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Notebook Medicine

Inner life

This medical illustration from the Centers for Disease Control and Prevention shows a Clostridium difficile bacterium. (Lois S. Wiggs & Janice Carr/Centers For Disease Control And Prevention/AP)

Associated Press/Photo by Matt Rourke

David Martin walks with his turkeys raised without the use of antibiotics at his farm in Lebanon, Pa.


Inner life

We all have our own personal rainforest full of bacteria in our stomachs, and we haven't been taking care of them

Mrs. Duncan slowly raised her head when I entered the exam room. The last two days of nonstop diarrhea were evident in her dry, cracked lips and withered skin. When I learned she recently received an antibiotic for a sinus infection, a likely diagnosis became clear. Sure enough, the next day a stool test showed that a bacterium called Clostridium difficile (C. difficile) was causing my patient’s gastrointestinal woes.

An infection that affects about half a million Americans per year, C. difficile shows the importance of the microbiome, the 100 trillion bacteria that live on and in our bodies. It’s astounding that each of us is home to 10 times more bacteria than human cells. Scientists are increasingly appreciating the crucial role our own personal rainforests play in human health.

In my patient’s case, an antibiotic had disrupted the delicate balance of microbial life in her gut, enabling the toxic bacterium C. difficile to proliferate and attack her colon. C. difficile is only one of the many harmful results of disturbing the body’s bacterial ecosystem. Emerging evidence suggests our microbiomes play a role in many health conditions, including obesity, immune disorders, and mental illness.

Since the 1950s, livestock farmers have known that adding low-dose antibiotics to animals’ feed accelerates their growth. Indeed, by 2011, 80 percent of all antibiotics sold by weight in the United States were used for meat and poultry production. There is now evidence that a similar phenomenon happens in people. For instance, a study showed that children repeatedly exposed to antibiotics in their first two years of life were more likely to be obese later in life. Research suggests gut bacteria affect weight by altering the level of hormones that control appetite and fat deposition. 

With the United States suffering from an obesity epidemic, biologists are increasingly looking to the microbiome for answers.

They are also turning to the microbiome to make sense of the rise in immune disorders such as food allergies, psoriasis, and multiple sclerosis. The immune system is our body’s defense against harmful viruses, fungi, parasites, and bacteria. But in allergic and autoimmune conditions, the immune system malfunctions, hurting the body it is supposed to protect.

According to what is called the “hygiene hypothesis,” the growth in immune-related disorders is at least partially due to children no longer being exposed to the same microorganisms they encountered in the past. Public health measures such as sanitation, trash collection, and clean water have successfully protected people from infectious diseases such as typhoid and cholera. But this also means people no longer encounter microorganisms that lived alongside humans for most of their history. Over many generations, these bugs became our immune system’s standard training partners. In their absence, the immune system sometimes gets confused and misbehaves.

Perhaps the most surprising discoveries about the body’s bacteria concern its relationship to the brain. It is well-known that the brain can profoundly affect the gut. Nausea, diarrhea, and appetite changes can result from emotions such as fear and sadness. But emerging research suggests the gut—specifically gut bacteria—can influence the brain.

In one study, researchers found that feeding mice a bacterium called Lactobacillus rhamnosus reduced behaviors associated with anxiety and depression. The bacterium, often found in yogurts and milk, increased receptors in the mice’s brains for a chemical called GABA that is targeted in commonly used anti-anxiety medications like Valium and Xanax. When scientists severed the mice’s vagus nerves, which transmit information from the gut to the brain, the Lactobacillus no longer affected mice’s behavior or brain chemicals.

In another study, researchers at UCLA found that women who regularly consumed beneficial bacteria through yogurt showed changes in their brains when they were imaged using a special MRI scanner. Commenting on the study published in Gastroenterology, lead author Dr. Kirsten Tillisch noted “our findings indicate that some of the contents of yogurt may actually change the way our brain responds to the environment. When we consider the implications of this work, the old sayings ‘you are what you eat’ and ‘gut feelings’ take on new meaning.” Based on such early research, some psychiatrists and other health professionals are prescribing probiotics—pills containing good bacteria—for conditions such as anxiety and depression.

Nevertheless, no robust studies to date show benefit for this practice.

So where do our bodies’ bacteria come from, and how can we cultivate the right mixture of little critters? Babies receive their first big burst of bacteria when they pass through the birth canal and then from their mother’s skin and milk through breast-feeding. After that initial colonization, our microbiomes change largely in response to what we eat.

A recent study in the journal Nature showed that a change in gut bacteria can occur quickly. Researchers assigned nine volunteers to eat a diet consisting of eggs, bacon, beef, cheese, and pork. Then after a break, the volunteers changed to a diet of only plants. Researchers found that within the first day of changing to a plant-based diet, volunteers’ guts became filled with bacteria associated with lower levels of inflammation in the body.

It thus appears that one way to form an optimal inner garden of microorganisms is eating a healthy diet. Another way is avoiding the inappropriate use of antibiotics. As my patient’s experience shows, when antibiotics eliminate large portions of our body’s bacteria, the results can be toxic.

—James Marroquin is a physician in Austin, Texas


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  • PAT W
    Posted: Mon, 04/11/2016 12:38 pm

    Great info. Thanks!

  •  William Peck 1958's picture
    William Peck 1958
    Posted: Mon, 04/11/2016 12:38 pm

    good info, thx. But I was interested in the turkey's role in this article.