A breakdown of bacterial species from your skin's microbiome. As a favor to

A breakdown of bacterial species from your skin’s microbiome. As a favor to pregnant women expectant fathers teenage boys on the internet everyone, this is the image I went with. Click to macrolaarggen (Ikean for embiggen).

Sometimes a headline will cause me to run through a series of reactions in rapid sequence. For example “Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health”:

Early studies show that swabbing a mother’s vagina and transferring it to her baby’s mouth, eyes and skin may stimulate microbiome development similarly to babies born naturally – and protect it from health issues later in life

I mean ick.

But take a step back. Not really. I tend to think of people like “Pig Pen” in Charlie Brown, shedding skin and bacteria into the environment. If we were to really think about each other’s microbiome, we might not have intimate contact with our significant other. Or any other animal. I always point out, when someone lets their dog lick them, that they (the dog) had probably just licked its rear, AKA dog-ass seeding. And no, a dog’s mouth is not cleaner than a human’s, unless your dog brushes and flosses with greater frequency than you.


What is birth but exposing the mouth, skin, and eyes of the baby to moms vaginal flora? So the ick factor is not really reasonable upon reflection, although anything that involves the eyes still gives me the willies.

The whole question of the microbiome and its relationship to health and disease is fascinating, but its application is closer to trying to construct a mnemonic memory circuit using stone-knives and bear-skins.

For the newborn, acquiring a microbiome is a complex and dynamic process with bacteria coming from exposure at birth, then from breastfeeding, then food, and finally becoming stable at about age 3. A C-section does result in a different microbiome in the baby, and is associated (with the usual association/causation caveat) with a variety of diseases later in life. But the microbiome differences between normal and C-section birth is gone in a year.

I have to admit I have always been enamored of the hygiene hypothesis and I find such speculation interesting, but not ready for prime time. Certainly I would never write a microbiome diet book.

And that is presuming that Mom’s microbiome, with all the issues related to what constitutes a ‘correct’ microbiome, is in fact the correct one for the child.

What is a normal microbiome and on what part of the body? Does diet and hygiene lead to an altered microbiome? Interesting studies suggest that people with no contact with the modern world have more complex microbiomes:

We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group.

And depressingly:

Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes.

But Yanomami evolution has been on a separate track than the West, so one would expect a different microbiome. So a different microbiome may not be a better microbiome. I wonder as we are evolving towards those massive craniums so popular in science fiction shows if we will become dependent on C-sections. We must if our children will be born with the same proportionately larger skulls. Or will there be other mutations that will make conception and birth of massive headed babies possible? Now there is a mental picture I don’t need.

In my experience, speculation is fun

It is interesting to speculate on how diet in the past and present has altered our microbiome. My favorite example is dental cavities. Cavities started showing up in humans about 15,000 years ago, although evidently Neanderthals were not good at flossing either. The theory is that a farming life lead to increase in carbohydrate intake which lead to more oral Streptococcus mutans, the leading bacteria in causing human cavities.

The issue of the microbiome and weight gain and loss is also interesting. Low levels of antibiotics in animal feed promotes growth, probably in part by altering the animal gut flora to a fat-promoting microbiome. How much the human microbiome is involved with the regulation of weight is uncertain, but most of the information suggests at least a part. I especially like the case of the patient with C. difficile who had a stool transplant from an obese donor and proceeded to gain 40 lbs. So a bit more plausible than taking on the characteristics of the person who donated your heart. But I would never get a hand transplant from a murderer. That is asking for trouble.

The data on antibiotics use and obesity in children is variable, but some antibiotic regimens are more likely to result in weight gain, probably by altering the microbiome, but then human genetics may determine the microbiome rather than the other way around. So maybe the host determines whether or not there is an obesity-promoting microbiome.

How could this go horribly, horribly wrong?

The assumption of these experiments is that altering a microbiome is only beneficial, but microbiomes do have the potential for harm.

One grumpy doc notes that the child could be at risk for acquiring sexually transmitted or other disease from vaginal transfer, but then would that not be the case for regular births as well? That is why we do prenatal screening, so I would not fret overly much about that.

There are a number of infections spread by the fecal-oral route and there are bacteria, such as B. fragilis and others, that might promote bowel and other GI cancers. People seem to assume there is a microbiome, perhaps from Eden, that has not known sin and search for it. I suspect that the idea that no good deed goes unpunished will apply here as well, that a microbiome that has benefits in one area will have downsides in another.

And some take it to extremes: DYI microbiome transplant. With an uncertain diagnosis of his GI problems (irritable bowel or inflammatory bowel disease?) one person tried, in the most half-assed way imaginable, to eradicate his own microbiome and substitute another. It is right up there with DIY surgery.

So vaginal transfer is an interesting and perhaps plausible idea, but far from being ready for prime time. But I would choose a microbiome from a thin person with no infections or family history of cancer for my transfer. And if you give your child your microbiome, you are banned for life from saying vaccines are too many too soon.

But our understanding of the complexity of the interactions of the microbiome and the human genome is in its infancy, and the wise person leaves well enough alone.



Posted by Mark Crislip

Mark Crislip, MD has been a practicing Infectious Disease specialist in Portland, Oregon, since 1990. He has been voted a US News and World Report best US doctor, best ID doctor in Portland Magazine multiple times, has multiple teaching awards and, most importantly,  the ‘Attending Most Likely To Tell It Like It Is’ by the medical residents at his hospital. His multi-media empire can be found at edgydoc.com.