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A Look at the Trillions of Microorganisms That Live in and on You

Scientists are continuing to learn what the microbiome does for our health, and how certain diseases and disorders are associated with changes in your microbes.
gut bacteria
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The fact that I can regularly find (and eat) probiotic cauliflower cheesy puffs might reveal that we’ve all gotten a touch microbiome-obsessed. Grocery stores sell probiotic chai tea, probiotic chia seeds, probiotic energy bars, and probiotic coffee, not to mention the booming kombucha market. I too have fallen prey to taking out my wallet for every nutrition label that reads bacillus.

That’s because there’s good reason to be excited about the microbiome, or the trillions of microorganisms that live in and on you. We now know that these microbes are crucially important to all facets of health. And scientists are continuing to learn about what these microbes do for us, and how certain diseases and disorders are associated with changes in their populations.


Still, when a field of science gets so trendy so fast, there’s a lot of hype to sift through. I talked to experts and asked them my burning questions about microbiome basics, probiotics, what we know about the microbiome and disease, and what the best diet is to feed our bugs—is it cheesy puffs or something else?

What exactly is the microbiome and what does it do?

Your microbiome is the community of microbes that live in and on you. They’re in your bowel, on your skin, your lungs, your genital tract and your bladder. Some are bacteria, some are viruses, and some fungi. All together, they’re called either the microbiome or microbiota. You can think of the microbiome as an ecosystem that lives in an environment called “you.”

Our microbiomes aren’t just passive guests, they help us out in immeasurable ways.

One, is that they help us digest our food, says Suzanne Devkota, the director of Microbiome Research at Cedars-Sinai Medical Center in LA. There are many things that we eat that our bodies don’t have the enzymes to break down, like plant matter. “If you didn't have gut bacteria, you could not be a vegetarian,” she tells me. “You would be essentially pooping out everything that you eat. They're seriously contributing to just normal health, and normal biological processes like digestion.”

There are also some vitamins that only bacteria can make, like Vitamin B components, and so having a diversity in our microbiome helps us prevent nutrient deficiencies. Newer research is finding that microbes make a lot of other active chemicals too, called metabolites. Microbes, for example, make something called short-chain fatty acids which are very important for overall gut health.


But not all bacteria make the same metabolites. When researchers talk conversationally about “good” and “bad” gut bacteria, they’re usually referring to bugs that make those compounds that we think help us stay healthy.

At the end of the day, a “good” or “bad” microbiome is extremely hard to define. “What is a healthy microbiome?“ Devkota says. “We know what kind of general components it should have, but we don't know what actually defines it. There's a lot of effort for people still to characterize the ‘normal microbiome’ or the healthy microbiome. We study a lot about disease and bacteria that are present in disease, but frankly we don't really know.”

Where does our microbiome come from?

You mostly get it from your mother, Jack Gilbert, a microbial ecologist at UC San Diego, tells me. Generation to generation, as people are born through the vaginal canal, breastfed, snuggled, and kissed, moms have provided their babies with her bacteria, which then colonized their bodies.

“We see this in lots of different animal species,” he says. “The physical interaction between a mother and a child can actually be a very significant component of the colonization of the new child by new organisms.”

As we get older, we also get our microbiome from our environment and from the food we eat. A recent paper found that when people move to America and adopt a Western lifestyle (and a Western diet) it has negative impacts on their microbial diversity, or they have less species of microbes inside them after a couple of generations. “A bad diet, lots and lots of sugary fatty foods … and the indiscriminate, unnecessary use of antibiotics and various other components may actually be eroding the organisms which live inside you,” Gilbert tells me.


And because we get our microbes in large part from our parents, if a woman gives birth to a new baby girl after losing microbial diversity, she passes that loss onto her children. “The degradation persists,” he says.

How does our microbiome change over time?

There are periods of our lives where the microbiome goes through larger changes, Devkota says, like puberty. “Your body is changing a lot, your microbiome changes in response,” she says.

When we’re adults, the microbiome is described as relatively stable. The types of bacteria you have as an adult are pretty much the types of bacteria you’ll have for the rest of your life. But what is changeable is the “relative abundance” of those types of bacteria.

Gilbert offers a nature metaphor: in Yellowstone National Park, there are animals like wolves, deer, bears, birds, and more. The composition of Yellowstone hasn’t changed much in the past decade—meaning, the same species still live there. But what does change over time, and fluctuate, is the abundance of each species, how many bears, wolves, and birds. Similarly, the composition of our microbiome probably doesn’t change much, but the amount of each species can change.

As an adult, your diet is one of the leading drivers of microbiome shifts you may go through week to week, day to day. If you spent a week eating south Asian food, and then a week eating Irish pub food, you would see changes in the abundance of certain microbes between those two weeks, Gilbert tells me, “because each of those diets is selecting for certain species that prefer the nutrients in one diet or the other.”


There are other factors like exercise, which can affect your immune system, that can change which microbes can survive and thrive; also alcohol consumption and medications can impact proportions of how many bacteria in each species are present.

“It is very easy to change the microbiome, but not change it from a rainforest into a desert, more like change it from a South American rainforest into a southeast Asian rainforest,” Gilbert says.

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Should I avoid antibiotics?

Our overuse of antibiotics both in medical contexts and food and agriculture has led to severe consequences, like antibiotic resistance and loss of microbial diversity, which has been associated with other health issues like food allergies.

But at the same time, antibiotics are sometimes needed, and it’s best not to say you’ll never use them. Gilbert says that his approach to antibiotics is to have an honest, open discussion with his doctor. Recently, his son had a persistent cough, but didn’t have a fever. He looked up details about how long a cough can last before medical professionals recommend going to a doctor, and once that time had passed he took his son to see someone. The doctor said based on how long it had lasted, and from hearing congestion in the lungs, she recommended an antibiotic.

They then had a conversation about whether it was truly necessary, how long he would take the antibiotic, and ultimately agreed to proceed. Gilbert thinks that if those conversations happened before each prescription, overuse would probably go down. One tip he has is to be polite and calm while talking, so that everyone feels like they have the space to express their opinions.


Should I take a probiotic after taking an antibiotic to help my microbiome bounce back?

There are some studies that suggest that taking a probiotic after an antibiotic dose can lead to a reduction in antibiotic-associated diarrhea.

Another recent paper found that when people took probiotics after an antibiotic it led some of the probiotic organisms to colonize the gut, which is very rare, Gilbert says. When we take probiotics, usually those bacteria are just visitors—they don’t end up living permanently in our bodies. But after antibiotics, some of the probiotics stuck around. We’re not sure yet if that colonization could be a good or a bad thing—but in some cases, it ended up slowing the recovery of a person’s natural microbiome.

“It suggests that probiotics works differently in different people,” Gilbert says of the study. “In some people it had no effect upon the reestablishment of the microbiome, and in some people it retarded it. Now there's a lot more work needs to be done to determine if that affects health, but it's an interesting finding.”

Until we know more, Gilbert says that if you experience diarrhea after you take an antibiotic, that you can try a store bought probiotic, if you want to. “It's unlikely it will hurt, but bear in mind, the science is still out on the potential implications for different people.”

I’ve heard of probiotics, but what’s a prebiotic and a postbiotic?

Probiotics try to give you the bacteria directly, while a prebiotic gives you the food and nutrients for the microbiome you already have. A postbiotic would be a supplement that skips the bacteria altogether and provides something beneficial that the microbiome makes, like a metabolite.

Devkota says that of the three, she is more of a believer in prebiotics, which are usually fiber based—either in fibrous foods, or in fiber supplements.


“Certain types of fiber are broken down by certain types of bacteria. If you feed them, you'll of course make them grow and multiply, and also that's a good thing,” she says. “I believe that if you feed the bugs you can manipulate them that way versus trying to introduce external organisms.”

Should we get probiotics from supplements or is it better to get them from fermented foods?

As Gilbert said before, probiotics rarely colonize—or make a home—in our bodies, but bacteria that are just passing through can still have effects. They can stimulate your immune system, or process nutrients and release chemicals into the gut. Some of those chemicals could be useful.

But where should we get these bacteria from? Gilbert says that the jury is still out on this. There have been some studies comparing the two, but Gilbert thinks it’s hard to define what the outcomes we’re hoping to find should be. “What actually was the effect, right?” He says.

“We do know that both have been shown to be useful in treating disease. But the efficacy of either one or the other is hard to determine.”

Gilbert doesn’t take probiotics, but he eats yogurt nearly every morning. “I like yogurt, it tastes good, and it makes my cereal better, and I prefer it to milk. There we are.”

Devkota says that when you get your probiotics from food, rather than pills, it can be easier to remember to include them in your diet. When you buy a bottle of probiotics, you might take them for a week and then forget. If they’re already in a food that you love, you’re more likely to stick with it. Also, when you eat fermented foods, you get the beneficial microbes and whatever compounds they’re making, together with a prebiotic: the food source the bacteria need to survive. “You've got the bug that's producing the metabolites, and you got the metabolites all right there in a one-stop-shop,” she says. “So I'm a huge fan of fermented foods. I think the whole fermentation movement is great, and I think there's only benefits to it, and no downside.”


Do our microbiomes drive our food cravings?

Gilbert says that we know the bacteria in our guts stimulate nerve endings which send signals to your brain. They also release chemicals into your bloodstream, which can also interact with brain functions. “There's lots of ways in which the bacteria in your intestine can alter how your brain works,” he says.

Gilbert tells me that he used to frequently travel to China, where it was hard to find one of his favorite foods: chocolate. “I love chocolate,” he says. “It's one of my favorite things in the world. But within a week of being in China, my chocolate craving would go away.”

Is it because while he was there, he only ate Chinese food and the population of his chocolate-loving microbes plummeted? One animal study found that when you altered chocolate availability, it changed the types of bacteria that were present in the microbiome. And if you took chocolate-eating microbes and transplanted them into another animal, that animal would start craving chocolate too.

“It's suggestive that there could be a relationship there,” Gilbert says. “Although there's lots more work that needs to be done before we know.” Perhaps there could be a future in which people’s dietary preferences could be manipulated by changing their gut bacteria, but the science isn’t there yet.

Still, these studies that suggest that microbes can directly affect what you want to eat come from animal models. Devkota says that based on that evidence, she still thinks that microbes do play a role in what we want to eat, though just to a degree. “I don't believe it's a cop out for people's hedonistic desires,” she says. “I think that if you're deficient in something I think your microbes can help you sense that.”


People with certain diseases have different microbiomes. Do their microbiome cause the disease? Or does the disease change their microbiome?

“That sort of the question that that's the Holy Grail question,” Devkota tells me. One of the barriers to answering it, is that it’s incredibly hard to study. An ideal case would be to follow someone over time who eventually develops some disease, and have microbiome samples from them the whole time. Instead, researchers usually end up comparing healthy people to those with a certain condition, and Devkota says “it ends up being an association where you can't really distinguish what came first.”

There is some research that shows that microbes are necessary for certain disease to happen, like in the case of inflammatory bowel disease.

Mice who live in bacteria-free environments don’t get IBD, even if they’ve been genetically altered to develop it. They don’t get IBD until you put microbes back in them “As soon as you put the microbes in them, they'll develop disease,” Devkota says. “That tells us that, at least for inflammatory bowel disease, microbes are a critical component.”

Most complex diseases like cancer, diabetes, and neurological diseases require more than one factor. For IBD, it’s likely the microbiome and something else, either a genetic disposition or dietary trigger. For other diseases, the disease itself may push a shift in the microbiome, though it could go the other way, or be more of a two-way interaction.


What about using the microbiome for treating disorders and diseases? And do fecal transplants work?

There have been a handful of studies that show that if you take the microbiome from an individual who has been diagnosed with a certain disease, and transplant their microbiomes into mice, you also see symptoms of their disease in the mice. “We did this in Parkinson's a couple of years ago,” says Sarkis Mazmanian, a medical microbiologist at the California Institute of Technology.

This is compelling evidence that doing the opposite might help people one day: putting the microbes of healthy individuals into those with disease through their poop, called a fecal transplant. There’s also evidence that there are differences between people’s microbiomes with mental health issues and healthy controls.

But there’s still a lot of ambiguity as to what’s causing what. “Maybe it's those gastrointestinal issues that are reshaping the microbiome,” Mazmanian says. “And maybe it's the genetic components of all these diseases that are reshaping. The answer is we just don't know.”

Mazmanian thinks that currently the best support for fecal transplants is in treating IBD. But trials of fecal transplants for conditions like Alzheimer’s, Parkinson’s, major depressive disorder and schizophrenia are ongoing, and in animals it seems like putting the microbiomes of healthy individuals into sick ones could help.


Researchers are also finding that the microbes found in people’s poop can be reliable biomarkers for disease, which could help predict and diagnose what disorders people have. If microbes had predictive power, that would be especially helpful, because you could start to give someone treatment and care before symptoms took hold.

For now, Gilbert tells me, we should think of the microbiome is part of a larger puzzle when it comes to any disorder. “It's a part of the puzzle we've ignored for a long time, and it definitely is something that is necessary if we want to be able to treat people's health seriously,” he says.

But the microbiome will probably not be a “cure,” Gilbert says. “We may be able to alleviate some symptoms, but there are many underlying other factors, which will influence health…socioeconomic status, family relationships, diet and lifestyle, which could be affected by microbiome, and many other factors, genetics and family history. So just giving someone a fecal microbiome transplant wouldn't be a cure.”

There’s currently no FDA-approved microbiome therapeutic. But with all the growing evidence surrounding the microbiome Gilbert says that it likely won’t be long before people start to try and make drugs.” Supplements that don’t have to be regulated by the FDA are already on the market, and can make nebulous claims about health based on small-scale clinical trials. For some things, it probably won’t hurt to try these probiotics, Gilbert says, like cases of minor diarrhea or other GI upset. But for larger health issues, Gilbert tells me he’s still on the fence. “I think there's potential unintended consequences,” he says. “We just don't know until we've done more research on it.”


A recent study found that melanoma patients were 70 percent less likely to respond to cancer immunotherapy if they were taking probiotics, Stat News reported. This was a small study, in a very specific population, but the truth is that we don’t know all of the effects and interactions probiotics will have, which is why they should be studied properly before we give them out as medication.

I still want to buy a probiotic at my grocery store, how do I pick which one to get?

There are lots of different bacteria strains and they have lots of different potential effects. Unfortunately it’s difficult to say which one is best for an individual person, because the effects could be different in you compared to your best friend. A recent study in Cell (that was widely reported as finding that probiotics are useless), actually found that how and if a probiotic works depends on what microbes are already present in your body.

In an ideal setting, to choose a probiotic, you would know the makeup of your own microbiome, what populations are a bit lacking, what a probiotic you’re taking does in your specific body, and how they interact with the bacteria that already exist in your body.

Devkota hopes that we’ll soon reach a point in medical care where microbiome data is routinely gathered, say at your yearly check up. Then you can see how it changes over time, and if changes happen in association with certain health problems.


Until then, you can buy some at-home microbiome tests, but take them with a grain of salt. Rather than interpreting results from one test, changes over time will be more useful information to you, and remember that the research is continually evolving about what having certain microbes over others means for your health.

Mazmanian does take probiotics, but he agrees that the literature that exists don’t reveal whether currently available probiotics are either good or bad. “I know it's a generalized statement, and there are people who I've met who swear by the probiotics they take,” he tells me. “I don't feel anything with the probiotics that I take. I still take them, but I'm generally healthy. So, maybe those people who do have abdominal issues, let's say gas, bloating, whatever, may get some benefit.”

For more serious symptoms, there’s even less evidence about what probiotic might help. Mazmanian tells me that most commercial probiotics were developed decades ago, and not necessarily for their biological criteria, but for factors like, shelf life. To muddy the waters even more: A lot of the probiotics on the shelves don’t contain the bacteria they claim to. Or, they don’t have the amount they say, or the bacteria were once in there but aren’t viable anymore. But, Kenya also says he’s seen nothing that’s convinced him that probiotics that exist now are harmful to someone in the general population who is otherwise healthy.

“They haven't shown great efficacy when they have been tested in the most rigorous settings, and that's a controlled clinical trial,” Mazmanian says. “The next generation of probiotics that we and others are developing may have more efficacy. I think we're probably a handful of years away from what’s called ‘next generation probiotics.’ Whether they be over the counter or require a prescription—they’re going to be a little bit of both, I think. I think in the immediate future, we'll have new options with probiotics.”

What’s the best diet for our microbiome?

If you’re facing decision fatigue in the microbiome aisle of Whole Foods, there’s another way to serve your microbiome, and that’s through what you eat. So what the best diet to feed your microbiome? The short answer: Fiber.

In a food culture that’s obsessed with adaptogens and protein, only five percent of Americans meet daily fiber recommendations, and it could be leading to changes in our microbiomes.

There is a lot of data that shows that the microbiome in the U.S. especially is less diverse, meaning we have less different kinds of bacteria than in other parts of the world. “Is that good or bad? Well, this is one of those situations where we're connecting the dots.” Devkota says.

The ‘western diet’ extends to any developed environment, and it’s different than other diets, and the microbiome has shifted to match that, and not for the better. Microbiome shifts in themselves aren’t a bad thing. One study compared the western diet microbiome to microbiomes in rural populations like the Hadza hunter-gatherers of Tanzania, and found that the non-western microbiome goes through seasonal shifts, driven by seasonal changes in the food supply.

Our microbiomes doesn’t go through these same seasonal shifts, because we get all the foods we want at all times of the year. When people immigrate to America from places like Asia or Latin America, subsequent generations have higher rates of so-called Western diseases, like metabolic and inflammatory diseases, compared to those who stayed in their native countries. “That's largely attributed to diet— diet and lifestyle,” Devkota tells me. "Coming to the U.S. mainly is a risk factor for most people, which is kind of scary but true.”

Try and get your fiber intake up to at least 25 grams a day, the experts tell me. You can do this by taking a fiber supplement, or by eating more fruits and vegetables. “Salad is an incredibly powerful way to increase fiber,” Gilbert says. “It's really powerful for feeding the bacteria which will produce beneficial chemicals in your gut.”

He also recommends eating a wide diversity of healthy foods to make sure you’re giving all the diversity of bugs in your body enough to eat. “If you can count more than five colors on your plate, natural colors, then you're doing pretty good,” he says.

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