GUT CHECK: THE TRUTH ABOUT YOUR MICROBIOME AND DISEASE
Sorting fact from fiction in the race to heal disease through gut health
DR. BOBBY DUBOIS
MAY 2025
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We’ve all seen the headlines—“Fix your gut and fix your life,” “The microbiome controls everything from your mood to your metabolism.” The claims are sweeping, the promises grand. But what does the evidence actually say? Is it truly the fountain of health, or are we just not sure yet?
As someone who’s spent a career in science and medicine, I usually stick to topics with clear evidence and answers—ways to improve sleep, how exercise lowers heart disease risk, the evidence around coffee consumption, and why the “eight glasses of water a day” rule lacks solid backing (if interested, listen to these podcast episodes here.). But the evidence about the microbiome is promising, but for most diseases, inconclusive.
Let’s walk through the core questions: Is the microbiome important? Can it change based on what we do or eat? Do those changes cause disease, or are they just along for the ride? And critically, can treating the microbiome treat disease?
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A Lot of Buzz, But Are We There Yet?
There are more bacterial cells in our body than human cells—at least according to studies like this one from PLoS Biology (link). That’s a big deal. Even more stunning, the genetic material from our microbiome may outnumber our own DNA by 150 times. This tiny universe in our gut, mouth, skin, and even lungs plays a role in digestion, immunity, and vitamin production. The microbiome helps us digest tough fibers, protects us from pathogens (Nature article), and synthesizes key vitamins like B and K (NIH overview).
But there is no ideal microbiome—no magic number or type of bacteria we all should aim for. It varies from person to person and even shifts with age. That’s part of what makes it so hard to study.
The One Slam Dunk: C. Difficile Colitis
The best evidence for microbiome-based therapy? Clostridium difficile infections. After a course of strong antibiotics, some patients’ guts are taken over by this dangerous bacteria. Mortality rates historically ranged from 6–30%. Enter fecal transplants—yes, transferring stool from a healthy person to a sick one. It sounds odd, but it's remarkably effective, with success rates of 80–90% according to this PubMed review (link). Here, resetting the microbiome isn’t just plausible—it’s life-saving.
Microbiome
The microbiome is the community of trillions of microbes—like bacteria, viruses, and fungi—that live in and on the human body, mainly in the gut.
Mice, Microbiomes, and Weight Loss Claims
Here’s where the hype starts to outpace the science. A popular set of studies showed that giving gut bacteria from obese mice to skinny ones made the latter gain weight (link). Even giving bacteria from obese humans to mice had similar effects (link). But when researchers tried fecal transplants from lean people to obese humans? No change in weight (study). Exciting animal data, yes—but not yet human-proven. Mice are not humans, and the mice they studied where genetically altered and raised in very artificial ways.
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What About Inflammation, Autoimmunity, and Chronic Illness?
This is where things get murkier. In inflammatory diseases like ulcerative colitis and Crohn’s, microbiomes often look disrupted. A meta-analysis of probiotic use found no benefit for Crohn’s, but some promise for ulcerative colitis (study). Other conditions—multiple sclerosis (link), rheumatoid arthritis (link), and even diabetes (link)—show links between microbiome shifts and disease, but again, it’s not clear what’s cause and what’s effect.
A major challenge? Probiotic treatments are not standardized. One study may use one strain, another a different mix, making comparisons difficult. In diabetes, a systematic review of 33 trials showed some improvement in blood sugar or lipids—but no consistent pattern, and none replaced traditional medications like metformin (review).
Is Gut Health the Key to Everything?
Unpacking the bold claims and limited science behind the microbiome movement.
So, Should You “Fix” Your Gut?
There’s little downside to increasing fiber intake, eating fermented foods like yogurt or sauerkraut, and steering clear of unnecessary antibiotics. These actions might not reverse autoimmune disease or obesity, but they support overall gut health and can’t hurt.
But no, I don’t rush out to buy expensive probiotic supplements. I do enjoy my homemade yogurt and a spoonful of sauerkraut now and then—but not because I think it’s a miracle cure.
If you wish to listen to my podcast on this topic, here is a link.
