The Human Biome and What We Don’t know

My old mentor, a well known functional medicine physician, used to always conclude his talks with a quote by Vaclav Havel:  “Keep the company of those who seek the truth – run from those who have found it.”   I think about that concept every single day, especially when I read any kind of definitive statement about the biome: i.e.  “it’s the chemicals in our food,” or “the rates of obesity continue to grow because people eat too much.”  I’ve pointed out before on this blog that nothing having to do with the human gut biome is simple and the causes of these illnesses are multifactorial.  We have barely started to scrape the surface of a system that involves trillions of organisms, all of which interact with each other, with our bodies, with our food, etc.,  sometimes in ways we have not as yet even discovered, let alone understood.

In this vein, I loved a recent article I read on Medical Express summarizing some of the new biome research going on at the University of Southern California.[i]  It starts by telling the story of a woman – a friend of one of the researchers – with gastrointestinal issues, who tried 3 different kinds of yogurts, looking for relief.  One had worked wonders for a friend of hers…but in her, it caused constipation.  The second caused diarrhea. The third made her feel great.  All the yogurts contained lactobacillus.  Why she should respond so very differently to each, and so very differently from her friend – we have no clue at the moment.   As the article says, “The microbiome is a complex and dynamic system – and as unique to each individual as a fingerprint.”  (I’d be willing to bet every last one of you reading this post has had this exact experience, in some form or another.   You do great on something, a food, a probiotic, a prebiotic, etc. which turns out to be awful for someone else you know.)

The article goes on to discuss both the promise of probiotics (and manipulation of the microbiome)…and the incredible difficulty we’re going to have reaching that promised land.

For example, Dr. James Boedicker of USC, has is working on a mathematical model “…to predict what happens when different species commingle.”  He points out that you can’t just study each species individually, as each species affects every other species in its vicinity.  His group measured the metabolic output of 4 individual species of bacteria:  “If living together has no effect…then the overall metabolic rate would simply be the average of each species’ individual rate.”  On the contrary though, they found that the overall metabolic output was markedly higher than that average.  That is, living together caused enormous changes in how these bacteria behave.

The importance of this kind of finding cannot be understated.  As this article points out, figuring all this out – how the various species affect each other – could explain everything from different responses to probiotics, to different responses to drugs and chemotherapy, and can help us predict what will work and won’t work for each person as the individual he or she is.

And of course, most of the current research concerns only the bacterial microbiome.  We literally know next-to-nothing about the other –omes of the gut (the virome, the mycobiome, the macrobiome, etc.), let alone how all these various organisms affect one another.

Too boot, none of this takes into account the interactions between the organisms of the biome and the food we eat.  Just a week ago or so, I wrote about another new study on personalized nutrition:  “As these researchers point out, we currently have very little information on nutrients that affect gut bacteria. Really it comes as no surprise that there was little consistency in microbiome changes between people.  That is, microbiome responses to food were completely individualized:  I eat a banana, you eat a banana – our gut bacteria respond completely differently.”

As another USC researcher says, “We can determine the microbiome of anything pretty quickly, but we don’t know what it means.”  That pretty much sums things up.



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