The human microbiome, explained: How bad science and junky diets gave rise to serious disease


We’re just as much bacteria as we are human. Some studies even suggest that our body contains more microbes than it does actual cells. In fact, when we combine the billions of these tiny organisms (also known as “germs”) living off our bodies, they add up to about the same weight as our brains.

By that logic, dousing the house in antibacterial spray or smothering hands with antibacterial sanitizer is — loosely speaking — a bit anti-human. More and more, scientists are realizing that the human microbiome is closely tied to our overall health, and killing swaths of microbes may not be doing us any favors.

“We’re too clean for our own good,” Dr. John Y. Kao, an associate professor of medicine at the University of Michigan, said in a phone interview. “There was this time where we turned on the TV and all you see is, ‘Oh, look at what’s on your keyboard — all these microbes, ew.’ Now, academia is really trying to counter that propaganda.”

Over the last decade, there has been an explosion of studies about microbes and human health in the science world. That’s partly because the last few years have unlocked advanced, lower-cost DNA-sequencing methods for scientists, experts say.

“It’s a really hot field right now. Research is pouring out about it,” Ginger Hultin, a registered dietician and the spokesperson for the Academy of Nutrition and Dietetics, said in a phone interview. “I think it’s a trend that’s here to stay, and for really good reason.”

“We’re too clean for our own good.” — Dr. John Y. Kao

To put it in the words of one 2013 study, we’re living in “a new era in medical science,” where the “forgotten organ” — our gut microbiota — is garnering serious interest.

Research has so far shown that a poor or altered human microbiome is associated with inflammatory bowel syndrome, chronic diarrhea, stomach pains, gas, bloating, food allergies and more. Some are researching the connections between the human microbiome and autism, Alzheimer’s disease, depression, our immune system or our metabolism. So no, it’s not just about problems in the bathroom.

“It’s everything. Everything has been somewhat directly or indirectly linked to the human microbiome — even cancers,” Dr. Kwang Sik Kim, a professor of pediatrics at the Johns Hopkins University School of Medicine, said in a phone interview. “This is an exciting time, and [this research] is extremely important — only 10% of the human body is human. The other 90% are microbes.”

Your microbiome is hugely important, so stop killing what’s living in it.

Part of the reason we should care about microbiomes is, technically speaking, we are one. Microbiomes are environments where tiny organisms called microbes live, the word “microbes” encapsulating bacteria, viruses, fungi and more.

Basically, our gut is a robust, highly individual world of living species. There are an estimated 5 million different genes in the average human microbiome, and our experiences as infants determine which bacteria get introduced to our guts.

“[This research] is extremely important: Only 10% of the human body is human. The other 90% are microbes.” — Dr. Kwang Sik Kim

“After our first year, [the microbiome] has pretty much been stabilized for life,” Kao said. “So what happens in that first year is really important.”

We’re all born sterile — without gut bacteria — and then our roster sheet of encountered microbes begin populating our bodies. “Whether you’re breastfed or not, what you eat and everything you come in contact with from then on makes your unique microbiome,” Hultin said.

Which may be why, as Kao previously mentioned, buying into the antibacterial dogma of the West may have given rise to diseases that aren’t as prevalent in other parts of the world. That idea is called the “hygiene hypothesis.”

“If you grow up in an environment when you’re little that has poor hygiene, your immune system actually turns out to be more robust,” he said. “You’re less likely to develop allergies, you’re less likely to develop inflammatory bowel disease … [your immune system] is more regulated when you grow up in an environment where you have dirtier surroundings. Your microbiome has seen more pathogens that train [the immune system] to be more healthier when the individual grows up.”

Your microbiome — and your health — may hinge on what you eat.

Much of the science on the human microbiome is still preliminary, partly because the field really only “caught on within the last five years,” Hultin said. And though many recent studies have provided key information on how gut bacteria affects the rest of the body, scientists and doctors aren’t necessarily sure how to apply it to their patients yet.

“The translation of the concept into practice for the public has not yet been clearly materialized,” Kim said. “That’s an important message for people to know.”

That said, research has unveiled a few widely accepted tidbits that make the human microbiome well worth our attention.

Having diverse gut bacteria is good. The opposite is probably bad.

“Generally, we would say that thousands of species are present in your gut. And if you maintain those diverse species in your gut, then you’re pretty healthy,” Kao said. “When we look at diseased states, that’s when diversity generally drops.”

Take Clostridium difficile colitis, which Kao called “the poster child for low diversity associated with disease,” as an example. It’s a type of infection that affected about half a million people across the U.S. in 2011 and it can cause a host of illnesses, including dehydration, kidney failure, holes in the large intestine and even death.

“When the diversity drops, you have overgrowth of these bacteria that are not normally overrepresented in the gut and they cause problems by producing toxins that break down the barrier in your gut,” he said. “It causes bacteria to translocate, develop inflammation and diarrhea.”

A common treatment for the disease is fecal transplantation (also known as bacteriotherapy). It’s exactly what it sounds like — transferring fecal matter from one person to another — but it often works, since it adds healthy microbes back into the gut.


We really need this bacteria to lead healthy lives. That means we need to feed them.

The microbes in our guts do a lot for us. They help us take energy from our food, produce amino acids and possibly fend off diabetes, cancer or dangerous toxins.

“We’ve known for a long time that gut bacteria make vitamins for us. They specifically create vitamin K and B12,” Hultin said. “That’s really amazing.”

It’s hard to argue otherwise. Vitamin K assists our body in clotting blood, and vitamin B12 is crucial for our metabolism. A lack of B12 can cause anemia, numbness and tingling or even poor balance. So yes, maintaining a healthy microbiome is important. The good news is that it may not be all that hard, either.

“If you want to maintain healthy diversity in your gut, you’ve got to feed [the microbes] and you’ve got to feed them well,” Kao said. He often uses the tagline, “Have you fed your microbiome today?”

The science points to advice we’ve all probably heard before — we need to eat lots of different fruits and vegetables, particularly for the plant fiber. That’s because these foods are sources of “prebiotics,” which help give rise to healthy bacteria called “probiotics.”

“Prebiotics feed the bacteria in the gut. They’re all plant-based, high-fiber foods,” Hultin said. “The richest in this type of prebiotic are things like onions, garlic, bananas, Jerusalem artichokes — those are actually sunchokes — and wheat bran and wheat flour.”

Probiotics have already had their 15 minutes of fame in the world of health trends, giving rise to foods like yogurt, kefir, kombucha, sauerkraut and kimchi. But the prebiotics found in plant fibers are essentially what keep those probiotics running — so, if you’re not getting your fruits and vegetables, you’re essentially starving the bacteria in your microbiome. That’s a big problem in the modern world, Kao said.

“In the old days of hunting and gathering, people averaged around 250 grams a day in fiber,” he said. “Now, we’re averaging 15 grams a day. It’s not enough. ... A slice of lettuce and tomato between hamburgers is just not going to do it.”

In the days of hunting and gathering, people averaged around 250 grams a day in fiber. “Now, we’re averaging 15 grams a day. It’s not enough.”

What the science doesn’t say

Businesses have, predictably, jumped on the microbiome bandwagon to sell Americans solutions. Cookbooks have wholesale packaged the idea into a sellable “microbiome diet,” while some companies advertise “microbiome purification shakes” or 30-day diet plans. Microbiome cosmetics have also surfaced.

“I think where the trendiness is getting a little bit out of control right now is people are making too far of a reach for where science is currently,” Hultin said. “I mean, there are companies out there right now looking at your microbiome and telling you what diet to eat, and there’s just not good research to back that up yet.”

What else might not check out

1. It’s probably not worth it to pay for a “diversity score.”

These days, people can purchase a gut check from companies. They’ll generally be given a diversity score that’ll compare their range of gut microbes to others who got tested. They can be expensive — tests on uBiome range from $89 to $399, though the more expensive kits also test other parts of the body such as the mouth or skin.

But even if the microbiome sequencing is accurate, is it worth the cost?

“I may get in trouble for saying this, but I’ll give my honest opinion: no,” Kao said. “We don’t know what to really do with that information at this point.”

2. Probiotic supplements might not change your microbiome.

Despite the probiotic supplement industry’s estimated $36.6 billion value, there isn’t enough hard evidence showing that they could dramatically improve the human microbiome, according to Hultin, Kao and Kim. In general, dietary supplements aren’t regulated by the FDA like drugs are.

“I don’t think there’s a study that shows that taking probiotics alone will increase your diversity,” Kao said. “We don’t know if the probiotics even live once you consume them … but there’s nothing wrong with taking them.”

3. The connections between the microbiome and weight loss are still rocky.

There appear to be links between gut microbes and obesity, but conclusions are still vague. Several studies on mice have pointed to connections between an undiverse gut microbiome and weight gain, but similar results “are remaining to be seen in people,” Kao said.

“With weight loss and weight gain, we’re just not there yet,” Hultin said. “Most of the research is being done on animal models, but it’s complicated to move from animal studies to human studies.”