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Inuit Gut Microbiome Shares Features With Gut Communities From Westernized, Urban Center

NEW YORK (GenomeWeb) – The microbial community in the gut of individuals from the Canadian Arctic Inuit population appear to be unexpectedly similar to those in gut microbiomes from individuals in an urban, westernized environment, new research suggests.

As they reported today in mSphere, researchers from the University of Montreal used 16S ribosomal RNA gene sequencing to characterize the gut microbial composition in dozens of individuals from the city of Montreal or from an Inuit population from Resolute Bay, an Arctic village that's home to just a few hundred people. They discovered that the Inuit population shares broad gut microbial community features with those found in urban individuals, at least at the phylogenetic level, though more subtle differences did arise.

"We anticipated bigger differences," senior author Jesse Shapiro, a biological sciences researcher at the University of Montreal and Canada Research Chair in microbial evolutionary genomics, said in an interview. "There was quite a lot of resemblance between the Inuit microbiome and the typical western microbiome."

The researchers used the Illumina MiSeq instrument to do 16S rRNA gene sequencing on stool samples collected by the study's first author Catherine Girard, a graduate student advised by Shapiro and co-author Marc Amyot at the University of Montreal, during one of her regular visits to the small community in Canada's Nunavut territory in late July and early August.

The study's participants included 16 adult Inuit individuals, along with two individuals of European descent and one individual with mixed Inuit and European ancestry. Most of the Inuit individuals consumed traditional diets comprised of protein- and fat-rich fare from fish and game animals, based on survey responses, although at least three individuals ate foods from the traditional diet no more than once per week.

"The majority of participants from Nunavut adhered to a modern traditional Inuit diet, and frequently consumed raw game, especially sea mammals," the authors noted. "The Inuit diet is limited in plant-derived foods and is enriched in animal protein and is an excellent source of vitamins, minerals, and micronutrients."

The team analyzed the microbial community identified in the gut samples alongside gut microbes discerned from 16S sequencing on stool samples from 26 individuals with European ancestry from Montreal.

In both populations, the bacterial diversity was diminished in individuals who were overweight, the researchers reported. And their results pointed to considerable overlap between the gut microbial community members in individuals from the Resolution Bay and Montreal.

The reason for these similarities needs to be explored further. The team suspects that they may be due to the relatively low levels of fiber found in Inuit and western diets relative to hunter-gatherer populations that consistently consume roots, tubers, and other plant material, though they have not ruled out the possibility that the merging microbiome features could reflect some the introduction of packaged or processed food to the Inuit diet.

"Even though it's one of the northernmost communities on earth, and extremely remote, [Resolute Bay] is certainly not uncontacted," Shapiro said. "There is some access to imported, packaged foods, even though it's very limited."

Some differences did turn up when the researchers took a closer look at gut microbial membership and abundance. For example, the team saw a jump in the abundance and diversity of Prevotella bacteria in Inuit individuals with more westernized diets and in individuals from Montreal. Past studies have linked the Prevotella genus to high-fiber diet, the group noted, though it has also been identified in individuals with gut inflammation.

Differences in Akkermansia genus representation also turned up, depending on individuals' location. Some strains were more plentiful in Inuit gut microbiomes, while others predominated in gut microbiomes from the Montreal population.

Several past studies have uncovered more pronounced gut microbiome differences in indigenous, remote, and/or hunter-gatherer populations from the Central African Republic, the Venezuelan Amazon, or Papua New Guinea — particularly enhanced microbial diversity.

"The few publications so far on different traditional diets — on hunter-gatherers in Africa or South America — that have a very distinct diet from the western diet have had very distinct microbiomes," Shapiro said.

He and his colleagues noted that gut microbial community diversity was only somewhat enhanced in the Inuit individuals, though they cautioned that more extensive or long-term sampling of the Inuit population might reveal gut microbiome differences that were not detected in the current analysis.

The team is currently collecting samples about once a month for a longitudinal, year-long study of the Inuit gut microbiome to get a better sense of the microbial community shifts that might accompany seasonal changes in the traditional Inuit diet.

It is also doing metagenomic sequencing analyses on the Inuit samples, in an effort to tease apart more subtle differences in the microbiomes and to identify genes that may be involved in processes such as dealing with environmental contaminants such as mercury that can make their way into northern food chains.

"The human genome does not encode any enzymes for metabolizing or detoxifying mercury. But bacteria, of course, encode many," Shapiro said, noting that "the human microbiome might have a role in transforming mercury and metabolizing it in different ways — either to more toxic forms or less toxic forms."

Over the longer term, members of the team are collaborating on a Massachusetts Institute of Technology-led effort to do standardized microbiome sample collection and analyses on individuals from hunter-gatherer populations around the world to explore the relationship between diet, human migration, human genetics, and microbial community composition.