What Bugs Are in Your Gut? (Humans from different cultures and geographic locations differ in the diversity of bacteria in their guts, but the metabolic functions that those microbial communities serve are similar)

What Bugs Are in Your Gut?
Hundreds of samples of human feces reveal how gut microbes change as
we age and vary between people in different countries.
By Ruth Williams | May 9, 2012
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Humans from different cultures and geographic locations differ in the
diversity of bacteria in their guts, but the metabolic functions that
those microbial communities serve are similar, according to a report
out in Nature today (May 9). The findings come from a large-scale
sequencing project carried out on 531 samples of human excrement from
Africa, South America, and the United States.

“It’s a humungous paper, with multiple key findings,” said food
scientist David Mills of the University of California, Davis. “An
impressive and complex piece of work,” agreed molecular biologist
Jeremy Nicholson of Imperial College, London. Neither researcher
participated in the study.

The scale and complexity stem from the research team’s aim of
answering a multifaceted question—“What is the degree to which these
microbial communities… vary within a person, as a function of
postnatal development, physiological status, cultural tradition, and
where a person lives,” said geneticist Jeffrey Gordon of the
Washington University in St Louis, who led the study.

To this end, the researchers collected samples of feces from villagers
in rural Malawi, Amerindians in Amazonian Venezuela, and metropolis-
dwelling Americans. They then performed high-throughput sequencing on
DNA taken from the samples to determine both the species and strains
of microbes present and which microbial genes were most abundant.

The team found a common pattern for how the microbiomes of babies
develop in the three countries. “It takes 6 to 9 months to get the
first 6 or 700 bugs and then another couple of years to get the adult
set,” explained Nicholson. “[Gordon] finds there is the same sort of
developmental time span between countries,” he said, “but that the
resulting microbiomes are nonetheless distinct between, let’s call it,
a third-world population and a westernized population.”

One of the most striking differences was the degree of microbial
diversity, with both the Amerindians and Malawians having far greater
diversity than the Americans. “But, ironically, [Americans] might have
more diversity in terms of the food eaten,” said Mills, which might
have been expected to correlate with microbial diversity. Gordon
suggested the Westerners’ lack of diversity could result from “our
lifestyle, our degree of hygiene, [and] our use of antibiotics,”
though further research is needed to test these possibilities.

Despite these differences between the gut microbiomes of the three
cultures, there were also striking similarities, said Gordon. For
example, “across all three populations, we see this age-dependent
change in vitamin biosynthesis,” he said. In infants, gut bacteria
tend to carry more copies of genes involved in folate biosynthesis,
while the guts of older individuals harbor microbes carrying more
genes for folate metabolism. Conversely, genes involved in vitamin
B-12 synthesis became more prevalent in the gut microbiome with age.

“What’s really fascinating about those results,” said Mills, “is that
it is reflecting what the host needs.”

The documenting and detailing of human microbiomes across ages and
cultures is an important resource for future studies, Mills added. One
obvious question arising from the work is, what difference do these
bugs make, if any, to people’s health? According to a presentation by
Liene Bervoets at the the 19th European Congress on Obesity in Lyon,
France, this week, obese children have a markedly different
proportions of the bacteria Bacteroides fragilis and Bacteroides
vulgatus in their guts than normal weight children. “Whether changes
in gut microbiota are a cause or consequence of obesity remains to be
established, but it is clear that the microbiota aid in energy
harvesting from our foods,” Bervoets said in an email to The

Gordon and his team now plan to investigate how variations in our gut
microbiomes might affect such energy harvesting. “Our long term hope…
is to understand the inter-relationship between the microbiome, the
nutritional value of foods that are consumed, and the nutritional
status of people,” he said.

T Yatsunenko et al. “Human gut microbiome viewed across age and
geography,” Nature, doi:10.1038, 2012.