All living things contain trillions of microscopic bacteria, viruses and fungi that collectively are called the microbiome. Our bodies contain multiple microbiomes, and the gastrointestinal, or gut, microbiome is the most complex and diverse. While research into the gut microbiome is in its relative infancy, scientists believe it is connected to our body’s immune function, physiology and nutrition, along with other possible links. The gut microbiome regulates our metabolism and may be linked to heart disease, colon cancer, obesity, type 1 and 2 diabetes, multiple sclerosis, dementia, allergies and asthma, and inflammatory bowel diseases, including Crohn’s disease and irritable bowel syndrome.

The healthy microbiome is an ecosystem much like a healthy pond, says George Weinstock, director of Microbial Genomics at The Jackson Laboratory for Genomic Medicine in Farmington. When the microbiome is filled with diverse bacteria, it can successfully fight off harmful bacteria. But like a pond, if much of what keeps it healthy dies, it no longer functions optimally. The gut microbiome affects our bodies from birth and throughout our lives. Babies come into contact with some microbes while still in the womb, and are exposed to microbes when passing through the birth canal and breastfeeding. Just like a healthy pond, as we grow, our gut microbiome diversifies, and that diversity is a sign of a healthy gut.

While it’s been known for years that genetics play a role in whether people are obese or thin, new research has found a connection to the gut microbiome. Scientists working with thin mice and obese mice transferred fecal matter from the obese mice to the thin mice and the thin mice gained weight, says Mary Anne Amalaradjou, associate professor of food microbiology at UConn. Researchers believe the microbiome of the obese mice processes energy more efficiently and store the excess energy as fat. 

Not surprisingly, the advice for building and maintaining a healthy gut should sound familiar. Breastfeeding for at least the first six months of life helps establish a diverse gut microbiome, and eating a well-balanced diet rich with fiber promotes gut health. Eating fermented foods and walnuts daily has been shown to foster good gut bacteria, Amalaradjou says. Just some examples of the many fermented foods include cheese, yogurt, kimchi and sourdough bread, and beverages such as beer, wine, apple cider and kombucha.

Amalaradjou recommends eating your way to health rather than popping a daily probiotic pill. What you eat is what you feed your gut microbiome, she says. “I love food and I hate pills. It’s easier and foods have a variety of bacteria in them. You don’t get just one. If you buy the pill, you only get what the pill says it has,” she says. “Just like our fingerprint, our microbiome is unique. The probiotic you take may not help. You may have to try a couple before you figure out what works for you.”

Taking antibiotics wipes out the beneficial as well as the harmful bacteria in our guts. Doctors routinely recommend probiotics along with an antibiotic prescription, but probiotics are not regulated by the Food and Drug Administration because they’re considered supplements. Not all probiotics are equal, and even the best probiotics may provide limited benefits, Weinstock says.

When researchers study the gut of people who take probiotics, they can’t find the beneficial bacteria, he says. Some of the cells in the probiotic are dead and others pass through the body without taking up residence in the gut, he says. Two studies published in the journal Cell call into question what has been the standard of care. One study concluded that not everyone who takes probiotics ends up with the bacteria in their gut and, a second study found that the gut of people who received an antibiotic and did nothing returned to normal more quickly compared to those who took a probiotic.

Perhaps our grandmothers were right when they said, “You are what you eat.”


Hygiene hypothesis: outdated?

The “hygiene hypothesis,” first suggested in 1989, has developed as a way to explain why people in wealthier countries have higher rates of autoimmune diseases such as type 1 diabetes, allergies and asthma than those in developing countries. Parents in economically advantaged countries clean and disinfect regularly and encourage hand washing — even before the global coronavirus pandemic. Unless they grow up on a farm, most children raised in the U.S. and Europe spend far less time outside and playing in the dirt than their counterparts in developing countries.

Widespread antibiotic use impacts the gut microbiome, and a peer-reviewed article published in Perspectives in Public Health says it’s time to abandon the hygiene hypothesis. “Evidence suggests a combination of strategies, including natural childbirth, breastfeeding, increased social exposure through sport, other outdoor activities, less time spent indoors, diet and appropriate antibiotic use, may help restore the microbiome and perhaps reduce risks of allergic disease,” the report concludes.

So, even while we’re living through a global pandemic and sanitizing surfaces and washing our hands frequently, encouraging kids to play in the dirt can promote good gut health, says Mary Anne Amalaradjou, associate professor of food microbiology at UConn. 

If, in the first years of life, children are not exposed to enough or the right microorganisms from other people and the natural environment, the controlling mechanisms of the immune system can fail, write the authors of the article. Consequently, the body attacks not only the harmful organisms that cause infections, but also innocuous targets such as pollen, house dust and food allergens, they write. People began perceiving they were being too clean, which led to their lost confidence in hygiene, they say, adding, “This is happening at a time when infectious disease issues mean that hygiene is becoming more, rather than less, important.”

So, keep washing your hands, but don’t worry about a little dust and dirt in your home.

This article appears in the December 2020 issue of Connecticut MagazineYou can subscribe to Connecticut Magazine here, or find the current issue on sale hereSign up for our newsletter to get our latest and greatest content delivered right to your inbox. Have a question or comment? Email editor@connecticutmag.com. And follow us on Facebook and Instagram @connecticutmagazine and Twitter @connecticutmag.