for life1,2, reinforcing the concept that when physically, emotionally, and economically feasible, breastfeeding should be the primary mode of infant nutrition through the first six months. But here we will focus on effects of lactation on the mother’s vaginal microbiome. This is an area that is, by comparison, vastly under-explored, but equally deserving.

Only a handful of studies in humans have examined the relationship between lactation and the vaginal microbiome. Animal studies are of limited utility because of the radically different vaginal microbiome between humans and animals; no species other than humans are known to have a lactobacillus-dominant microbiome. But a study of rhesus macaques – monkeys often used in reproductive science inquiries because of their “menstrual-like” cycle and close similarities to humans in terms of placental and fetal development – showed that lactation causes a shift in the vaginal microbiome to more closely resemble that of a male urethra3.

Lactation is a period of low estrogen levels. Since estrogen is the driver of vaginal epithelial cell maturation, the withdrawal of estrogen leads to vaginal epithelial thinning and a reduction in glycogen production. Because glycogen breakdown products (glucose, maltose, maltotriose, and small dextrans) are the primary fuels for lactobacilli, these changes in vaginal epithelial structure and function are expected to reduce the number of lactobacilli, allowing for increases in diversity and quantity of other bacterial species which are considered pathogenic. Many of these pathogenic bacteria produce enzymes such as sialidase capable of breaking down intercellular adhesions, reducing the barrier integrity of the epithelium.

In fact, this shift in the vaginal microbiome during lactation is exactly what is seen. Jie and others recently showed a reduction – or a near absence – of lactobacilli during lactation in a study of nearly 1200 Chinese women4. A separate study showed an increase in Prevotella – a species associated with bacterial vaginosis – in lactating women5.

It is worth noting that many women experience vaginal dryness during lactation due to low estrogen levels. Women who use hyperosmolar lubricants for sex during this period will exacerbate the vaginal epithelial damage and dysbiosis due to the nature of these products.

Lactation is a period of increased vulnerability to sexually transmitted infections due to the double hit of a naturally thinner vaginal epithelium and a dysbiosis comprised of low lactobacilli followed by rising levels of epithelium-degrading pathogens. Breastfeeding women who have new sexual partners or partners with known infections should be especially cautious, using barrier protection for the duration of lactation. Any lubricants used should be iso-osmotic.


1. Houghteling PD, Walker WA. Why is initial bacterial colonization of the intestine important to infants’ and children’s health? J Pediatr Gastroenterol Nutr. 2015;60(3):294-307. doi:10.1097/MPG.0000000000000597

2. Dawod B, Marshall JS, Azad MB. Breastfeeding and the developmental origins of mucosal immunity: how human milk shapes the innate and adaptive mucosal immune systems. Curr Opin Gastroenterol. 2021;37(6):547-556. doi:10.1097/MOG.0000000000000778

3. Hallmaier-Wacker LK, Lüert S, Roos C, Knauf S. Lactation and menstruation shift the vaginal microbiota in captive rhesus monkeys to be more similar to the male urethral microbiota. Sci Rep. 2019;9(1):17399. doi:10.1038/s41598-019-53976-8

4. Jie Z, Chen C, Hao L, et al. Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omics. Genomics Proteomics Bioinformatics. Published online June 9, 2021:S1672-0229(21)00099-1. doi:10.1016/j.gpb.2021.01.005

5. Austin MN, Meyn LA, Avolia HA, et al. Impact of Dapivirine and Placebo Vaginal Rings on the Microbiota of Adolescent, Lactating, and Postmenopausal Females. J Infect Dis. 2022;225(12):2208-2218. doi:10.1093/infdis/jiab590

Back to blog