The key to good health lives in your gut

Plus, major revelations from the world’s largest microbiome study

This month marks nine years since my book Boost Your Health with Bacteria was published. It was one of the first books to focus on the importance of the human microbiome, and it shared a message I’ve been delivering for years…

The microbiome, the environment in which your gut bacteria thrive, serves as the foundation to good health. And a compromised microbiome leads to a whole host of chronic diseases.

At the time, I hoped the book would help the conventional medical community embrace the importance of the microbiome and pay serious mind to gut health. Little did I know, thousands of people around the world would be enthusiastically analyzing their own microbiomes less than a decade later. But that’s what’s happening, courtesy of the American Gut Project.

This ongoing, crowdsourced project, which began in November 2012, has spawned the largest published study to date on the human microbiome. The new research shows how key factors like diet, antibiotic use, and the gut-brain axis, can influence the microbial and molecular makeup of your gut.1

So far, the findings are fascinating, and we can glean quite a bit from them. But first, let me give you a little background and tell you how this monumental study came to be.

Crowdsourcing the microbiome

The project was started by three researchers at the University of California San Diego School of Medicine. Their goal was to learn more about the bacteria that live in the human gut—what type, how many, and how they’re influenced by diet, lifestyle, and disease.

The American Gut Project is a follow-up to the Human Microbiome Project—a five-year NIH initiative started in 2008 that identified and characterized gut microorganisms and their role in human health and disease. The major difference with this project is that instead of studying the microbiome in a lab, it enlists real, everyday people from all over the world.

Essentially, American Gut Project participants agree to have their microbiome data anonymously added to a public reference database. And as the largest public database for the microbiome, it may be a catalyst for future studies on the human gut and how it influences our health.

As of mid-2017, more than 11,000 people from 45 countries have collected their own fecal, oral, or skin swabs and mailed them back to the researchers. Participants also answered surveys about their health status, disease history, lifestyle, and diet. In return, they got a personalized report analyzing their microbiome.

The researchers believe that the success of their project shows citizen science can be a viable tool, and a good way to engage the public in medical research. And I agree. Especially when it comes to something as diverse and variable as the human microbiome.

In fact, researchers said they were “blown away” by the microbial diversity of the participants. And although microbiomes are extremely complex and different, they did note some common trends.

Dietary diversity

The more vegetables, fruits, and herbs you eat, the more diverse your microbiome becomes. The researchers found that people who ate more than 30 different plant types per week had substantially more diverse microbiomes compared to those who ate fewer than 10 plant types a week.

Researchers have not yet concluded if increasing the diversity in your microbiome can directly benefit your health. But considering there are over 1 trillion types of bacteria in your gut, adding to the levels of “good” bacteria with healthy food seems like a no-brainer.

I realize that eating 30 different plants a week sounds like a lot. But think about it—you could pack a third or even half of that into one big salad filled with a variety of leafy greens, veggies, legumes, nuts, and even fruits. And you’d enjoy all of the other health benefits of these fantastic foods.

Avoid antibiotics

The researchers also found that people who took antibiotics in the month before they sent in their sample had less diverse microbiomes than those who hadn’t had an antibiotic for a year. No surprise here. Antibiotics kill off all of the bacteria in your gut—good and bad.

I recommend you avoid antibiotics unless absolutely necessary. This includes not only prescription pills, but also the antibiotics given to conventionally raised livestock. Organic meat is antibiotic-free and the way to go. In order to be certified organic, farms and ranches must meet the following standards to be certifiably organic for poultry, cattle, and pigs:

• They must be raised organically on certified organic land
• They must be fed certified organic feed
• No antibiotics or added growth hormones are permitted
• They must have outdoor access

Overall, I recommend eating organic foods whenever possible.

And if down the line you do need to take antibiotics, be sure to boost your intake of high-quality, multiple-strain probiotics afterwards. This helps the good bacteria in your gut repopulate faster. My stand-by brand is Dr. Ohhira’s, which contains 12 probiotic strains and is backed by over 25 years of research. For more information, visit my website,

The gut-brain connection

Additionally, the researchers looked at the microbiomes of people diagnosed with  mental health issues like depression, schizophrenia, post-traumatic stress disorder, or bipolar disorder. Their microbiomes were compared to people who didn’t have mental health disorders, but did have common characteristics such as body mass index, age, gender, and country.

Researchers found that demographics didn’t really matter—people with mental disorders had similar microbiomes across continents, age groups, genders, and more. This was particularly true for people with depression.

There’s been plenty of other research on the gut-brain axis—particularly in regard to depression. As much as 95 percent of the feel-good chemical serotonin is produced in your gut rather than your brain… meaning the healthier your microbiome, the healthier you may also be mentally.

This opens up exciting possibilities. For instance, we may soon discover that simple dietary changes can help thwart depression—with gut-friendly plants that nourish the microbiome. We already know probiotics can play a pivotal role in improving your mood, as I detailed in my July 2015 Reality Health Check e-letter (“When it comes to brain health, go with your gut”).2 To revisit this article, simply type the title into the top right search bar via

Looking to the future

Researchers are still collecting and analyzing samples in an effort to determine concrete findings in regard to our microbiomes and exactly how they are affected by diet, exercise, lifestyle, and a number of other factors.

One of the study’s co-founders, Dr. Rob Knight, said, “The human microbiome is complex, but the more samples we get, the sooner we will be able to unravel the many ways the microbiome is associated with various health and disease states.”

Knight continued, “The American Gut Project is dynamic, with samples arriving from around the world daily.”

We want to eventually go beyond making maps of the microbiome to making a microbiome GPS that tells you not just where you are on that map, but where you want to go and what to do in order to get there in terms of diet, lifestyle or medications.”2

If you’d like to participate or learn more about what’s going on inside your microbiome, visit the study’s official website, Sample kits are $99 and results take about three months to process.

If you’d like to read more of my extensive coverage on the microbiome, probiotics, and overall gut health, enter “microbiome” or “probiotics” into the search bar at

Three simple ways to support gut health

Along with eating more plants and avoiding antibiotics, you can also keep your microbiome in top shape by following my three easy, but critical, steps:

1. Avoid sugar at all costs. Sugar can destroy bacteria in your gut faster than antibiotics do.

2.Fill up on lean protein and healthy fats, and consider incorporating natural probiotic foods like sauerkraut, kimchi, or fermented vegetables into your diet.

3. Take a high-quality, multi-strain probiotic like Dr. Ohhira’s. Take one capsule, twice a day.


1“American Gut: an Open Platform for Citizen Science Microbiome Research.” mSystems, 2018; 3 (3): e00031-18.

2“First Major Results of ‘American Gut Project’ Published.” Duke Anesthesiology. 2018, May 15.