So far, it is a mouse study, but most people have the same microbe
(Methanobrevibacter smithii) in their guts .... Effectively, it appears
to lower metabolism by extracting more calories from the same amount of
food.

Possibly, some overweight people may have an abundance of this bacteria.
And that would/could make weight control a little more difficult. And,
this would be another explanation for the syndrome of "eating tiny
amounts of food and still gaining weight"

Possibly, the application to humans is less simple than that, however.

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Stomach bug makes food yield more calories
Mice with a hefty dose of a certain gut bacteria are fatter.

When you eat a cake, do you get the same calories out of it as everyone
else?

http://www.nature.com/news/2006/060522/full/060522-19.html

Scientists have identified a key microbe in our guts that helps us glean
more calories from food. The discovery backs the idea that the type of
microbes in our gut help to determine how much weight we gain, and that
seeding the intestine with particular bugs could help fight obesity.

Our intestines are teeming with bacteria and other microorganisms that
help to digest the food we eat. But scientists are only just beginning
to tease out what each microbe does amidst the swarming life in these
dank, dark tubes.

Samuel Buck of Washington University in St Louis, Missouri, and his
colleagues focused on one microbe called Methanobrevibacter smithii,
which is effectively a waste-removal bug. It eats up the hydrogen and
waste products released by other microbes, and converts them into the
methane that escapes from our rear ends everyday. "It's a minor
component of the gut flora with a major impact," Buck says tactfully.

M. smithii may have a dirty job, but Buck and his colleagues have now
shown that it is a vital one. They found that by clearing waste products
it helps other gut bacteria digest some of the fibrous components of
food that we cannot, and turn them into material that our bodies can
use. Without these bugs, waste accumulates and blocks the activity of
other gut bacteria.

The researchers found that mice with a hefty dose of M. smithii in their
guts are fatter than those that don't have the bacteria.

Calorie counting

The discovery suggests that calorie counts on food labels could be
misleading, because different people may glean a different number of
calories from an identical banana or cheeseburger, based on the
individual mix of microbes in their gut.

Up to 85% of people harbour M. smithii or its cousins in their gut.
Samuel's team is now interested in examining whether overweight people
have more of this kind of bacteria, or underweight people less.

If their theory holds up in people, then it might be possible to gain or
shed pounds by planting different microbes in our guts. At this stage,
though, that is "total speculation" says Buck.

Buck presented the results at the American Society for Microbiology
meeting in Orlando, and will publish them shortly in the Proceedings of
the National Academy of Sciences.

Fatty acids

The researchers took mice that had been grown in a sterile environment,
with no microbes in their guts, and injected them with a very common
strain of human intestinal bacteria, called Bacteroides
thetaiotaomicron. Some of the mice also received a dose of of M. smithii.

About 100 times more microorganisms took up residence in the colon of
mice injected with both B. theta and M. smithii than in those injected
with B. theta alone. This suggests that the presence of waste-removing
M. smithii was somehow helping other bacteria to thrive. "There's
something cool going on," Buck says.

When both microbes were present, B. theta boosted the activity of genes
involved in breaking down and metabolizing fructans — a food component
common in onions, wheat and asparagus that the human gut cannot digest
by itself. B. theta converted the fructans into fatty acids, some of
which were taken up by the mouse gut and either used as fuel or stored
as fat.

In humans, around 10% of our calories come from such
microbe-manufactured fatty acids.

After a few weeks, mice with both types of microbe had approximately 40%
more of a particular fatty acid called acetate in their blood, and
carried 15% more fat.