A no-bullshit guide to caring for your gut microbiome

Written By Katharine Schulz

There’s a lot of hype about the gut microbiome these days. The advent of cheap DNA sequencing has led to an explosion of microbiome research, which is uncovering manifold ways that our gut microbes impact our health. It has also led to the proliferation of microbiome startups, many of which are puffing out overblown claims and capitalizing on the desperation of the chronically ill. The thing is, while gut microbiome science is unbelievably shiny and promising, it’s still in its infancy and it remains riddled with unknowns. 

Hype aside, the research has made it abundantly clear that our gut microbiome is worthy of our awe and care. I’m writing this post because I want you to know how to care for it and I want you to stop wasting your money on snake oil. 

WHY IT MATTERS 

The term “gut microbiome” refers to the trillions of microbes (i.e., bacteria, fungi, viruses, protozoa) that inhabit our intestines. We have a symbiotic relationship with these microbes: we provide them with a hospitable environment to call home, and they provide us with superhuman powers. For example, they extract nutrients from our food that we otherwise couldn’t access, synthesize health-promoting metabolites (e.g., vitamins, short-chain fatty acids), protect us from pathogens, and train our immune systems to distinguish between harmful and harmless substances.

It may sound like science fiction, but our gut microbes influence our brain function and behavior. They communicate with nerves in the gut-brain axis (i.e., a superhighway of nerves that links our guts to our brains) by producing neurotransmitters, like the “happiness hormones” serotonin and dopamine. Research suggests that our microbes may use this line of communication with the brain to influence what we eat. Different microbes prefer different foods, so if they release neurotransmitters that make us feel real good after we eat their favorite food (e.g., sugar), they can train us to eat more of it.

There are well established links between the gut microbiome and a variety of diseases, including obesity, depression, anxiety, allergies, and autism. Often, it’s unclear whether alterations in the microbiome are a cause or consequence of disease. However, fecal microbiota transplantation (i.e., poop transplant) experiments in mice suggest that changes to the microbiome are a causative factor in at least some cases. For instance, if mice get a poop transplant from an obese person, they gain weight. If they get a poop transplant from a depressed person, they start acting depressed. And if they get a poop transplant from an autistic person, they start acting autistic (e.g., engage in more repetitive behavior and less communication).

The gut microbiome is an ecosystem, and ecosystems are considered “healthy” if they contain a rich diversity of organisms that exist in balance with one another. When the balance in the gut microbiome gets thrown off, this is referred to as “dysbiosis”. It’s like when an algae bloom takes over a lake. Dysbiosis can damage the lining of the gut and cause “leaky gut”, a condition in which gaps in the intestinal lining allow foreign substances to leak into the body where they can trigger an immune response and inflammation. Chronic leaky gut puts the body at risk for various inflammatory and autoimmune diseases.  

HOW TO CARE FOR IT

As of April 2025, the only tried-and-true way to improve your gut microbiome is to improve your lifestyle. Healthy diet, good sleep, and exercise have all been shown to boost microbiome diversity and increase the abundance of “beneficial” microbes. The power of diet is particularly strong: dietary changes can measurably affect the microbiome in less than 24 hours. To eat for your microbes, you’ll want to: 

  1. Pack in fiber - “Fiber” is any part of a plant that our bodies can’t completely break down. Our microbes feed on fiber and produce byproducts, like short chain fatty acids, that keep the lining of our guts healthy (i.e., not leaky). Fiber isn’t just one thing, and different microbes prefer different types of fiber. So, to support a healthy/diverse gut ecosystem, it’s essential that we not only eat a lot of fiber, but that we also eat a diversity of different kinds of fiber. This is best accomplished by eating a diversity of different plants (i.e., vegetables, legumes, nuts, seeds, whole grains, fruits, herbs). Experts recommend that we eat at least 30 different plants each week (based on this study).

  2. Toss the toxins - Research has shown that a variety of diets (e.g., the Mediterranean diet, plant-based diets) can support a healthy microbiome. The Western diet (aka the Standard American Diet) is not one of them; it’s been shown to reduce microbiome diversity and cause dysbiosis. The problem with the Western diet is that it's low in fiber and high in toxic shit that ravages the microbiome, like sugar, red/processed meat, pesticides, and additives (e.g., emulsifiers, preservatives, artificial sweeteners, food dyes). One of the most effective ways to reduce the toxic shit in your diet is to cut out ultra-processed foods. To do so, start reading nutrition labels: if a product contains ingredients that you wouldn’t find in a kitchen, don’t eat it. You could also consider going organic, getting off sugar, and/or reducing your red/processed meat consumption.    

Of course, food isn’t the only potentially toxic substance that we put in our mouths. Pharmaceuticals are another biggie. Antibiotics are notorious for damaging the gut microbiome, but they’re not the only drugs that cause problems. A 2018 study that looked at the effect of 923 non-antibiotic drugs on gut microbes found that over 25% of them suppressed the growth of “beneficial” bacteria. NSAIDs (e.g., ibuprofen, aspirin) are a noteworthy example. People pop ‘em like candy, but research has shown that they damage the intestinal lining and can cause dysbiosis and leaky gut. 

DON’T WASTE YOUR $

The fact that microbiome science is still in its infancy hasn’t stopped eager startups from rolling out a variety of microbiome-based products. Unfortunately, most of these products aren’t ready for prime time yet and the only thing they’re going to help you do is empty your wallet. We know that diversity is key for ecosystem health, but beyond that, we still don’t know what makes a gut microbiome “healthy”. 

The issue is that ecosystems are inherently complex. In a healthy ecosystem, there are a variety of organisms that fill each ecological role. For example, a healthy forest will contain multiple predators that subsist on rodents (e.g., owls, snakes, and foxes). This “functional redundancy” ensures that ecosystems remain balanced even if a species is wiped out. The same is true in the gut: there are many different microbes that perform similar/overlapping roles. To further complicate matters, individual microbes can take on different roles in different environments, and a microbe that’s beneficial to us in one environment can be pathogenic in another. 

Due to this complexity, we can’t say that a person’s microbiome is healthy or unhealthy based on the presence or absence of individual microbes. This is why today’s at-home microbiome tests, which use DNA sequencing to detect specific microbes present in the gut, rarely provide helpful/actionable information. These tests are neither legit (i.e., they’re not evidence-based) nor reliable. Reviewers have found that, if you test the same poop sample using several different kits, each kit may give you a different result.     

Probiotics are microbes that people ingest in the name of health. While research supports their use for a couple specific indications (e.g., preventing antibiotic-induced diarrhea), taking a random probiotic doesn’t do much for most people. And when we introduce foreign microbes into the gut ecosystem, we run the risk of throwing off its delicate equilibrium. So the disappointing truth is that, until we have a more nuanced understanding of the gut microbiome, taking probiotics is unlikely to help you and it might even harm you. 

Probiotics are regulated very loosely in the US and they often don’t contain what they say they do on the bottle. So if you insist on taking them despite their apparent lack of efficacy, be sure to do your research and find a trustworthy brand. Better yet, just stick with fermented foods (e.g., sauerkraut, kimchi, miso, yogurt, kefir). Unlike probiotics, fermented foods have stood the test of time (humans have been eating them for almost 10,000 years), and they’re guaranteed to contain live microbes. Studies have shown that fermented foods reliably reduce inflammation and increase gut microbiome diversity.   

CONCLUSION

To summarize: Our gut microbes give us superhuman powers and influence our mood, behavior, and susceptibility to disease. The best way to care for them is to adopt a healthy lifestyle: think fiber in, toxins out. Save the money that you’d otherwise blow on bogus products, like microbiome tests and probiotics, and use it to fill your fridge with organic vegetables and fermented foods.    

The gut microbiome is a fascinating new frontier. It challenges our notion of being a distinct individual and reminds us that all aspects of our health are intricately connected. For anyone who wants more gut stuff, I recommend the following resources:

Katharine Schulz
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