Another key role of the microbes that live within us has been identified by researchers. In a
study comparing mice raised in a "germ free" environment and mice
raised under more typical lab conditions, scientists observed that the mircobiome serves as a mediator of host
gene expression through the epigenome, the chemical information that
regulates which genes in cells are active.
In our guts, and in the guts of all animals, resides a robust
ecosystem of microbes known as the microbiome. Consisting of trillions
of organisms — bacteria, fungi and viruses — the microbiome is essential
for host health, providing important services ranging from nutrient
processing to immune system development and maintenance.
‘The gut bacteria metabolizes plant nutrients to form short-chain fatty acids that are important chemical messengers, communicating with the cells of the host through the epigenome.’
Writing online in the journal Molecular Cell
, a team of
researchers from the University of Wisconsin-Madison describes new
research helping tease out the mechanics of how the gut microbiome
communicates with the cells of its host to switch genes on and off.
upshot of the study, another indictment of the so-called Western diet
(high in saturated fats, sugar and red meat), reveals how the
metabolites produced by the bacteria in the stomach chemically
communicate with cells, including cells far beyond the colon, to dictate
gene expression and health in its host.
"The bugs are somehow
driving gene expression in the host through alteration of the
epigenome," explains John Denu, a UW-Madison professor of biomolecular
chemistry and a senior researcher at the Wisconsin Institute for
Discovery, and a co-author of the new study. "We're starting to
understand the mechanism of how and why diet and the microbiome matter."
study, which was led by Kimberly Krautkramer, an MD/Ph.D. student in
the UW School of Medicine and Public Health, revealed key differences in
gene regulation in conventionally raised mice and mice raised in a
germ-free environment. The mice were provided with two distinct diets:
one rich in plant carbohydrates similar to fruits and vegetables humans
consume; the other mimicking a Western diet, high in simple sugars and
A plant-based diet, according to Federico Rey, a UW-Madison
professor of bacteriology and also a co-corresponding author of the new
report, yields a richer microbiome: "A good diet translates to a
beautifully complex microbiome," Rey says.
"And we see that the
gut microbiome affects the host epigenome in a diet-dependent manner. A
plant-based diet seems to favor host-microbe communication."
new Wisconsin study shows that a small set of short-chain fatty acids
produced as the gut bacteria consume, metabolize and ferment nutrients
from plants are important chemical messengers, communicating with the
cells of the host through the epigenome. "One of the findings here is
that microbial metabolism or fermentation of plant fiber results in the
production of short-chain fatty acids. These molecules, and potentially
many others, are partially responsible for the communication" with the
epigenome, says Denu.
In the study, the gut microbiota of the
animals that were fed a diet rich in sugar and fat have a diminished
capacity to communicate with host cells. According to the Wisconsin
team, that may be a hint that the template for a healthy human
microbiome was set in the distant past, when food from plants made up a
larger portion of diet and sugar and fat were less available than in
contemporary diets with more meat and processed foods.
"As we move
away from plant-based diets, we may be losing some of that
communication between microbes and host," notes Rey. "With a
Western-type diet, it seems like the communication between microbes and
host gets lost."
Foods rich in fat and sugar, especially processed
foods, are more easily digested by the host, but are not necessarily a
good source of food for the flora inhabiting the gut. The result is a
less diverse microbiome and less communication to the host, according to
A surprising finding in the study is that the
chemical communication between the microbiome and host cells is far
reaching. In addition to talking to cells in the colon, the microbiome
also seems to be communicating with cells in the liver and in fatty
tissue far removed from the gut. That, says Denu, is more evidence of
the importance of the microbiome to the well-being of its host.
kicker experiment in the study, says Denu, was providing mice raised in
a germ-free environment with three different short-chain fatty acids
that the study showed to be important messengers to the epigenome. The
supplement was enough to promote the kind of healthy interplay between
microbiota and host cells seen in mice given a diet high in plant fiber.
helps show that the collection of three short-chain fatty acids
produced in the plant-based diet are likely major communicators," adds
Denu. "We see that it is not just the microbe. It's microbial