What You Need To Know About The Infant Microbiome

Turns out there's a little bit more to know about bodies than we originally thought.


Hey Mamas, today we’re going to get into some nitty-gritty details about healthy gut biomes. Turns out there’s a little bit more to know about bodies than we originally thought (pretty much the new mom mantra, are we right?). So we’re making it our mission to inform you about bacteria, gut health, and fostering healthy, biome-y babies. We talked to Anita Tee, who helped us understand all the good nuances of gut health. Anita is a published scientist and clinical nutritionist who is an expert in child nutrition and has just completed interviews for global child nutrition crises. We looove her here at Little Spoon. So, mamas (& papas!), buckle in and prepare for science ‘cause we’re all about to get educated

What is a biome? 

Ok, first of all, when talking to Anita, one of our key takeaways was that when we’re talking gut biomes, we’re talking microbiomes and all the goodness it entails. We’re not just talking about gut bacteria (a term people love to throw around!). Basically a human microbiome is the name we give a group of living microorganisms like yeast, fungus, viruses, bacteria (blah blah blah) that call our body home. Don’t freak out! They live in everyone in weird places like our mouths, our skin, our guts, and around our vaginal tracts (fun!). These organisms work together to make sure you function properly. Feeling smart yet?

In this article we’re specifically talking about the many components (not just the bacteria!) of the gut microbiome. “Recent studies regarding gut biomes have stunned scientists.” Anita tells us.
“There’s now strong evidence to suggest microorganisms begin taking shape while your baby is still a fetus within the womb.” As Anita explains to us, this is such a cool discovery because, until recently, scientists believed the womb to be sterile (5,6). Apparently a mama’s microbiome has a major-major role in fetal development and can affect your baby’s health for the rest of their life. 

We don’t know about you, but when we heard this we thought: great. One more thing to worry about(7). 

Why You Should Care?

Here’s the stats as Anita gave them to us: by the time you’re an adult, about 1-3% of your body mass comprises of microorganisms (!!!). That means, that in a 200-pound person, these little critters make up around 2-6 pounds(1). “In the human colon alone,” Anita confided, “there’s around 1 pound of bacteria. It’s only in the last few years that the scientific world has started to come to terms with how important these living organisms are to our health(2).” 

Anita explained that a bunch of stuff goes into developing your baby’s microbiome (like amniotic fluid, umbilical cord stuff, placenta, & on & on)(8). But what you need to know is that basically, what’s happening in your womb-biome affects your baby’s biome.  

“A mama’s biome undergoes major change during pregnancy(11),” Anita said. Hormones, chemical-internal-stuff, infections, inflammations, and diet all affect the mama’s biome, and, by extension, the baby’s(12). Basically, if there’s an imbalanced ratio of species in mama it can cause a similar imbalance in baby, possibly increasing risk of asthma, allergy-related diseases, and even obesity once the child is born(13). 

Of course, it’s impossible to have complete control over the normal changes the body goes through when you’re building a human (need we mention hormones?)! Taking charge of those that you can, however, can make a huge impact. 

Kickstarting Your Baby’s Microbiome

For example, Anita mentioned that “reducing your risk of infections and increased inflammation can be done through simple changes to the diet before pregnancy (if you’re just getting started), during pregnancy (throughout each of those wonderful months), and even after pregnancy (for breastfeeding and cuddling!).” That sounds doable!   

“In the prenatal microbiome,” Anita said, “a mama’s diet has a significant influence on the fetal microbial colonization. Just one of the more recent studies that have come out show that women who follow a high fat diet (saturated, processed, trans fats), may have babies born with less of one of the healthier genera of bacteria in their gut, which is associated with inflammatory conditions later in life(18,19,20).” Well, we can certainly do that. 

That being said, the best way for a mama to control her microbiome, and build her baby’s during pregnancy, is to focus on nutrient intake. A healthy mama-and-baby-beneficial diet would look something like this:

  • Low in refined and processed sugars
  • Low in white and processed carbohydrates
  • Low in highly processed packaged foods 
  • Rich in a variety of fruit and vegetables, that represent all of the colors of the rainbow
  • With the addition of whole-grains like rolled oats, quinoa, barley, millet, amaranth, and brown rice
  • With lean protein like chicken, turkey, ostrich, lean beef, eggs
  • Healthy fats like olives and their oils, avocados and their oils, coconut, nuts and seeds
  • Portions of legumes like lentils and beans

A combination of the latter foods at every meal feeds your own and baby’s bodies to allow them to grow and develop as they should. As they feed the healthy little critters in your digestive tract, they may move into baby’s, and begin to flourish there. 

Making The Most of A Child’s Microbiome

Mamas, don’t worry. Once your child is no longer in-utero, there are a couple of things you should consider to help support diverse biome-growth in your kid. 

(1) Breastfeeding

It turns out that even once your child is not physically part of you, your body has a lot to do with their health! Breast-feeding has been shown to promote distinct microbiomes and increase immune responses as well as metabolic development (24,25)! 

(2) Probiotics… yes for your baby! 

We’ve talked about the feasibility of breastfeeding before, so if it’s not the path you’ve chosen for baby, don’t worry. And even if it is, probiotics also have been shown to help get guts flowering in kids as well as adults.

“In children, the species Lactobacillus rhamnosus DSM 6594 has been well-studied in its effect,” Anita said. “It’s a mouthful, but just think of it as L. ram-no-sus, with the number DMS 6594. We’ve seen multiple clinical trials of its effects in infants and children, where it helps their  bodies to better find and attack foreign invading pathogens that may increase their risk of illness. You’ll want to look for this single strain in at least a concentration of a billion CFU (109 CFU), as this high concentration means that even though some of the bacteria may be destroyed during normal transit through the digestive system, many of them reach their end goal, which is to be deposited into the large intestine where they can settle in and get to work.” The higher the concentration, the better. 

But it can be tricky to figure out which probiotics will work best for your kid, especially because we’re still researching and learning about the impact they can have. We suggest talking to your pediatrician before introducing any new probiotics into your infant’s diet. There’s still research being done on this topic, so it’s best to ensure you are consulting with your pediatrician and considering a probiotic that has been designed for infants (read: has some clinical proof of results in a baby’s bod, not just an adult’s!). (By the way – if you decide that you do want to move ahead with probiotics for your baby, look no further than our Gut Feeling Booster which has 3 billion CFU’s of Lactobacillus rhamnosus DSM 6594.)

(3) Some other tricks of the trade 

There are also a few things that support gut-health that seem outside of the box, but are proven to help. Exposing your infant to furry animals, a variety of outdoor spaces, and other children in the first four months of life have been shown to positively influence microorganism diversity within infant tummies. Another way to support this diversity is to prevent your baby from being overly clean (seriously)! Basically, all of this is just various ways of exposing your baby to new elements of the world and, in the process, helping their gut get accustomed to life(22,23). 

Your Health is Baby’s Health

Fortunately, with all of the research that has gone into the microbiome, we know that it’s easy to alter for the betterment of baby’s health. You can put strategies in place that can both promote balance in your own microbiome as well as that of your fetus, infant or toddler(17). 

It’s true whether you’re just starting out, whether you’re weeks away from your bundle’s arrival, or you’ve already spent many happy moments with your little one. We can’t stress enough the importance of thinking about the influence of your gut biome for every part of pregnancy and child-raising both for mama and baby. It doesn’t hurt to check in with your healthcare provider about how you can maintain the health of your gut bacteria, whether your little one needs some extra care in that department, and how probiotics may be just what you both need to be healthy and flourish. 

We did the research so you don’t have to. Still, if you want to compare our stuff to the original, here are our sources: 


  1. National Institutes of Health. NIH Human Microbiome Project defines normal bacterial makeup of the body. 2012. 
  2. Sender, R., et al. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol. 2016 Aug; 14(8): e1002533.
  3. Willyard, C. Could baby’s first bacteria take root before birth? Nature 553, 264-266 (2018).
  4. D’Argenio V, Salvatore F. The role of the gut microbiome in the healthy adult status. Clin Chim Acta. 2015 Dec 7; 451(Pt A):97-102.
  5. Nuriel-Ohayon M, Neuman H, Koren O. Microbial Changes during Pregnancy, Birth, and Infancy. Front Microbiol. 2016; 7():1031.
  6. Neu J. The microbiome during pregnancy and early postnatal life. Semin Fetal Neonatal Med. 2016 Dec; 21(6):373-379.
  7. Saavedra JM, Dattilo AM. Early development of intestinal microbiota: implications for future health. Gastroenterol Clin North Am. 2012 Dec; 41(4):717-31.
  8. Mor G., Aldo P., Alvero A.B. The unique immunological and microbial aspects of pregnancy. Nat. Rev. Immunol. 2017;17:469–482. 
  9. Mshvildadze M., Neu J., Shuster J., Theriaque D., Li N., Mai V. Intestinal microbialecology in premature infants assessed with non-culture-based techniques. J. Pediatr. 2010;156:20–25. 
  10. rdissone AN, de la Cruz DM, Davis-Richardson AG, Rechcigl KT, Li N, Drew JC, Murgas-Torrazza R, Sharma R, Hudak ML, Triplett EW, Neu J. Meconium microbiome analysis identifies bacteria correlated with premature birth. PLoS One. 2014; 9(3):e90784.
  11. Tapiainen T, Paalanne N, Tejesvi MV, Koivusaari P, Korpela K, Pokka T, Salo J, Kaukola T, Pirttilä AM, Uhari M, Renko M. Maternal influence on the fetal microbiome in a population-based study of the first-pass meconium. Pediatr Res. 2018 Sep; 84(3):371-379.
  12. Chu DM, Antony KM, Ma J, Prince AL, Showalter L, Moller M, Aagaard KM. The early infant gut microbiome varies in association with a maternal high-fat diet. Genome Med. 2016 Aug 9; 8(1):77.
  13. Mor G, Aldo P, Alvero AB. The unique immunological and microbial aspects of pregnancy. Nat Rev Immunol. 2017 Aug; 17(8):469-482.
  14. Dominguez-Bello MG, Costello EK, Contreras M, Magris M, Hidalgo G, Fierer N, Knight R. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci U S A. 2010 Jun 29; 107(26):11971-5.
  15. Dominguez-Bello M.G. et al. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc. Natl. Acad. Sci. USA. 2010; 107: 11971-11975.
  16. Backhed, F., et al. Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe. 2015 May 13;17(5):690-703.
  17. Zmora N, Zeevi D, Korem T, Segal E, Elinav E. Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease. Cell Host Microbe. 2016 Jan 13; 19(1):12-20.
  18. Xe, R., et al. Maternal High Fat Diet Alters Gut Microbiota of Offspring and Exacerbates DSS-Induced Colitis in Adulthood. Front Immunol. 2018; 9: 2608. 

Looking for more tips on parenting, nutrition & all the WTF moments of this life stage? Sign up for our weekly Is This Normal by Little Spoon newsletter.

    Tags: baby gut problems, baby microbiome, infant gut health, infant gut microbiome, infant microbiome development