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Microbiome

Guess Where You Got Your Microbes

Nature goes to extremes to ensure you get some heirloom microbes.

Key points

  • Your microbiome is passed down from your mother at birth.
  • A healthy microbiome is important to support a healthy mental state.
  • There are three redundant mechanisms to ensure proper transmission of microbes.

“Only mothers can think of the future — because they give birth to it in their children.” —Maxim Gorky

The gut-brain axis depends on a healthy set of microbes — the microbiome — to generate a positive mood, clarity of thought, and a strong memory. That’s a major reason why nature goes to shocking lengths to pass on a microbiome.

Some insects, for instance, have special cells called bacteriocytes: fat cells that contain an entire microbiome in miniature, preserving the microbial heritage of the host insect. These bacteriocytes position themselves near the eggs, and during birth, the bacteriocytes burst and spill their precious cargo. Thus anointed, the eggs absorb the bacteria and begin the cycle anew.

These bacteria go to work immediately to scrounge nitrogen from the environment, providing vitamins and nutrients to the newborn larva. That ability to thrive on detritus has made insects — and their attendant microbes — some of nature’s most successful collaborations.

In the beginning

Some 1.5 billion years ago, animals formed and immediately recruited microbes to fight off pathogens and digest fiber. Animals and bacteria have some genes in common, and over time both the host and the bacteria dropped the redundant genes to become more efficient.

That had two important consequences:

  • The host became dependent on the microbes. For instance, humans no longer have the genetic machinery to create most vitamins — those jobs have been outsourced to microbes.
  • The microbes became dependent on the host. Because they lack essential genes, these bacteria could no longer live outside of the host and are no longer found in the environment.

That’s why passing down a microbiome is a biological imperative. There must be a mechanism to pass on this essential but vulnerable heritage, and — across the entire animal kingdom — that job typically falls to the mother.

AI Generated
Source: AI Generated

Humans are no exception. During pregnancy, the mother develops a distinctive vaginal microbiome, custom-built to anoint her baby. Certain lactobacillus species become dominant and the population becomes less diverse, amplifying microbes that are gut related. As you’re born, you get a healthy dose of these bacteria while squeezing down the birth canal.

Once born, you’re exposed to the outside world, which is cold, dry and highly infectious. You, of course, are naked. You have no real consciousness, and you won’t remember this day, but you know enough to cry.

Try not to think about it

Birthing can be an untidy business, and you are almost certain to pick up your mother’s fecal bacteria as well. Many animals pass on their microbes through mother’s poop, which is gross, but superbly efficient.

This bacterial appetizer is there to kickstart your own microbiome and to teach your immune system what to tolerate. If your mother is in good health, you’ll get a lucky head start on life.

If you were born by caesarean, you missed a lot of that messy stuff. Instead, you were whisked away to a nursery where you picked up a bacterial population unique to your nurse’s gloves and your hospital room.

Some studies have shown that children delivered by C-section may lack important bacteroides species for up to the first 18 months of life, making them more likely to suffer from asthma and allergies. C-section babies seem to react differently to stress and are more susceptible to depression and anxiety, thanks to the gut-brain axis.

Not all outcomes are so bleak: new research has shown that at around six weeks, the microbiome of most of these children normalizes, with some of that due to breastfeeding. That’s because breast milk also contains microbes, carefully curated from the gut, that get passed down to the baby along with prebiotics to feed them.

The microbial triumvirate

These three inoculations, from the vagina, fecal matter, and breast milk, constitute your microbial starter kit, preowned and passed down from your mother, her mother, and her mother before her. Unless you become violently ill or take antibiotics in the first days of your existence, these bacteria will stick with you for life.

Which of these microbial samplers is most important? A recent Dutch study looked at 714 mother-baby pairs, from month 6 of pregnancy to 1 year old. They found that the major impact was the fecal route.

Such is life. It may start crappy but hopefully improves from there. Now that you know how you got one and why you need one, you might want to take better care of your microbial life partner. Feed it well. Your mind, mood, and memory depend on it.

References

Sinha, Trishla, Siobhan Brushett, Asier Fernández-Pato, et al. “Maternal Influences on Infant Gut Microbiome and Health.” Nature, August 12, 2026, 1–12.

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.

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.

Chu, Derrick M., Jun Ma, Amanda L. Prince, Kathleen M. Antony, Maxim D. Seferovic, and Kjersti M. Aagaard. “Maturation of the Infant Microbiome Community Structure and Function across Multiple Body Sites and in Relation to Mode of Delivery.” Nature Medicine advance online publication (January 23, 2017). doi:10.1038/nm.4272.

DiGiulio, Daniel B., Benjamin J. Callahan, Paul J. McMurdie, Elizabeth K. Costello, Deirdre J. Lyell, Anna Robaczewska, Christine L. Sun, et al. “Temporal and Spatial Variation of the Human Microbiome during Pregnancy.” Proceedings of the National Academy of Sciences 112, no. 35 (September 1, 2015): 11060–65. doi:10.1073/pnas.1502875112.

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