Clearly diet plays a big role in determining which critters hang out in our digestive tracts. "The Yanomami tribe don't sit down and eat big meals, three times a day, like we do," Dominguez-Bello says. "They eat a little bit all day long. They just grab a banana when they want. Or go eat some fish soup with plantains."NPR:
Dietary fiber serves as food for many of the bacteria that live in our guts, says microbiome researcher Jeff Leach of the Human Food Project. Eat a variety of veggies, and eat the whole thing, he recommends.
"It doesn't hurt as a general rule to eat more fiber," Leach tells The Salt. "When we starve our bacteria they eat us. They eat the mucus lining – the mucin in our large intestine."
Microbiome researcher Rob Knight adds that when we do keep our bacteria well fed, they, in turn, give off nutrients that nourish the cells that line our guts.
Fiber was also central to Leach's suggestion to Stein to eat more garlic and leek. Those vegetables contain high levels of a type of fiber called inulin, which feeds actinobacteria in our guts. In fact, inulin is considered a prebiotic, since it feeds the good bacteria, or probiotics, that live inside us.
Garlic actually has antimicrobial properties, which paradoxically, could also be good thing for our microbiomes. One study shows that garlic hurts some of the bad bacteria in our guts while leaving the good guys intact.
Whole grains are another good source of fiber — but evaluating its benefits is a bit trickier. Whole grain consumption seems to be associated with high levels of a type of bacteria prevotella, Leach says. "Prevotella has been associated with inflammation in HIV patients [and] it's been associated with rheumatoid arthritis." We don't know why that is, Leach says. "So the jury's still out on whole grains."
Another way to build a better microbiome may be to eat foods that naturally teem with probiotics. Michael Pollan mentions the puported benefits of organic veggies fresh from the soil in his piece on the microbiome for The New York Times Magazine.
But this can get tricky, Knight says. In the absence of pesticides, a lot of veggies turn on their natural defenses in order to fight off insects, and those defenses can be toxic to humans.
Two studies give us a glimpse into our ancestors' microbiome — you know, those trillions of bacteria that live in the human gut. And the take-home message of the studies is clear: Western diets and modern-day hygiene have wiped a few dozen species right out of our digestive tracts. One missing microbe helps metabolize carbohydrates. Other bygone bacteria act as prebiotics. And another communicates with our immune system.
In other words, Americans' digestive tracts look like barren deserts compared with the lush, tropical rain forest found inside indigenous people.
"The concern is that we're losing keystone species," says microbiologist M. Gloria Dominguez-Bello, at the New York University School of Medicine. "That's a hypothesis, but we haven't proved it."
In 2009, her colleagues and a medical team with the Venezuelan government took a helicopter to a remote Yanomami tribe at the border of Venezuela and Brazil. Members of the tribe have lived as hunter-gatherers for more than 11,000 years in a mountainous area of the Amazon rain forest. Dominguez-Bello's colleagues took samples from 12 of the villagers' fecal matter. Back in New York City, the team used DNA analysis to figure out which species thrived in the hunter-gatherers' guts.
The biggest surprise was how many different species were present in the Yanomami's microbiome. The tribe had about 50 percent more ecological diversity than the average American has, Dominguez-Bello and her colleagues reported Friday in the journal Science Advances.
As cultures around the world become more "Western," they lose bacteria species in their guts, Dominguez-Bello says. At the same time, they start having higher incidences of chronic illnesses connected to the immune system, such as allergies, Crohn's disease, autoimmune disorders and multiple sclerosis.
"So the big question is: Are these two facts related?" Dominguez-Bello asks. "It's not clear if more diversity in the microbiome is healthier. But maybe we have lost species with important functions."
Dominguez-Bello says there's likely another reason, besides diet, for the diversity in the Yamomami's GI system: The tribe had never been exposed to antibiotics before the 2009 visit.
"Antibiotics kill bacteria in the gut, and sometimes species don't come back," Dominguez-Bello says, "This is especially true with children, whose microbiomes are in the process of getting assembled. Impacts on the microbiome at a young age can have long-lasting consequences."
But Jens Walter, a microbiologist at the University of Alberta, isn't convinced antibiotics are the major reason for the bacteria extinctions in Western guts. His data point to a more subtle culprit.
Walter and his collaborators have characterized the gut microbes in two indigenous populations in Papua New Guinea. Unlike the Yanomami tribe, these groups regularly use antibiotics. But they still have high levels of diversity in their microbiomes, Walter and his team reported Thursday in the journal Cell Reports.
The Papua New Guineans' microbiome had about 47 species that are essentially absent in the Americans they studied. The Americans, on the other hand, had only four species in their microbiome that were missing in the Papua New Guineans.
Experiments to test whether changing gut microbes in humans could affect the brain are only just beginning:
But other researchers have been trying to figure out a possible connection by looking at gut microbes in mice. There they've found changes in both brain chemistry and behavior. One experiment involved replacing the gut bacteria of anxious mice with bacteria from fearless mice.
"The mice became less anxious, more gregarious," says Stephen Collins of McMaster University in Hamilton, Ontario, who led a team that conducted the research.
It worked the other way around, too — bold mice became timid when they got the microbes of anxious ones. And aggressive mice calmed down when the scientists altered their microbes by changing their diet, feeding them probiotics or dosing them with antibiotics. They found changes in a part of the brain involved in emotion and mood, including increases in a chemical called brain-derived neurotrophic factor, which plays a role in learning and memory.
Dr. Emeran Mayer, a professor of medicine and psychiatry at UCLA has been studying the effects of probiotics on the brain in humans. Along with his colleague Kirsten Tillisch, Mayer gave healthy women yogurt containing a probiotic and then scanned their brains. He found subtle signs that the brain circuits involved in anxiety were less reactive, according to a paper published in the journal Gastroenterology.
"I'm actually seeing new neurochemicals that have not been described before being produced by certain bacteria," says Mark Lyte of the Texas Tech University Health Sciences Center in Abilene, who studies how microbes affect the endocrine system. "These bacteria are, in effect, mind-altering microorganisms."
In the mice, many of their autism behaviors were no longer present or strongly ameliorated with probiotics, says Paul Patterson at the California Institute of Technology in Pasadena, Calif. His research will be published soon in the journal Cell.
One team of researchers in Baltimore is testing a probiotic to see if it can help prevent relapses of mania among patients suffering from bipolar disorder.
"The idea is that these probiotic treatments may alter what we call the microbiome and then may contribute to an improvement of psychiatric symptoms," says Faith Dickerson, director of psychology at the Sheppard Pratt Health System.
» NPR: "What If Americans Ate Like South Africans And Vice Versa?"
» NPR: "How Bacteria in the Gut Help Fight Off Viruses"
» New York Magazine: "Cute Family. And You Should See Their Bacteria."
» Stanford Medicine: "Low-fiber diet may cause irreversible depletion of gut bacteria over generations"