U probes bacteria in the gut

U researchers helped examine different lifestyles and diets’ impact gut bacteria quantities.

by Hannah Weikel

The average human gut contains about 100 trillion microbial bacteria that work together and impact bodily health.
A group of researchers from around the world joined the University of Minnesota’s Blekhman lab to study these little bugs and how they differ across lifestyles and continents.
Their work compared digestive microbiomes of African BaAka hunter-gatherers, Bantu agricultural workers and a sample of Americans from the Human Microbiome Project.
The researchers hoped to pave the way for future research into how bacteria can prevent conditions like diabetes, obesity, allergies and asthma.
The study, released last month in Cell Reports, used the Central African Republic’s Bantu people — who live a traditional lifestyle but with more agriculture and Western medicine — as a midpoint between BaAka and American lifestyles.
Other studies have shown a depletion in number and diversity of bacteria associated with Western diets and antibiotics, but the patterns were never shown on a gradient between three different groups, said chief researcher Andres Gomez.
The team’s work began when researcher Klara Petrzelkova contacted Gomez in 2009 after learning about the techniques he and his colleagues at the University of Minnesota use to map the genomes of gut microbiomes.
At the time, Petrzelkova was working with gorillas in the Dzanga-Sangha Protected Areas in Central African Republic to examine their gut microbiomes with help from two local groups — the BaAka and the Bantu —who later became the focus of the new study, she said.
“The Bantus and the BaAkas were helping us track the gorillas and collect [fecal] samples,” Gomez said, “but when I found out the lifestyle the BaAka have, they were true hunter-gatherers with very little Western influences. And I knew the Bantu had a different lifestyle with growing and agriculture and consuming antibiotics. The idea came to me about comparing both of their microbiomes.” 
The BaAka consume mostly wild game and foraged fruits and vegetables, while the Bantu eat agriculturally grown vegetables, cattle and antibiotics, Gomez said. 
According to the study, the researchers collected fecal samples from 28 BaAka and 29 Bantu people and found many similar bacteria in both groups but some number variance, which demonstrated a transition in the Bantu people as they lose some “traditional microbes.”
Antibiotics and a low-fiber diet common in Americans has led to a loss in the number and types of gut bacteria, said Michael Sadowsky, the University’s BioTechnology Institute director.
Gomez said they found types of bacteria that were abundant in the BaAka, still present but depleted in the Bantu and gone completely in Americans.
“We showed that transition,” he said. “We proved that there is an intermediate point in the two extremes.”
The bacteria in a human gut are good indicators of diet and health, he said. And if Americans continue consuming foods in the same way, their gut microbiomes won’t be able to gain any new bacteria types.
However, bacteria can be reintroduced after they’re gone by a “microbiome transfer” — a procedure that flushes the gut and replenishes desired bacteria with a pill — which is also being done at the University, Sadowsky said.
Gomez said they hope to determine which bacteria — or the absence of — allow “modern diseases” to occur exclusively in Westernized populations.
The researchers used a program called PICRUSt to predict the function of a bacterium based on its genome. Dan Knights, a University researcher and assistant professor in the Department of Computer Science and BioTechnology Institute, developed the method.
Knights said each disease has a distinct makeup in a gut, but there isn’t enough research to know whether some diseases are caused by the lack of certain bacteria or if the diseases kill those bacteria.
“It’s certainly clear that people in modern society have a different set of bugs and that it’s less diverse on average. And it’s also quite clear that we have higher rates of metabolic and autoimmune disorders,” he said. “But what we don’t know is which bugs … you want to restore to reduce the risk of those diseases.”