A Gut Feeling

The Microbes Living Within Your Intestines Can Affect
Your Mental and Emotional Well-Being


March 2015

By Lisa James

Energy was never a problem for MaryAnne. “My life was always very, very busy,” says the retired financial services executive. Neither was cognition, nor memory.

But that all changed when she hit her late 50s. “I started feeling sluggish,” recalls MaryAnne, now 67, who lives in New York City and asked that her last name not be used. “I couldn’t find words, I would say that I couldn’t even read a book.” She also would forget things, such as whether or not she had fed her dogs. “Brain fog—it’s hard to explain, especially when you’re used to being fully functional,” she says.

Sound familiar?

A lot of people jest about having “senior moments.” But it’s no laughing matter when memory loss and impaired thinking, as well as lack of energy, start to interfere with one’s life; it’s even more ominous when such slippages represent the prelude to serious disorders such as Alzheimer’s disease. And suffering from anxiety or depression is no joke, either.

Scientists, logically enough, have looked to the brain as the key to difficulties with cognition or mood. But cutting-edge research, much of it published just within the past few years, now points to a surprising new culprit—the micro-organisms living within one’s intestines, also referred to as the gut flora or microbiome.

The Gut-Brain Connection

The microbiome is more extensive than most of us realize.

“When you look in the mirror you think of yourself as one person,” says William Miller, MD, of Phoenix, Arizona, a physician in private practice for more than 30 years and author of The Microcosm Within (Universal Publishers). However, Miller notes that the microbial cells we carry, which colonize our bodies inside and out, outnumber our own cells ten to one. “We can’t live without them and they can’t live without us,” Miller says. “If I took out your spleen, you’d be fine. If I sterilize your gut, you couldn’t survive.”

Probiotics for Digestive health

The microbiome is best known for supporting healthy digestion. “It nourishes and sustains your gastrointestinal tract,” says Raphael Kellman, MD. “And it keeps you at your ideal weight by helping you digest your food, maintain an appropriate appetite, regulate the calories that enter your system and keep your metabolism working at optimal speed.” What’s more, poor microbiome function has been linked to metabolic syndrome, type 1 diabetes and rheumatoid arthritis.

While scientists are a long way from identifying all of the probiotic bacteria within the gut, some types have been well-documented. Among them are many of the Lactobacillus species, including acidophilus, brevis, bulgaricus, casei, lactis, plantarum and rhamnosus, and the Bifidobacterium varieties, including
bifidum, coagulans (also known as L. sporogenes) and lactis. (Two other probiotic species, S. salivarius K12 and M18, are found in the mouth, nose and throat, where they help defend against upper respiratory infections.)

These probiotics are supported by prebiotic fibers; among them is FOS, which has been found to not only promote a healthy gut flora mix but to also enhance absorption of minerals such as calcium and magnesium.

These microbes affect the brain through pathways known as the gut-brain axis or “the microbiome-gut-brain axis; the three are inextricably linked,” says Raphael Kellman, MD, of The Kellman Center for Integrative and Functional Medicine in New York City and author of The Microbiome Diet (Da Capo Lifelong).

How does this axis work? For one thing, the gastrointestinal tract is equipped with its own nervous system. “The neurons in the gut are so innumerable that many scientists are now calling the totality of them ‘the second brain,’” says David Perlmutter, MD, FACN, ABIHM, of the Perlmutter Health Center in Naples, Florida, board-certified neurologist and author of Brain Maker (Little, Brown). He says these neurons communicate with the brain via the vagus nerve. According to a review done at McMaster University in Hamilton, Ontario, “There is now strong evidence from animal studies that gut micro-organisms can activate the vagus nerve and that such activation plays a critical role in mediating effects on the brain and behavior” (Advances in Experimental Medicine and Biology 2014).

The digestive tract produces neurochemicals such as serotonin, best known for promoting feelings of well-being in the brain. In the intestines, serotonin is involved in “controlling motility and contractions,” says John Bienenstock, FRCP, FRCPC, FRSC, Professor of Pathology and Molecular Medicine, Director of the Brain-Body Institute at St. Joseph’s Healthcare Hamilton and one of the AEMB authors. He says irritable bowel syndrome, marked by pain and bowel irregularities with no obvious physical cause, is now thought to be caused and/or maintained by the nervous system, including the brain. Kellman says, “A big part of the reason IBS is associated with depression and anxiety is because of the microbiome. It’s part of the same problem.”

Gut microbes also influence the brain through their interaction with the immune system, including that system’s inflammatory response. “The microbiome actually educates and modulates the immune system,” Kellman explains. “That can then set off an inflammatory cascade, and that’s transmitted to the brain.”

One factor in chronic inflammation is leaky gut syndrome, in which a dysfunctional bowel wall allows substances to enter the blood that shouldn’t be there. Perlmutter says one of those substances, lipopolysaccharide (LPS), “induces a violent inflammatory response if it finds its way into the bloodstream.” But healthy gut flora “bolster the intestinal wall’s integrity and prevent gut permeability.”

All of these actions represent the microbiome’s profound effects on the brain. One study found that gut microbes may induce the brain to produce cravings (Bioessays 10/14). In another, a lack of gut flora enhanced anxiety and stress in rats (Psychoneuroendocrinology 4/14).

Microbes Under Attack

We start acquiring our gut flora in life’s first moments, a process with long-term health implications.

“The current thinking is that the moment we move through the birth canal and are exposed to organisms in the vagina, our microbiome begins to develop,” says Perlmutter. He cites studies in which babies born by Caesarian section had microbiomes “dominated by an abundance of the potentially harmful bacteria” found on the skin, and notes that these children “have triple the risk of developing ADHD.”

Being raised in an overly clean environment, often as the result of efforts to defend against harmful organisms, can instead harm a child’s developing microbiome. “What constitutes the microbiome is a process that occurs early on in life. If it’s a very sterile environment the microbiome is affected,” says Kellman.

Unnecessary exposure to antibiotics through both medicine and agriculture doesn’t help matters. “The overuse of antibiotics absolutely disrupts the microbiome and it can have adverse effects both in terms of the microbiome’s effects on inflammation and in terms of brain health,” says Kellman.

Stress can alter the microbiome as well. Bienenstock says the effects of chronic stress “are felt in the brain resulting in things such as anxiety, but are also felt by the bacteria in the gut. The brain is, through stress, producing imbalance in the gut bacteria, which in turn produces problems in the brain.”

No one can undo such early influences as having been given a lot of antibiotics as a child, but that doesn’t mean microbiome function can’t be improved in adulthood. “Trauma to the microbiome can, to some degree, be offset by probiotics found in fermented foods, by prebiotic foods that enhance probiotic organisms and by the use of probiotic supplements,” says Perlmutter.

Better Microbial Balance

Direct testing of the microbiome is in its infancy. “There are thousands of different types of bugs and we only know most of them by their genetic signatures. Seventy percent of them have not really yet been cultured,” says Bienenstock. Because the technology is so new, researchers are only beginning to identify these organisms.

“We’re not even quite sure of what we’re missing, but 90% of what is there was being missed,” says Miller.

There are indirect ways to test for poorly functioning flora. Perlmutter says his clinic tests for LPS “in people with disorders such as multiple sclerosis, Alzheimer’s, autism and ADHD, and we find more often than not that those markers are significantly elevated.” Kellman will test for levels of a fatty acid called butyrate (“a healthy microbiome should be producing a significant amount of butyrate”) as well as markers such as zinc and B vitamin levels: “If these levels are low, you know the microbiome is not healthy.”

One way to help the microbiome is by avoiding substances that kill off beneficial bacteria. Perlmutter cites unnecessary antibiotic usage and acid-blocking drugs as harmful factors. He says it’s a good idea to reduce exposure to environmental toxins as much as possible (especially pesticides and chlorine), believing it “prudent to be cautious and assume they are inflicting damage until we have solid research to prove otherwise.”

Another way to encourage microbial health is through the use of supplemental probiotics. In rodents, various formulations have shown the ability to ease stress and encourage greater neuronal plasticity, a key factor in cognitive function (Neurogastroenterology and Motility 11/14, PLOS ONE 9/14). Kellman says that just as important is the use of prebiotics, “natural compounds that are fuel and energy for the microbiome.”

But neither probiotics nor prebiotics will help without significant changes in diet.
Both Kellman and Perlmutter advocate greater consumption of such fermented foods as kefir, kimchi, pickles and other fermented vegetables, sauerkraut and live-cultured yogurt, all of which naturally contain probiotics. Both also stress vegetables in addition to healthy proteins and fats; Kellman calls plants that contain the prebiotic fibers inulin and arabinogalactan—in particular asparagus, carrots, garlic, Jerusalem artichokes (also called sunchokes), jicama, leeks, onions, radishes and tomatoes—as “microbiome superfoods.”

Kellman says his Microbiome Diet “produces significant brain improvements” as well as weight loss and greater energy levels. “When you improve the microbiome, that’s the pathway to optimal health,” he says.

MaryAnne took her complaints of low energy and brain fog to Kellman. He helped her address a number of issues, including thyroid dysfunction and sensitivity to gluten, a grain protein that can promote leaky gut.

“We started to change the whole diet,” she says. “My diet before that was pretty horrendous. I’d start the morning off with oatmeal and sometimes I wouldn’t eat until 10 at night; in between there would be a lot of junk food.”

MaryAnne says that as a child she would avoid fruits and vegetables. But after following Kellman’s recommendations, “My taste buds have changed. I don’t eat the stuff that I used to eat.

I don’t have any processed foods. I’m really pretty good with no gluten; every once in a while I’ll have a piece of bread.”

What does MaryAnne eat now? “I do a lot of beans and lentils,” she says. “I do flax seeds, that type of thing. I’ve come to love brussels sprouts, broccoli, avocado. My immune system was really bad, but I started eating garlic and onions every single day.

I eat a lot of eggs; I’ll make omelets with onions, radishes. I use ghee (clarified butter) and coconut oil. I’ll have salads. I drink a little kefir in the morning, have sauerkraut once in a while. I’ll have a glass of wine (another fermented food) every couple of days.”

In addition to probiotics and prebiotics, MaryAnne takes glutathione, an antioxidant, and digestive enzymes. “I wasn’t digesting food,” she says. “Even the crummy food I had, I wasn’t even digesting that.”

As a result of her efforts, MaryAnne says her energy levels improved quickly, as did her gluten-related stomach pains. “The brain fog went away after a while,” she notes.

“The concentration, the being unable to finish a sentence, that probably took a couple of months.”

Today, “I feel very energized. I can do things again. I do a lot of volunteer work now. The concentration, the reading, the writing, all of that is back,” says MaryAnne. “My stress relief is I’m out with the dogs and seeing people and having a good time. I don’t even take my phone to the park. Friends ask why they can’t reach me in the morning and I say I just like to think.

“A lot of this happened because I had a good doctor,” MaryAnne adds. “I’m a supporter of finding a really good doctor who can be your partner in this healing process.”

Many researchers believe that microbiome support represents a breakthrough, including its ability to bolster brain function. “We are going to have a terrific yield in terms of health, not just length of life but our ability to lead lives in which we feel well at older and older ages,” says Miller.

“The body works holistically,” says Perlmutter. “We have to step back and say that maybe the answers we’ve been looking for all these years may lie in the gut.”

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