Fecal yogurt and more microbiome musings

Yesterday I was kind of harsh on the microbiome researchers whose work has been so widely discussed in the NY Times and elsewhere. I went so far as to call it “fatally flawed” because the researchers picked their research subjects for “normalcy” and went so far as to manipulate the subjects by requiring that 80% of them get dental work to remove bacteria from their mouths before said subjects were analyzed. I believe this was a mistake in those studies, but I also think “fatally flawed” was probably a bit over the top on my part.

Perhaps more importantly, I believe that these microbiome studies raise a dizzying array of interesting questions and point to future endeavors related to, well, germs.

Maybe…in fact probably a lot of germs are our friends!

One possibility of this way of thinking is so-called “fecal transplants”.

Now I’m not that squeamish, but I was always of the feeling that the mouth and feces should be kept separate.

Very far apart in fact, right?fecal transplant

Even so, scientists are already doing fecal transplants and studying the results based on the notion that the microbiomes of some healthy people might colonize the gut of other less healthy people making them healthier….perhaps less prone to GI diseases and maybe even skinnier!

It’s an astonishing paradox when you think about the concept of germs as medicines!

Most of us have probably seen the commercials nowadays for yogurts that have all kinds of beneficial bacteria in them and that’s now extended to supplements whereby consumers swallow pills intended quite literally to “infect” or to use a friendlier word “colonize” their guts with specific germs that are supposed to provide healthful outcomes.

A logical future prediction is yogurt with fecal transplants in it.

This may not be as far fetched as it may sound to some.

I also find it fascinating to think that human beings actually consist of a combination of human cells and equal or even greater #s of bacteria living inside and on us. I believe this is a true case of symbiosis, but we know relatively little how these bacteria that are our own symbiots.

A related, equally interesting area is the “virome” of the human body consisting of actual viral particles in our bodies, but also massive amounts of viral DNA in our genomes. What’s the scoop there?

Stayed tuned and pass the yogurt! No feces for at least for now please though.

A version of this piece was first published by me at Science2.0

1 Comment


  1. I ran into this concept when writing about our relationship with bacteria a few years ago. One doctor, Michael Kennedy, told me what he had seen: http://nctim.es/fbacteria

    Kennedy said he has worked with doctors who’d go to unusual means to replace the normal flora in patients who had their beneficial bacteria killed by broad-spectrum antibiotics.

    One doctor would take stool samples from incoming patients who had not taken antibiotics, and use them to culture E. coli populations in a kind of broth.

    “He would give this to patients whose colons were populated with highly resistive strains of bacteria, because everything else had been killed by antibiotics. He would mix this broth with the sensitive E. coli in a kind of milk malt to hide that he was giving them something awful,” Kennedy said.

    In about three days, the normal population of E. coli would return.

    “He had a theory that antibiotic resistance is an acquired characteristic, not a natural state, and the antibiotic-resistant bacteria had given up something,” Kennedy said. In other words, the antibiotic-sensitive bacteria were better adapted to living in an antibiotic-free environment, so they would crowd out the resistant bacteria.

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