New Science Shows Infants are Born with Gut Bacteria — How Do You Make it Healthy? : Exclusive Article by J. E. Williams

Friday May 4 | BY |
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New studies show that babies are born with intestinal flora already in place, which can greatly influence later health and personality.

What goes on in the anaerobic world of the gut? It’s long been assumed that the fetus lives in a sterile world, protected from a myriad of infectious and friendly bacteria that fill its mother’s gut and cover the surface of her body. A baby’s first gut flora was thought to be collected at birth from its passage through the mother’s birth canal, via nursing, and from the environment into which it is born.

Now it appears that we are, in fact, born dirty. Bacteria are already colonizing our guts in the womb, where they begin to shape our immune systems and influence our risk of disease through our entire lives. This collection of bacteria is called our “personal microbiome.”

My clinical questions are: Can we restore a diseased gut to normal if the mother’s diet was loaded with refined foods, and if her gut was out of balance due to antibiotic use? How can we ensure a baby is given the healthiest start in life?

Studies Show Humans Develop Microbiome Before Birth
The evidence that mammals, including humans, might develop their microbiome before birth came from studies in mice published by Esther Jiménez of Madrid, Spain. Jiménez’s team found bacteria in the meconium of healthy mice babies, suggesting that the bacteria had transferred from the mother’s gut to the fetus during pregnancy.

Another study from Spain suggests the same thing happens in humans. The research team found newborns’ bacterial communities already very developed. Half of the samples were dominated by bacteria that produce lactic acid, such as lactobacillus, which is the type we believed rules every baby’s gut. But the other half mostly contained a family of friendly enteric bacteria, such as Escherichia coli.

Since microbiomes significantly influence our immune response to disease, these findings are really important. The Spanish researchers were surprised to find that infants born with more lactic acid bacteria were significantly more likely to develop asthma-like symptoms, while those born with more enteric bacteria were at a greater risk of eczema.

Mother’s Lifestyle Affects Newborn Gut
These first bacterial communities also appeared to be linked to the mothers’ lifestyles. University-educated women in the study, who were more likely to live in hyper-clean environments, gave birth to babies with a lactic acid bacteria-dominated microbiome. The majority of women who had not been educated beyond age 12, and who were more likely to live in rural, less sterile environments, had babies whose guts were dominated by enteric bacteria.

Nobody knows how the bacteria gets from the mother to the fetus, but these studies give us an important clue that a pregnant woman can influence the makeup of her baby’s microbiome before it is born. The first bacteria to colonize the gut influence the bacterial species that follow, and effect lifelong health. In addition, lifestyle and diet influence our mirobiome. Smoking encourages an enteric microbiome, while eating organic foods promotes lactic acid bacteria.

Healthy Gut Bacteria Affects Health and Personality
Having the right kind of bacteria in your gut is worth working for. Altered microbiomes have been linked to a host of disorders, including IBS and obesity, allergies, asthma, cancer, and even autism. The bacteria that line our intestines are known to be vital for health, but they also influence personality. Research suggests that a healthy gut flora is necessary for normal behavior. Apparently, gut bacteria trigger changes in brain proteins linked to mood and anxiety.

Your health and personality are very complicated. I’m not surprised that bugs play a role. So I keep looking for ways to restore, revitalize, and regenerate the gastrointestinal microbiome. It’s a big job that takes time, lots of patience, and a lot of bugs.

For more information, check out the microbiome conference page.

Kev’s Comments:

This concept is fascinating and at the same time a little scary.

I’m not going to add to what Dr. Williams said, but I’m going to give you some tips on how to start improving your gut whether or not you’re a mom.

  • Fermented foods play an important role in keeping your gut flora in balance. These foods provide healthy bacteria as well as give you nutrients like B vitamins and amino acids that work to keep your immune system strong.
  • Probiotics help keep your gut strong as well. Probiotics are more concentrated than fermented foods in many cases, but sometimes aren’t as potent because we don’t know how long they’ve been in a capsule or what happened at the factory. They could be incredibly potent, or not so much. Your best bet is to find a company you trust or one that your health practitioner recommends. We like HealthForce as well as some of the physician only brands.
  • Avoid GMO foods. Jeffrey Smith explains a study where pesticide (BT) producing bacteria were found in the guts of a small sample of humans after they ingested GMO food that was engineered with that particular bug. Apparently, the DNA of the bacteria is so volatile it may be able to be picked up by healthy bacteria in your gut. As an expecting parent, the thought of this happening in mom’s tummy is unacceptable.
  • If you’re having gut issues, consider HCL. HCL will help you digest your food better, but it may also help keep your stomach acid low enough to kill harmful bacteria before they slip into your gut and colonize.
  • Take some enzymes. Enzymes help break down your food so it can be absorbed easily. Poorly digested foods causes inflammation in the gut — this then can lead to a weakened immune response which may not be able to fight off bad gut colonies. The easier it is for your gut, the less likely you’ll have issues with your flora.
  • Don’t stress. Seriously. Stress negatively affects gut flora. (Maybe it’s just like your family… who doesn’t want to be around you when you’re stressed either… LOL!)

If you incorporate some of these aspects (or all of them) into your routine, you’re on the right track to a healthy gut. And please don’t forget to use the resources of a good practitioner who can test and monitor your progress.

Your question of the day: What do you think about this science…

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Picture courtesy ymc_photos via

Dr. J. E. Williams


Dr. Williams is a pioneer in integrative and functional medicine, the author of six books, and a practicing clinician with over 100,000 patient visits. His areas of interest include longevity and viral immunity. Formerly from San Diego, he now resides in Sarasota, Florida and practices at the Florida Integrative Medical Center. He teaches at NOVA Southeastern University and Emperor’s College of Oriental Medicine.

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  1. Julia says:

    April, you beat me to it. 🙂 I was about to say the exact same thing. I’m currently doing the GAPS diet myself. Her book is great. I also have “Breaking the Vicious Cycle” by Elaine Gotchsall – not sure how to spell her name, but she teaches the specific carbo diet which is very similar to GAPS. These diets definitely work!

  2. Hello says:

    I really like these microbiome articles. They’re so fascinating. Thank you.

  3. Gen says:

    I wish I would have known these things (and more) when I had my daughter 27 years ago. She had colic so bad for several months and all the pediatrician wanted me to do was give her this horrid pink stuff.

  4. Hello says:

    Anyone with IBS or irritable bowel disease should be aware that HCL can exacerabate symptoms. And can be particularly dangerous if you are experiencing intestinal bleeding as it can increase bleeding or cause it for those with very sensitive bowels.

  5. George says:

    I am not a medical scientist, I never had the finances (nor did the family) to attend a university and absorb all the holy writ of the medical world. They should not find this discovery so surprising. The foetus is being prepared for life in the ouitside world, so it is logical that certain conditions be in place for that transition. As usual Kev has some sage advice for the woman in this time.

  6. Ray says:

    I also went along with Kev’s first tip (and all the other ones) about fermented foods and the Body Ecology sort of things until I read this: especially about the harmful effects of fermented food.
    Whilst I am not persuaded one way or the other by all these conflicting views, I would like to hear about the personal experiences of other readers. And perhaps further elaboration from Kev.

  7. Hello says:

    Are olives considered fermented? Anyways, I’ve been eating a lot of olives lately.

  8. sunshine says:

    i would like to see Ray’s info addressed also i have read alot about fermented foods not being so good for you too – what is that all about – totally against bodyecology diet and what we learned about creating good bacteria in the gut.

  9. Rebecca Cody says:

    Yes, Dr Natasha Campbell-McBride spoke at our Nutritional Therapy Association conference a couple of years ago and she did a lot of research on this, especially as it relates to autism. There are more neurons in the gut than in the brain, so it’s no wonder that an imbalance of gut bacteria causes behavior and personality problems.

    She credits Elaine Gottschall with her original diet, but she has since tweaked it and added the introductory phase to it.

    One of her suggestions was for women to put good quality (preferably homemade) plain, live yogurt of kiefer on their genital area after bathing and allow it to dry naturally, to seed the urinary tract and birth canal with healthy bacteria. She said this is what the women did when she was a little girl growing up in Russia. Every week they went to a communal bath house – women one night, men another – where they bathed and I think used it as a sauna. Yogurt was used this way as part of the weekly cleansing.

    She has developed a certification class for professionals who want to work with her diet to heal lots of problems, including autism. It all started with her son almost 20 years ago, when he was diagnosed as autistic. The doctor told her there was nothing she could do and he would only get worse. But, being a doctor, she went to the research literature and found a lot of answers. Her son shows no signs of autism now. She has healed many, many people over the years of ADD, ADHD, autism,dyslexia, etc.

    For more details, go to

  10. Anna21 says:

    Like Ray, I have also read some negative things about fermented foods, but I eat them now anyway!

    Oddly enough, probiotics & fermented foods used to make me feel nauseous but now when I eat them I feel great! I think it depends on one’s biochemistry. Some people thrive on fermented foods, yet others seem to have immune reactions to some strains of yeast (or something else) that are commonly in fermented foods. Or it could possibly a herxheimer reaction.

    Regardless of whether or not you choose to eat fermented foods, you still need to find a way to populate your gut with healthy flora.

    Also, you may find that it is not wise to follow someone else’s diet dogma. The right kind of diet for one person may be detrimental to another. It’s a good idea to experiment with different diets & foods (GAPS, vegetarian, vegan, gluten-free, fermented, etc.) until you find the right combination for your unique biochemistry.

    Listen to your body and heed kevin’s & Dr. William’s wise recommendations to get periodic blood tests to ensure you are on the right path.

  11. Carolyn says:

    ha – that’s the science project my kid passed on doing a decade ago with puppies. Glad to see someone picked up the ball. You might want to check out Dr Thomas Borody in Australia – he does fecal transfusions for refractory gut diseases.

  12. Ira Edwards says:

    Microbiome? A more specific term would be “endobiome.”
    This population of interacting populations acts as an organ of the body with many functions. Killing off some populations and excess growth of others is a factor in numerous pathologies. Neglect of this, and careless damage to the endobiome will continue until it is recognized as a vital and fragile organ of the body. Naming it will help with that recognition, which is why I call it the endobiome.
    Ira Edwards Medford, Oregon

  13. Gail says:

    Hi, just a query on one of Kevin’s last comments re HCL. You suggest adding HCL would keep stomach acid “low” enough to kill bad bacteria before entering the intestine. Was that a typo when you really meant “high”.?

  14. Jean Hart says:

    I agree strongly with the entire article!
    Good work Kevin & Dr. Williams!
    As for “bad” fermented foods, yes, there “may” be some
    out there, but just remember that Asians & Germans
    have eaten fermented foods for ages, and they’re not sick as a culture….!
    I keep my gut well-populated with pro-biotics and only
    catch a very mild cold about every 3-4 years. The gut
    is the first line of defense when it is well populated. If one gets a sore throat, that’s the first
    clue that they don’t have enough good gut flora to stop the virus or invading organism. The body will
    naturally “shunt” the invader out through loose bowels when the gut is well-populated!
    To Healthy Guts! 🙂

  15. Charlotte says:

    Gail: I’m pretty sure he meant keep the pH low enough 😉
    Personally, I usually feel pretty food when I eat fermented foods.

  16. Alice J. McDowell says:

    “Probiotics help keep your gut strong as well. Probiotics are more concentrated than fermented foods in many cases, but sometimes aren’t as potent because we don’t know how long they’ve been in a capsule or what happened at the factory.”

    Yeah right, just like this article ( said that fermented foods are really healthy specially in digestive track, cool information.

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