A new baby, a new microbiome

by Christina on August 10, 2016

“During infancy the microbial equivalent of a land grab is occurring in the gut. Species that are successful in establishing early can persist for decades, and perhaps throughout life.” ~From “The Good Gut” by Justin and Erica Sonnenburg

I’ve been thinking a lot about how to optimize my newborn’s gut microbiome.

Max 1 weekI thought about it a bit after baby #1, and there has been a lot more talk about the gut microbiome in the past couple of years. For example this article from last year, and the Sonnenburg’s excellent book The Good Gut that also came out last year.

We now know that one’s gut microbiome is really important for long-term health, specifically for inflammatory bowel disease, obesity, type 2 diabetes, but also much more that continues to be discovered.

We also know that creating the optimal gut bacteria actually starts in the womb and at birth, and this time likely has lifelong effects.

In terms of specifics, this is what we know for optimizing your newborn’s gut bacteria:

  1. Deliver vaginally (if possible): this first exposes the infant to mom’s vaginal bacteria, which then colonizes the gut. In contrast, a c-section birth exposes the baby to different skin flora. If vaginal birth is not possible, one day we may consider a providing baby with vaginal swab after delivery (see more on this below). As this article points out:

    During vaginal delivery, facultative anaerobic species such as Escherichia coli, Staphylococcus, and Streptococcus colonize the infant gut and produce anaerobic environs in the first few days of life that allow strict anaerobes like Bacteroides and Bifidobacterium spp. to thrive.

  1. Breastfeed: Breast milk contain important bacteria that colonize the gut, as well as prebiotics called human milk oligosaccharides (HMOs) that help optimal bacteria grow in the infant gut. Even if full time breast feeding is not possible, even a little can go a long way. As the Sonnenburgs say in The Good Gut: 

    “Breast milk, and specifically the quintessential microbiotia accessible carbohydrate (MAC) human milk oligosaccharides, is a microbiota superfood.”

  2. Avoid antibiotics: Antibiotics kill both good and bad bacteria, damaging the diversity of the gut flora. Doctors are learning the dangers of antibiotic use and we are really trying to limit their use to the times they are truly needed (and there are certainly those times).
  3. Give probiotics: There may be some benefit to giving infant probiotics, and once babies start on solids they can be fed both prebiotic and probiotic foods.

I’m sure there will be a lot more that’ll be coming out on all this. I also wonder if doing a vaginal swab colonization after c-sections will start happening more (I’ve already had a few patients ask about this).

{ 5 comments… read them below or add one }

Emily August 11, 2016 at 2:55 am

Wow so interesting about the vaginal swab! It makes sense, and to me it doesn’t seem like it would do harm (since most babies are highly exposed to that from vaginal birthing anyways!). And, whats really stopping anyone from doing this as a do-it-yourself if the provider doesnt want to do it?

My roommate (also a medical student!) keeps me up to date on gut biome research, we really wanted to go to a conference in DC this year but it was too expensive. Maybe someday! Still wondering about my question on your last post. I am a 4th year student and really struggling to decide between EM and FM for future specialty. I think I would miss the continuity of care in FM if I did EM, but I;m not 100% sold yet. What are your thoughts on balancing your own personal wellness and family live with a career in Fm?


Christina August 11, 2016 at 6:39 pm

Hi Emily!
It’s really nice to hear from you and sorry for the delay on your last question (things have been a bit busy!!)! EM vs FM is a tough decision – both are great. I liked EM for a lot of reasons, but overall felt really strongly about having more long-term relationships with patients and focusing on preventive issues/lifestyle change/nutrition. There’s only so much you can do in those areas in EM. I thought FM was ideal because you can still definitely do a lot of urgent care type work, a lot of procedures, but have the more holistic and long term relationship with people. If you find the right job I think it’s definitely possible to have a balanced life in FM. A lot of my colleagues are able to work part time. For me EM also had the drawback of shiftwork/night shifts and a changing schedule, and I’m such a person of routine (and I hate working nights) that would be hard for me. Keep me updated and let me know what other questions you might have!


Min August 11, 2016 at 1:21 pm

Hi! Great post. I have not commented in years, and now you have 2 kids. I am an Integrative Doctor and Asshtangi from Sydney. If you are attending the IFM gut conference in Chicago in October, I will see you there!


Christina August 11, 2016 at 6:35 pm

Hi Min! Great to hear from you. Where are you practicing these days? I wish I could make it to the IFM conference but unfortunately not this year – hopefully one soon.


Min August 11, 2016 at 8:37 pm

Hi Christina
Still in Sydney (Bondi). Keep those posts coming! Take good care. Amazingly a couple of paeds are give probiotics to prem babies to prevent necrotising enterocolitis.
Take care


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