Skip to main content

Verified by Psychology Today


From Mom on Your Birthday: A Microbiota

Moms go to great lengths to pass on their microbial genes.

Horse owners are often startled when they see a foal eat its mother's poop, but it's perfectly normal. Eating poop is an efficient, if indelicate, way to inherit the mare's microbiome. Horses spend their entire day grazing. In order to process the laughably low energy content of grass, a mature horse has a cecum containing up to eight gallons of cellulose-degrading bacteria – and that had to come from somewhere. Lots of animals – especially young ones – eat poop, including rabbits, koalas, pandas, pigs, geese, elephants, hippos, dogs, mice and monkeys. And, often, humans.

Olha Rohulya/iStock
A mare and her foal grazing.
Source: Olha Rohulya/iStock

When a baby is squeezed down the birth canal, we know that it picks up vaginal microbes along the way. But with all that squeezing, the baby often picks up mom's fecal microbes as well. Natural birth is far from antiseptic. From an evolutionary standpoint, that makes sense: The world is lousy with pathogens, and babies are totally doomed without protective microbes. They need to be saturated with their mom's microbiota as quickly as possible. A messy birth provides an important starter set for the baby's microbiota.

Babies born by C-section have a different microbiota, more like a nurse's glove. These kids have an increased likelihood of asthma and allergies than babies born vaginally. They often have higher gut permeability and lower microbial diversity, both associated with depression and anxiety.[i] Muddying the issue, mothers are typically given antibiotics before a C-section, so some of the microbial changes may be attributed to that as well. New research shows that many of the differences disappear after a couple of months and fortunately, C-section babies get a second chance to establish a good microbiota: Babies are born to suckle.

Natalia Deriabina/iStock
A great way to get a microbiota.
Source: Natalia Deriabina/iStock

Breast milk is like warm kefir

Breast milk is an amazingly rich concoction of sugars, fats, and immune factors. It is a carrier for the main payload—a starter microbiota that includes bacteria and fungus from the mother and her mother before her.[ii] They are specially plucked from the mother's gut by dendritic cells and then ferried to the milk ducts via the lymphatic system.[iii] These microbes are accompanied by a rich broth of prebiotics to feed them. Most of the sugars in milk are for those microbes, not the baby. That seems sadistic, but it's not: The microbes convert those indigestible sugars into energy-packed fatty acids that feed the baby and nourish the gut lining.

Wait a minute

Don't we all have an immune system designed to kill microbes? Even mom's microbes? How does the immune system know which ones are the good guys? The answer is: It has to grow into it.

In anticipation of these mother-approved microbes, the baby's immune system lets down its guard. It learns to accept this initial batch of microbes. Mom's microbiota thus provides an early lesson in tolerance.

Milk also includes antibodies and white blood cells that the mother has built up against previous illness – the baby's first vaccination. Thus, mother's milk is a prebiotic, probiotic, and antibiotic formula that has played a starring role in 200 million years of mammalian history. That arrangement allows us to share genes with microbes. A lot of genes — the microbiota has 100 times as many genes as we do. Those microbes haven’t evolved separately from us. We have co-evolved, ensuring that both sets of genes are passed down. We need each other.

Making up your mind

Microbes play a role in brain development, a statement that should give us all a shudder.[iv] In 2004, Nobuyuki Sudo showed that germ-free mice raised in a sterile environment develop an abnormal stress response. Sudo was able to normalize that stress response by feeding them bacteria from healthy mice.[v]

In 2015, Roman Stilling and Pauline Luczyinski showed that germ-free mice develop abnormal amygdalas, with unusual brain chemistry.[vi] Abnormal amygdalas are associated with anxiety, depression, and autism. As well as the amygdala, studies in John Cryan and Ted Dinan's lab have shown that a germ-free mouse may have an unusual hippocampus, a part of the brain involved with both memory and emotion. Somehow, the microbiota is affecting the development of important memory and anxiety centers of the brain.

Mice are not people, but we can't do germ-free experiments on humans. These studies, however, show a foundational connection between the microbiota and the brains in all mammals studied. The odds are, something similar happens to people.

After about 1000 days, a baby has settled on its own unique microbial formula. After then, it is difficult to alter the basic structure of your microbiota, but not impossible. In future articles, I'll discuss some strategies to improve your microbial balance.


[i] Neu, Josef, and Jona Rushing. “Cesarean versus Vaginal Delivery: Long Term Infant Outcomes and the Hygiene Hypothesis.” Clinics in Perinatology 38, no. 2 (June 2011): 321–31. doi:10.1016/j.clp.2011.03.008.

[ii] Boix-Amorós, Alba, Fernando Puente-Sánchez, Elloise du Toit, Kaisa M. Linderborg, Yumei Zhang, Baoru Yang, Seppo Salminen, et al. “Mycobiome Profiles in Breast Milk from Healthy Women Depend on Mode of Delivery, Geographic Location and Interaction with Bacteria.” Appl. Environ. Microbiol., March 1, 2019, AEM.02994-18.

[iii] Funkhouser, Lisa J., and Seth R. Bordenstein. “Mom Knows Best: The Universality of Maternal Microbial Transmission.” PLOS Biol 11, no. 8 (August 20, 2013): e1001631. doi:10.1371/journal.pbio.1001631.

[iv] Dinan, Timothy G., and John F. Cryan. “Gut Instincts: Microbiota as a Key Regulator of Brain Development, Ageing and Neurodegeneration.” The Journal of Physiology 595, no. 2 (2017): 489–503.

[v] Sudo, Nobuyuki, Yoichi Chida, Yuji Aiba, Junko Sonoda, Naomi Oyama, Xiao-Nian Yu, Chiharu Kubo, and Yasuhiro Koga. “Postnatal Microbial Colonization Programs the Hypothalamic-Pituitary-Adrenal System for Stress Response in Mice.” The Journal of Physiology 558, no. Pt 1 (July 1, 2004): 263–75.

[vi] Stilling, Roman M., Feargal J. Ryan, Alan E. Hoban, Fergus Shanahan, Gerard Clarke, Marcus J. Claesson, Timothy G. Dinan, and John F. Cryan. “Microbes & Neurodevelopment--Absence of Microbiota during Early Life Increases Activity-Related Transcriptional Pathways in the Amygdala.” Brain, Behavior, and Immunity 50 (November 2015): 209–20. doi:10.1016/j.bbi.2015.07.009.

More from Scott C. Anderson
More from Psychology Today