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Where does your microbiome come from?

Like your genome or your fingerprint, your microbiome is completely unique to you—the kaleidoscope of genetic material of bacteria, fungi, viruses, and archaea that you harbor cannot be found anywhere else on Earth.

5 minutes
14 Citations
IntroductionYour Microbiome Is Unique To YouEarly Microbes Train a Developing Immune SystemImplications For Long-Term HealthCitations

Your body is home to a diverse community of trillions of microorganisms, including 38,000,000,000,000 (that’s 38 trillion!) bacteria.1 Most of them reside in your gut, where they help aid in essential functions like digestion, immune response, and nutrient absorption. You’ll also find smaller communities in places like the mouth, skin, vagina, and penis.

Organs we once thought were sterile—the lungs, the eyes, the ears—are all teeming with distinct microbial life, too. Your body isn’t just an ecosystem; it’s a planet full of ecosystems! These bacteria represent 50% of you by cell count, and collectively, their genes constitute part of your microbiome. But where did they come from, and how did they end up in (and on) your body?

To answer that question, we need to go back to the very beginning—your beginning.

Like your genome or your fingerprint, your microbiome is completely unique to you—the kaleidoscope of genetic material of bacteria, fungi, viruses, and archaea that you harbor cannot be found anywhere else on Earth. Unlike your genome, it is (mostly) passed down by a single parent.

Your microbiome, as it turns out, is mostly maternal in origin. It makes sense if you think about it. The first microbes you’re exposed to are your biological mother’s—through the birth canal, skin-to-skin contact, and breastfeeding.2

The exposure to these foundational microbes is called seeding, and it continues to be influenced by the environment into which you’re born. Nature, nutrition, family members, pets, and even the hospital room where you take your first breath can all contribute to your microbial mosaic.

By the age of two or three, your community of flora will stabilize into what’s called your steady state microbiome. External factors like diet, exercise, medicine, and sleep will continue to alter the composition for the rest of your life, but your dominant species should remain relatively unchanged, especially if you treat them well.

Seeding is an essential part of your early biological development. These first microbes colonize your gastrointestinal system and quickly reproduce, ensuring long-term residency through strength in numbers. They also form the foundation of your immune system.3 Without them, your body wouldn’t know how to distinguish between benign (read: harmless) substances and pathogenic (read: harmful) invaders.

Translation? Immunity is not just innate—it’s also learned—and our microbiome plays a critical role in training our bodies to recognize threats. Performing that role well requires a healthy and diverse community of resident microbes. It also requires adequate exposure to a diverse range of microbes outside of our bodies (that’s a whole other story).

Whatever your microbial community experiences during the seeding process may impact the training of your immune system. For instance, some scientists now believe that many allergic conditions and autoimmune diseases may stem from early disruptions in microbiome development triggered by antibiotics, cesarean delivery, and even the use of infant formula.4 But nothing is conclusive.

Regardless, seeding and the gut microbiome clearly have significant implications for our long-term health. That’s why it’s so important to identify the inputs and unravel the mechanisms involved. Fortunately, scientific understanding has come a long way in a very short amount of time, thanks to next-generation tools like metagenome sequencing, and exploratory initiatives like the Human Microbiome Project.

Still, important questions remain:

  • Are there strains or species of bacteria that are particularly important for seeding?
  • Are there strains or species of bacteria that are detrimental?
  • How exactly is seeding impacted by vaginal birth, versus cesarean birth?
  • How exactly is the microbiome impacted by natural breast milk vs. infant formula?
  • How exactly do antibiotics affect the seeding process?
  • What about environmental disinfectants?

While additional research is necessary to answer these questions conclusively, preliminary data is already rushing in. In 2017, for instance, a team of scientists at UCLA found that 30% of the beneficial bacteria in a baby’s intestinal tract came from the mother’s breast milk, while an additional 10% came from the skin on the mother’s breast.5

In 2018, a study of more than one million Swedish children found a positive link between cesarean delivery and food allergy risk.6 However, a separate study suggested that the microbiome-related disruptions associated with c-sections have less to do with the method of delivery, and more to do with the corresponding use of antibiotics, and related changes in breastfeeding behavior.7

In 2019, scientists discovered that the maternal microbiome is actually reshaped during the late stages of pregnancy, presumably for the benefit of the fetus.8 Specifically, they found that progesterone—a hormone that prepares the body for conception, among other functions—has a direct effect on the richness of key bacterial genera, including Bifidobacterium.

Most recently, scientists discovered that food-allergic children have a distinct ‘microbial signature’ that is different from children who do not have food allergies, further contributing to the body of evidence that the human microbiome and prevalence of allergies may be linked.9 In this study, the researchers were able to isolate bacterial strains that help protect against allergic reactions by activating a special group of immune cells to express a protein that halts immune response in the presence of harmless substances (read: allergens).

In the near future, that could mean targeted interventions (read: probiotics and fecal microbiota transplants) for those at highest risk of becoming food allergic—namely, infants whose parents or siblings suffer from allergic conditions like eczema,10 asthma,11 and food allergies.12 It could even lead to treatments for children and adults who already suffer from food allergies. And indeed, these are in the early stages of development as we speak.

Other treatments and interventions related to seeding are also in the works, though their efficacy is far from conclusive. One of the most compelling—and controversial—is vaginal swabbing, sometimes referred to as bacterial baptism. The practice involves swabbing cesarean-delivered babies with the mother’s vaginal fluids immediately after birth.

The idea is to expose them to the microbes they would otherwise ‘miss out’ on, in the hopes that they will colonize the infant. In 2016, a preliminary study showed that post-C-section exposure to vaginal fluids was able to partially restore newborns’ bacterial communities, though the sampling size and sampling efforts were limited.13 Meanwhile, a more recent study argued that vaginal swabbing is unjustified, and potentially even unsafe.14

To sum up it all up, answers are coming—and fast—but there’s a lot more work to be done.The discovery of the microbiome marks an evolution of human (and women’s) health. New technologies and research inform us that we are vast, complex ecosystems—seeded first by our mothers, and sculpted further by the world around us. This new biology reveals the potential of bacteria to set ourselves—and our children—up for the healthiest life possible. By every indication, it won’t be long before that potential is unlocked.

  1. Sender, R., Fuchs, S., & Milo, R. (2016). Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology, 14(8), e1002533.
  2. Dunn, A. B., Jordan, S., Baker, B. J., & Carlson, N. S. (2017). The Maternal Infant Microbiome: Considerations for Labor and Birth. MCN. The American journal of maternal child nursing, 42(6), 318–325.
  3. Nash, M. J., Frank, D. N., & Friedman, J. E. (2017). Early Microbes Modify Immune System Development and Metabolic Homeostasis-The “Restaurant” Hypothesis Revisited. Frontiers in endocrinology, 8, 349.
  4. Huang, Y. J., Marsland, B. J., Bunyavanich, S., O’Mahony, L., Leung, D. Y., Muraro, A., & Fleisher, T. A. (2017). The microbiome in allergic disease: Current understanding and future opportunities-2017 PRACTALL document of the American Academy of Allergy, Asthma & Immunology and the European Academy of Allergy and Clinical Immunology. The Journal of allergy and clinical immunology, 139(4), 1099–1110.
  5. University of California – Los Angeles. (2017, May 8). Breast-feeding’s role in ‘seeding’ infant microbiome: Nearly one-third of beneficial bacteria in baby’s intestinal tract comes directly from mother’s milk. ScienceDaily. Retrieved March 23, 2022 from
  6. Mitselou, N., Hallberg, J., Stephansson, O., Almqvist, C., Melén, E., & Ludvigsson, J. F. (2018). Cesarean delivery, preterm birth, and risk of food allergy: Nationwide Swedish cohort study of more than 1 million children. Journal of Allergy and Clinical Immunology, 142(5), 1510–1514.e2.
  7. Stinson, L. F., Payne, M. S., & Keelan, J. A. (2018). A Critical Review of the Bacterial Baptism Hypothesis and the Impact of Cesarean Delivery on the Infant Microbiome. Frontiers in medicine, 5, 135.
  8. Nuriel-Ohayon, M., Neuman, H., Ziv, O., Belogolovski, A., Barsheshet, Y., Bloch, N., Uzan, A., Lahav, R., Peretz, A., Frishman, S., Hod, M., Hadar, E., Louzoun, Y., Avni, O., & Koren, O. (2019b). Progesterone Increases Bifidobacterium Relative Abundance during Late Pregnancy. Cell Reports, 27(3), 730–736.e3.
  9. Abdel-Gadir, A., Stephen-Victor, E., Gerber, G. K., Noval Rivas, M., Wang, S., Harb, H., Wang, L., Li, N., Crestani, E., Spielman, S., Secor, W., Biehl, H., DiBenedetto, N., Dong, X., Umetsu, D. T., Bry, L., Rachid, R., & Chatila, T. A. (2019c). Microbiota therapy acts via a regulatory T cell MyD88/RORγt pathway to suppress food allergy. Nature Medicine, 25(7), 1164–1174.
  10. Dhar, S., & Srinivas, S. M. (2016). Food Allergy in Atopic Dermatitis. Indian journal of dermatology, 61(6), 645–648.
  11. Emons, J., & Gerth van Wijk, R. (2018). Food Allergy and Asthma: Is There a Link?. Current treatment options in allergy, 5(4), 436–444.
  12. University of British Columbia. (2017, October 11). New genetic clue to peanut allergy. ScienceDaily. Retrieved March 23, 2022 from
  13. Dominguez-Bello, M. G., De Jesus-Laboy, K. M., Shen, N., Cox, L. M., Amir, A., Gonzalez, A., Bokulich, N. A., Song, S. J., Hoashi, M., Rivera-Vinas, J. I., Mendez, K., Knight, R., & Clemente, J. C. (2016). Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature medicine, 22(3), 250–253.
  14. Frontiers. (2018, May 30). Swabbing cesarean-born babies with vaginal fluids potentially unsafe and unnecessary. ScienceDaily. Retrieved March 23, 2022 from