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Digestive Health Blog

The Microbiome? The Metabolome? What does it all mean?

Updated: Aug 29, 2022






One of the most exciting areas of digestive health is also one of the most confusing. And this confusion, like many topics, is used to drive the sales of wellness products and theories that range from solid, scientifically sound to great theories to bupkis. I think most of us realize the bazillion targeted marketing campaigns from wellness related products are often just fancy sales pitches. I see many half-truths used to create a semblance of authority. But I've also worked alongside providers from many educational backgrounds in nutrition and alternative/complementary health. And we have all begun to coalesce around the science of nutrition and organisms that live within our bodies.


At Pearl Health Partners Digestive Health, we have the benefit of continuing to work alongside many of these schools of thought. So, it is our intent to bring expertise as a resource to other local practitioners and patients, specifically regarding the well-founded science of the microbiome and metabolome. What is a microbiome? Generally speaking, we are referring to microorganisms of different types that have evolved to live within and on our bodies. I specialize in those residing in the digestive tract, as this is the realm of a gastroenterologist allopath. We have studied the theories, experiments and outcomes from the revelation of single-germ theory all the way through the complex ecosystems we are only beginning to understand now that involve bacteria, fungi, phage (virus) and archaea. There are trillions of these organisms in us, and it seems like just as many research studies!


Are these organisms "good" or "bad"? Well, this is complicated. In an era of single-germ theory, we thought we knew a pathogen and its harms. So, we'd kill it, and that worked! But there was actually an ecosystem present, and treatments had unintended impacts on it. So, now think about some of the initial wellness approaches to send a stool sample and grow organisms to see what shows up with the intent of using that information as if it informs about health: it really is just a test of how well things grow. And presuming what is present is "good" or "bad" didn't pan out as we looked for objective health issues to study this way (inflammatory bowel diseases for example). This makes sense if you think about it, such as presuming that Candida is "overgrown" and presuming that condition, should it exist, was related to health issues. Next, we tried to study the DNA or DNA representatives (16S) using super computers (that's how much genetic material is present in a stool sample) to better identify what is present in stool, and in what amounts. This was enlightening, in that we could more accurately see what organisms were present, in whom and in what setting. The excitement of this era was astronomical over the preceding decade.


But it turns out that showing who has genetic material in the "garden" doesn't really tell you what is happening within it. And attempts to treat and modify those DNA results have had mixed and confusing results. Take the use of a fecal transplant: (sounds gross but SCIENCE!) We found we could knock down pathogenic, toxin driven colitis (Clostridium difficile). But then, we found we could sterilize the fecal material and transplant with similar results. Why? Some think that the viruses (bacteriophage) found in the sterilized sample may infect and destroy some types of bacteria such as C. Diff. In other attempts to use a fecal transplant to cure ulcerative colitis we would see that the results were mixed, but if a patient had a transplant from one of a few individuals they were much more likely to have a response.


Again, this makes sense when you think about it for a few reasons. These organisms are living things, who "eat" and metabolize/alter molecules. They are sometimes dependent on the presence and actions of other organisms. A true ecosystem or garden or forest. Study of these metabolic phenomenon are termed the "metabolome", and we've known how to do molecular biology for decades. All of a sudden, the research has exploded. We are learning all sorts of pathways of metabolism and alteration of molecules. The implications are enormous, relating to nutrition, immune function, digestive health but also to many other physiologic systems outside of digestive health. Take the above Ulcerative Colitis condition: research last year showed that one particular microbe (Bacteroides vulgatus) produced proteases (enzymes that break down protein) which when blocked reduced disease severity. This makes a ton of sense! We're getting closer...


So, you can see how the best theories have evolved, but also provided fertile ground for half-truths, false promotion and wild health claims along the way. It's our job to bring you up to speed on the range of theories well-supported by science (small), great theories but w/o much evidence yet (large) and false claims not founded in science (enormous). In my next post, we'll dive into the links between nutrition and metabolome that are well-supported by science.

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