Evidence is showing we can change our microbiome, the trillions of bacteria that have evolved to live inside us. Drinking kefir or kombucha, taking a course of antibiotics, and even playing with dogs could change your microbiome for better — or worse.

This is the second part of a two-part series. Read part one here: Is the Forest of Bacteria Inside You Your Most Precious Resource? »

Most patients worry their doctors will give them crap. But the folks who see Dr. Neil Stollman are absolutely begging for it.

Stollman is a gastroenterologist and chair of the Department of Medicine at Alta Bates Summit Medical Center in Oakland, California. He specializes in fecal microbiota transplants, or FMTs, which involve taking feces from a healthy patient and putting them into the body of a sick one.

Study after study has shown an FMT can cure a patient infected with the nasty bacterium Clostridium difficile (C. diff) almost overnight.

C. diff infections strike nearly 500,000 patients a year in the United States, and about 29,000 die. These infections are most common in patients who get intensive medical care along with antibiotics. And one in five people who contracts C. diff diarrhea will have to fight it off more than once. That’s where Stollman steps in.

“When a multiply recurrent C. diff patient gets to me, I never have to convince them — they are so far past the ‘ick factor,’” Stollman (affectionately called “the stool man”) told Healthline. “It’s a barrier more among doctors than among patients, surprisingly. Most of my patients have had to ask their doctors to send them to me.”

By the time patients make it to Stollman’s office, antibiotics have killed off the vast majority of the helpful bacteria that naturally live in their stomach, intestines, and colon, called the gut microbiome. These bacteria help the body digest food, fight harmful invaders, and keep inflammation in check. With no competition from good microbes, C. diff can thrive.

Stollman blends feces from a healthy, prescreened donor into a nightmarish smoothie, and patients receive the concoction rectally. It’s not fun by any means, but microbes from the donor stool quickly take up residence in the patients’ guts, bringing the microbiome back into balance and sometimes saving their lives.

Researchers are exploring ways to deliver FMTs using frozen stool or bacteria alone in the form of a pill.

Learn More: Grossed Out by Fecal Transplants? There’s a Pill Instead »

Scientists are beginning to recognize how important it is for humans to take care of the trillions of tiny microbes that call our bodies home. They’ve spent years studying how these bacteria influence everything from autism to acid reflux to types 1 and 2 diabetes.

Microbiome researchers are concluding that our microbial makeup can change over time, at least to some degree. We can get under the hood by tinkering with our diet, changing the way we give birth, and deciding how many probiotics and antibiotics we take.

FMTs are, right now, one of the only really direct ways to modulate the microbiome, and they’ve only been shown safe and effective for C. diff infections. But Stollman believes as the science gets more precise, doctors will design bacterial cocktails tailor-made for each patient and each illness.

“I’m going to be out of the fecal transplant business very soon,” he said. “In a few years we’ll be able to put your fecal sample in a processor and say, ‘Mrs. So-and-So needs a jar of X, a vial of Y, a jigger of Z.’ A fecal transplant is a shotgun version of that.”

Someday scientists will even create totally synthetic bacteria to fight our microscopic battles for us.

For now, research can guide us toward some noninvasive, commonsense ways to keep our microbiome healthy in every stage of life. As it turns out, getting a head start is key.

Find Out: Does MS Start with Faulty Gut Bacteria? »

The most important thing to ever happen to your microbiome happens the moment you’re born.

Babies born vaginally get their first major dose of microbes from their mothers as they pass through the birth canal. These beneficial bacteria include Lactobacillus, which helps breakdown the lactose in milk to make energy. More Lactobacillus colonize the mother’s vagina as her due date nears, ready to jump ship to her baby and help it digest breast milk.

Babies delivered via C-section surgery get their first dose of microbes from their mothers’ skin and the skin of doctors and nurses in the delivery room. Researchers worry that because C-section infants don’t get the bacteria their mothers evolved to give them, it will set these children on the road to poor development.

Studies are showing that our native bacteria help train our immune system to recognize friend from foe. Without proper training, the theory goes, the immune system is weak and the body is more likely to overreact to everyday substances like dust and peanuts.

“Evidence supports the idea that microbial colonization of the gastrointestinal and respiratory tract in the period [around birth] has an important role in the predisposition to chronic inflammation, autoimmune, allergic, and chronic illness,” Dr. Uma Perni, an OB-GYN at the Cleveland Clinic, told Healthline.

Worldwide, C-section rates vary quite a bit, but cesareans are the most common inpatient surgeries in the United States, where C-section rates increased from less than 21 percent in 1996 to nearly 33 percent in 2009. The World Health Organization (WHO) estimates countries should have no more than a 10 to 15 percent C-section rate.

Maria Gloria Dominguez-Bello, Ph.D., an assistant professor and microbiome researcher at New York University’s (NYU) Langone Medical Center, is testing a fast and easy work-around called the “gauze-in-the-vagina technique.”

It’s exactly what it sounds like: doctors soak a gauze pad in the mother’s vagina for one hour and remove it just before her C-section. When doctors remove the baby from the womb, they quickly swab it from head to toe with the gauze.

Dominguez-Bello reports the gauze technique doubles the numbers of vaginal bacteria C-section newborns get, though a traditional birth still delivers six times more.

Dominguez-Bello’s husband and fellow microbiome researcher at NYU, Dr. Martin Blaser, says an added danger of moving away from traditional modes of birth is the routine use of antibiotics. Pregnant women get antibiotics to fight Group B strep bacteria and to prevent infection after a C-section, and newborns get dosed to prevent a rare eye infection caused by a mother’s gonorrhea.

Antibiotics kill bugs indiscriminately, and many good microbes fall victim to this “friendly fire.”

Another best practice for keeping your baby’s microbiome healthy is breast-feeding. It’s no secret breast-feeding is beneficial — it gives babies vital nutrients, helps the immune system develop, and may even boost IQ. But breast-feeding also delivers good bacteria to jump-start microbial health.

“Breast-feeding is best for many reasons. Breast milk seeds the infant’s gut with beneficial nutrients, including microbes that are crucial for proper growth, development, and function. Some studies support the use of probiotic support in non-breast-fed infants,” Dr. Mary Rosser, an OB-GYN at Montefiore Medical Center in New York City, told Healthline.

Learn 8 Ways Greek Yogurt Benefits Health »

MaryBeth Reardon, R.D.N., L.D.N., a dietician in Massachusetts, also recommends probiotics for infants and children who took antibiotics or were bottle-fed. She uses probiotics — helpful bacteria in the form of a pill or naturally fermented food — to help kids in her practice with constipation and other gut troubles.

The evidence to support vaginal birth and breast-feeding for microbiome health is strong and growing every year. But recently, scientists have found evidence mothers can also give their babies a leg up on microbial development well before they go into labor.

Studies are demonstrating that a mother’s weight and diet, even before pregnancy, impact her personal microbiome, which in turn affects which bacteria she passes to her offspring. An unbalanced microbiome can affect a woman’s metabolism, predisposing her to weight gain and passing that risk on to her child. The microbiome may be the reason parental obesity is one of the biggest risk factors for childhood obesity.

“You are what you eat. We can control what goes into and onto our bodies. The gut microbiome of mom affects the developing fetus. Bad nutrition and extra weight change the microbiome of the maternal gut and offer an unstable and unhealthy balance,” Rosser said.

Read More: Will Antibiotics Make Your Baby an Obese Adult? »

If you think your baby is protected in its walled-in placenta, think again. A study published last year showed for the first time that the placenta harbors its own unique community of bacteria, similar to those found in the mouth. The authors found the placental microbiome is affected if the mother gets an infection. It’s also linked to the risk of preterm birth, suggesting bacteria in the placenta may play a role in premature labor.

Perni says doctors don’t have enough information to give women specific advice for how to keep their placental microbiome in ship shape, but research is ongoing.

Antibiotics are undoubtedly overused in America. Because they damage the microbiome, antibiotics can hamper a child’s immune system and metabolism. The most crucial period of development for the immune system is between birth and age 3.

Does that mean antibiotics are the enemy for kids? Yes and no, experts say.

Every year, American doctors write about 100 million antibiotic prescriptions for conditions the drugs can’t treat. In part, that’s because 36 percent of Americans incorrectly believe antibiotics can cure viral infections like the common cold. By age 2, the average child in the United States has taken about three courses of antibiotics.

This practice drives the growth of antibiotic-resistant bacteria, including Stollman’s nemesis, C. diff.

“Mom wants something, and the pediatrician is risk-averse. We live in America, and lawsuits are very common. The doctor can make the mom happy and protect him or herself legally by writing a 30-second script,” Stollman said.

See How Patient Demand for Antibiotics Fuels Drug Resistance »

When a child arrives at the doctor’s office with a fever, it’s most often caused by a virus. Without rapid diagnostic tests that can tell bacterial and viral infections apart, doctors often prescribe antibiotics on the outside chance it’s a serious bacterial infection like pneumonia or meningitis.

“We choose to treat out of an individual safety argument when collectively that can be catastrophic,” Stollman said.

However, Laurie Cox, Ph.D., a microbiome researcher in Blaser’s NYU lab, cautions that we shouldn’t throw the baby out with the bathwater.

“Antibiotics can have an effect on the microbiome and that might have health consequences, but a life-threatening infection could have health consequences as well,” Cox said. “Antibiotics can still be very useful and shouldn’t be completely avoided, but this new risk we’ve identified should be taken into account.”

“There probably is over-prescription of antibiotics in the United States, so if your doctor is saying, ‘It’s a viral illness, and I don’t recommend an antibiotic,’ you should really go with that,” Cox added.

Many pediatricians these days recommend a probiotic be taken along with any antibiotic drugs to prevent diarrhea.

What Are Probiotics Anyway? Report Calls for a Stricter Definition »

Often, basic cleanliness and common sense can make antibiotics unnecessary in the first place.

“Good hygiene can help you avoid antibiotics,” Cox said. “We know certain practices to reduce bacterial infection and illness, and a lot of that is proper sanitation, proper food handling.”

But just as with antibiotics, there can also be too much of a good thing. With parents everywhere rushing for the sanitizing wipes and cleaning spray at the first sign of dirt, household bacteria are becoming endangered species.

“If you’re totally wiping off your skin bacteria because you’re so worried about transmitting it, then you’re actually disrupting ancient pathways of colonization,” Cox said.

When scientists recently studied the microbiomes of previously uncontacted tribes in the Amazon, they found the people there had a much more diverse, and hence healthier, array of bacteria.

“The idea that germs are bad and should be destroyed is wrong. Kids need to be exposed to a wide range of bacteria in order for them to develop a strong immune system,” said Ross Pelton, R.Ph., a pharmacist and researcher. “Normal cleanliness, as in washing one’s hands and face, is part good hygiene. But washing regularly with antibacterial soaps and cleansers may have more negative effects than positive effects, as it can promote the survival of antibiotic-resistant bacteria.”

Did You Know? Triclosan Encourages MRSA Bacteria to Colonize Your Nose »

Moreover, the antibacterial compound triclosan, found in shampoos, soaps, toothpaste, and many other items, compromised liver function in mouse tests and made the animals susceptible to liver cancer after long-term exposure. In human tests, triclosan is present in 75 percent of urine samples.

Triclosan is no more effective at killing germs than plain soap and water, the experts say. And the old standby, bleach, may be overkill, too.

In a recent study, kids who lived in homes or went to schools where bleach was used for cleaning had higher rates of the flu, tonsillitis, and other infections compared to kids who weren’t exposed to bleach.

So, the dirtier the better? In an effort to “let them eat mud pies,” some parents are taking their toddlers to farms or petting zoos, and even having them eat dirt. Blaser and Cox say that probably won’t do any good.

“Really, it’s not the dirt that you need — we think it’s specific bacteria that we have co-evolved with. There might be soil organisms that your child might be exposed to, but they’re not going to colonize the gut well, and they will have a limited impact,” Cox said. “I think sometimes people look at it too broadly. They say either all dirt and bacteria is good or all cleaning is good. Really, we want the right bacteria.”

There is some good news, though. In small studies, children who were exposed to pets and their dander or who slept on animal fur early in life had a more diverse array of microbes and a lower risk of allergies and asthma.

Related News: Exposure to Dogs May Protect Kids from Allergies »

What if your parents missed the boat? If you were born by C-section, took antibiotics, and had a sterile childhood, are you doomed to microbial imbalance?

Not necessarily.

Early evidence suggests vigorous exercise can change the microbiome for the better. A 2014 study of competitive rugby players showed the athletes had a greater diversity of gut bacteria than non-athletes. Scientists have seen similar microbial changes in lab mice that exercise, though some research shows voluntary and forced exercise can affect the microbiome in different ways.

There are also tantalizing hints that traveling to a different environment can modify your microbes. In a recent study that tracked just two people over the course of a year, scientists saw a huge change in one’s gut bacteria when the subject traveled from a developed to a developing country. The changes were reversed when the subject moved back.

However, the thrust of most research on the adult microbiome has focused on the impact of diet. One study of colorectal cancer patients showed that eating more fruit and vegetable fiber was associated with a jump in diversity and the abundance of certain bacterial species.

Learn All the Microbiome Basics »

A 2014 study by Harvard University researchers found that putting humans on a diet of either only plant products or only animal products changes their microbiomes in a way that lets their bodies process either more protein or more carbohydrates.

The volunteers on the carnivorous diet saw a big increase in the relatively rare bacterium Bilophila wadsworthia, which has been linked to inflammation and autoimmune gut conditions such as Crohn’s and colitis. However, while the volunteers’ microbiomes changed when they switched diets, their microbes flipped back just as quickly when the study ended. This suggests we can change our diet to change our disease risk, at least temporarily.

“Eating a healthier diet is definitely going to change your microbiome in the direction we think is the right one,” José Clemente, Ph.D., an assistant professor at the Icahn School of Medicine at Mount Sinai, said. “We don’t know for how long you need to change your diet before the impact on your microbiome is significant.”

Diversity may be as important for your diet as its overall healthfulness.

“Eating a diverse, healthy diet helps keep a person’s microbiome healthy and diverse,” Pelton said. “Of major importance is the consumption of whole grains and unprocessed carbohydrates, as well as healthy fats and proteins. Foods to avoid include sugars, processed carbohydrates, trans fats, and an excess of omega-6 fats.”

But what about probiotics — those good bacteria that live in yogurt and in pricy capsules on the drugstore shelf? Blaser writes that the current use of probiotics “smacks of placebo effects,” and that we need larger, well-controlled trials to test their impact on health.

See 29 Hilarious Things Only Someone With Ulcerative Colitis Would Understand »

“Most of us don’t feel yet that there’s strong evidence that probiotics work for treating disease or for regulating weight or anything else, primarily because we don’t have a good idea of what probiotics are,” Lita Proctor, Ph.D., head of the Human Microbiome Project, told Healthline. “We don’t really know what these strains do.”

However, as early as 2010 scientists had reached a consensus that probiotics can be helpful in at least some cases: They can reduce the risk of diarrhea from antibiotics and reduce deadly bouts of necrotizing enterocolitis in premature babies, for example.

In 2014, an updated consensus showed the evidence backs probiotics for supporting a healthy digestive tract and a healthy immune system. There’s also some evidence of efficacy in treating irritable bowel syndrome (IBS).

MaryBeth Reardon says she finds probiotics helpful for IBS but also ulcerative colitis, yeast infections, chronic diarrhea or constipation, and even eczema and respiratory infections. Among her favorites are multiple strains of Lactobacillus and Bifidobacterium, as well as Saccharomyces boulardii, which has been shown to decrease inflammation and even boost weight loss in mice.

Reardon admits, though, that probiotics aren’t an exact science. “It is important to acknowledge what we have not yet begun to understand, and that is the relationship between an individual’s genome … and their unique population of microbiota,” she said. “No two are alike, so often we may just throw billions, sometimes trillions [of bacteria], into the gut (going low and slow as we introduce them, of course) after covering the bases with those most commonly found species or strains.”

For those who may be wary of probiotics, or unable to afford them, Proctor says naturally fermented foods like kimchi, tempeh, and kefir, and teas like kombucha, are both safe and teeming with helpful bacteria.

“In a general sense I’m a big fan of food-based probiotics,” Stollman said. “I discourage my patients from spending a lot of money on these specialty products. I encourage them to drink kefir. There’s some good data that kefir is probably better than most available probiotics, if not all.

“Food-based probiotics have several upsides — one is that they’re foods, so the FDA looks at them. The problem with the marketing of a supplement is that government oversight for supplements is nonexistent,” he added. “They also seem to have a better breadth or diversity of bugs and better survival.”

Microbiome science is still in its early stages.

“It may be possible that we can find some really good candidate organisms that can help us lose weight, for example, or improve our breathing, but they have yet to be discovered,” Blaser told Healthline.

However, we know that just as our microbes are working hard to keep us healthy, it will take effort to keep them flourishing. Who knows what’s waiting to be discovered hiding in our guts and how it might change the future of medicine?

“The microbiome really has been the undiscovered universe,” Reardon said, “and it will be so exciting to uncover its full potential in human health and disease.”

Find Out: Is Coconut Kefir the New Superfood? »