Welcome to the World in Your Gut

By Melissa Pandika | June 20, 2016 | Rally Health


Your gut contains a whole ecosystem of (mostly) helpful bacteria — about 30 trillion, in fact. That’s more than the human cells you have in your body, so it’s natural they’d have a major effect on our health. Researchers now think that our gut flora (a nicer-sounding name for these gut bacteria) might be linked to a huge number of conditions ranging from digestive disorders and allergies to heart disease and depression. In fact, in May 2016 the White House announced the National Microbiome Initiative to learn about all the microbes that live in and on us and how they influence our health.

Here’s one example of how doctors are already using bacteria as a new type of medicine. A very unfriendly bacteria called Clostridium difficile causes severe digestive problems and can be very difficult to treat. Researchers decided to take a new approach and “transplant” bacteria from the fecal matter (poop) of healthy people into patients with C diff. (More on how this works.)

This odd approach has a success rate that’s hard to argue with: 92 percent. Many patients only need a single transplant to cure them of a problem they’d sometimes been battling for years, but the treatment is still considered experimental. Researchers are also looking to treat colitis and other digestive disorders with these bacterial transplants.

Here’s some of the latest research on other conditions.

Allergies and asthma: It’s been known for a while that early experiences shape our immune system — the foods we eat during childhood, the pets we hug, even the soil we play in. When we’re exposed to different foods, germs, and other allergens early in life our immune systems seem to get better at figuring out “friend” from “foe” and avoiding allergies and asthma (they’re both overreactions by our immune systems).

For example, breastfed babies may be less likely to develop asthma and allergies than formula-fed babies. Not surprisingly, the guts of breastfed infants have more varieties of bacteria than those of formula-fed infants too.

Now, animal studies are starting to look at specific types of bacteria. Researchers have shown that feeding mice a certain strain of bacteria can reduce asthma-like symptoms. Another study found that giving mice antibiotics early in life made them vulnerable to a mouse version of peanut allergies, but feeding them different type of bacteria got rid of their symptoms.

Obesity and diabetes: There are signs that certain gut bacteria could influence the risk of diabetes, heart disease, and other problems linked to obesity. In a recent study, scientists colonized mice guts with bacteria from obese women and their healthy-weight twins. Mice that received bacteria from an obese twin had more body fat, weighed more, and had less diverse gut microbiomes than other mice.

How might gut bacteria tip the scales? One possibility is that different bacteria absorb nutrients differently from food. If they’re very efficient, they might trigger our bodies to store the extra energy as fat. Another idea is that our gut flora can change how much energy we burn. Researchers have found that an imbalanced gut microbiome in mice lowers the number of calories they burn while resting.

Another theory is that the bacteria affect our gut lining directly. Studies show that a high-fat diet may trigger bacterial by-products that weaken this lining, allowing harmful substances to enter the bloodstream and leading to steady, low-grade inflammation (associated with heart disease and obesity).

Stress, anxiety, and depression: As many people with digestive disorders like irritable bowel syndrome, Crohn’s, and colitis also suffer from depression and anxiety, research has begun to look at whether anxiety and depression may be influenced by your gut, too.

Researchers at McMaster University have looked at the stress-gut connection in mice. In one study, they exposed smaller mice to bigger, more aggressive mice for a few minutes a day for 10 days. The smaller mice lost their appetite and showed other signs of stress. Compared to calmer mice, these stressed-out mice had fewer types of bacteria in their guts. When the researchers gave them bacteria from calm mice, they showed striking improvements in behavior and stress hormones in their blood.,

A May 2013 study found that 35 percent of depressed participants had a “weakened” gut lining, which may be associated with inflammation. Studies suggest that inflammation may even play a role in depression and other psychiatric disorders.

What lies ahead

All this research suggests that “rebalancing” the gut bacteria could prevent or treat a range of conditions. But as with any emerging field, it’s complicated. For starters, we still don’t have a clear definition of a “normal” or “balanced” gut microbiome, says John Bienenstock, the McMaster professor of pathology and molecular medicine who conducted the studies on stress in mice.

“It’s early days yet in terms of brain and behavior,” he says. “We’re not absolutely certain of how to adjust the balances yet.” Plus, it’s still not clear whether the disturbances in the microbiome cause depression or obesity, or whether they’re the result of these health problems.

One day, physicians might even be able to design personalized diets based on our microbiome, but we’re not there yet. At this point, “I can’t just go down to a health food store and buy a particular probiotic,” Bienenstock says. Still, the field is moving very fast, he says.

So what does all this mean for you?

Consider probiotics for certain digestive troubles. Probiotics are live microbes that are supposed to be good for your health. Research shows some may help with irritable bowel syndrome and certain types of diarrhea, and possibly other digestive conditions as well (though they need more study). You can find probiotics in cultured and fermented foods like yogurt, kefir, sauerkraut, miso soup, and kombucha. Eating them might help with some digestive problems — but then again, you might not notice any dramatic changes. Probiotics have a good safety record in healthy people, but not all probiotics have the same effects. You should check with your doctor before trying any new supplements, especially if you have a serious illness or weakened immune system.

Look for live, active cultures. By definition, probiotics are live microorganisms. Some yogurt manufacturers heat-treat their products after fermentation, which kills the active cultures. Frozen yogurt typically doesn’t contain them, either, since the freezing also kills them. The National Yogurt Association’s Live & Active Cultures seal ensures that the yogurt meets a specific level of Lactobacillus bulgaricus and Streptococcus thermophilus, the bacteria used to make commercial yogurt.

When it comes to supplements, buyer beware. It’s unclear whether supplements work as well as probiotics in food. But since supplements don’t fall under FDA regulation, they “can be very concerning to someone with serious health conditions,” says Hattner. They can also be pricey, and “what’s on the label might not necessarily be what’s in the product.” For instance, a supplement label might state that the product contains 10 billion cultures — but they might be freeze-dried, and only a small fraction may “wake up” in the body.

Think about prebiotics. Probiotics alone may not be enough — “you have to feed them,” Hattner says. Called “prebiotics,” the food for probiotics is mainly fiber. Plus, research has already linked a high-fiber diet to a host of health benefits, including lower cholesterol levels, better control of blood sugar levels, and more regular bowel movements. Some examples of prebiotic-rich foods include garlic, onions, leeks, bananas, whole grains and flaxseed.

Start slow. Introduce probiotics gradually, especially since many supplements also contain prebiotics, which can make you gassy. You could begin with one serving of probiotic foods per day — for example, some yogurt with honey at breakfast or some pickles on a sandwich at lunch, recommends Kristi King, a registered dietitian and spokesperson for the Academy of Nutrition & Dietetics. The same goes for prebiotics — if you’re not eating much fiber now, you could add more vegetables and whole grains to your meals.

Editor: Deepi Brar

Melissa Pandika is a freelance writer based in Oakland, California.

Selected references:

  • Ursell LK, Metcalf JL, Parfrey LW, Knight R. Defining the Human Microbiome. Nutrition Reviews. 2012. [Link]
  • Ethan Gough, Henna Shaikh, and Amee R. Manges. Systematic Review of Intestinal Microbiota Transplantation (Fecal Bacteriotherapy) for Recurrent Clostridium difficile Infection. Clinical Infectious Diseases. 2011. [Link]
  • Okadach J-F. The “Hygiene Hypothesis” for Autoimmune and Allergic Diseases: An Update. Clinical and Experimental Immunology. 2010. [Link]
  • Madan, Juliette C. Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants. JAMA Pediatrics. March 2016. [Link]
  • Turnbaugh, Peter J., et al. A Core Gut Microbiome in Obese and Lean Twins. Nature. January 22, 2009. [Link]
  • National Center for Complementary and Integrative Health. In Depth: Probiotics. NIH website.
  • Ciorba MA. A Gastroenterologist’s Guide to Probiotics. Clinical Gastroenterology and Hepatology : the Official Clinical Practice Journal of the American Gastroenterological Association. 2012. [Link]
  • Sanders ME, Guarner F, Guerrant R, et al. An Update on the Use and Investigation of Probiotics in Health and Disease. Gut. 2013. [Link]
  • US Department of Agriculture and US Department of Health and Human Services. Dietary Guidelines for Americans, Eighth Edition 2015-2020.


Rally Health

Already a Rally member? Please log into Rally for more.

Would you like to see more? Explore


Articles on Rally Health’s website are provided for informational purposes only, as a free resource for the public. They are not a substitute for medical advice, diagnosis, or treatment. Rally Health does not accept solicitations or compensation from any parties mentioned in the articles, and the articles are not an endorsement of any providers, experts, websites, tools, or financial consultants, services, and organizations.