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Study Uncovers Inflammatory Features in Gut Microbiomes of Cheyenne, Arapaho Individuals

NEW YORK (GenomeWeb) – A study (pdf) appearing online today in Current Biology suggests members of Oklahoma's Cheyenne and Arapaho populations carry gut microbiomes with lower levels of anti-inflammatory bugs than those found in their non-native counterparts from the same region.

Researchers from the University of Oklahoma and elsewhere teamed up with tribe members from five Oklahoma towns to profile gut microbiome patterns in more than three-dozen individuals from these Native American communities. The microbial members, gene content, and metabolite profiles from these samples were then compared with gut microbiomes from 11 non-Native individuals from Oklahoma and from members of two South American tribes.

Although Native and non-Native individuals from Oklahoma shared some gut microbiome features, the team saw shifts toward microbial composition and metabolite profiles in the Cheyenne and Arapaho gut microbiomes that resembled those previously reported in inflammatory bowel disease studies.

"At the population level, there's something really interesting going on, and there's a compelling reason to look at this in more detail in collaboration with the tribes," senior author Cecil Lewis, a molecular anthropology, microbiome, and applied social researcher at the University of Oklahoma, told GenomeWeb.

For the most part, gut microbiome studies in North America have focused on individuals of European ancestry from urban settings or in clinical contexts.

Even so, Lewis explained, some of the same conditions that have prompted increased interest in the gut microbiome — including obesity, type 2 diabetes, and autoimmune disease — disproportionately affect some Native American populations.

"If we discover that the microbiome matters when it comes to these conditions and that's information we could use to improve quality of life," he said, "it seems pretty darn important to ensure that communities with these health disparities are included in the studies to make sure they apply to them equally well."

He and his colleagues spent several years partnering with tribal leaders, administrators, and potential participants from Cheyenne and Arapaho tribes in Oklahoma to discuss the science, study approach, and results from the research.

As part of the collaboration, the researchers collected fecal samples for gut microbiome profiling from 38 adult Cheyenne and Arapaho individuals from the towns of Clinton, Concho, Geary, Hammon, and Kingfisher, all in western Oklahoma.

Along with a stool sample, each participant provided information on his or her food consumption for the three days leading up to sample collection as well as age, body mass index, type 2 diabetes status, and other data.

The team used the Illumina MiSeq to identify gut microbial community members by 16S rRNA sequencing, while metagenomic sequencing with the Illumina HiSeq offered a look at the repertoire of microbial genes present in the gut microbiomes.

To get a look at the compounds produced by these communities, meanwhile, the researchers had samples tested for hundreds of fecal metabolites at the North Carolina-based metabolomics company Metabolon.

The gut microbial communities from Cheyenne and Arapaho individuals overlapped to some extent with gut microbiome features found in 11 non-Native participants from Norman, Oklahoma, the researchers reported. In particular, both the Native and non-Native gut microbiomes showed microbial composition patterns that have been linked to industrial agricultural lifestyles.

Compared with gut communities in previously profiled individuals from Native populations in South America, for example, individuals from Oklahoma had diminished microbial diversity and an abundance of microbes from the Firmicutes phylum.

Indeed, all but three of the top 15 genera detected in the Cheyenne and Arapaho gut microbiomes belonged to Firmicutes, though bugs from the Actinobacteria, Bacteroidetes, and Proteobacteria phyla turned up across the samples as well.

When they focused on differences in gut microbial communities in the individuals from the Cheyenne and Arapaho tribes and their non-Native counterparts, the researchers saw an over-representation of Blautia, Coprococcus, Dorea, and other genera from the Lachnospiraceae family.

In contrast, the non-Native individuals had higher levels of bacteria from the Ruminococcaceae family such as Faecalibacterium, a potentially anti-inflammatory microbe found at diminished levels in the guts of Crohn's disease patients in the past.

Likewise, the Native American samples contained metabolite profiles that previously have been correlated with Crohn's disease and other inflammatory bowel diseases, Lewis said.

He emphasized that the current analysis was not done as part of a clinical study, though it provides population-level clues to designing future studies of microbial features associated with obesity, type 2 diabetes, and other clinically relevant traits.

Still, the existing data are expected to help untangle relationships between microbial community membership and fecal metabolites, Lewis explained, since at least some of the metabolites detected seem to inhibit certain gut bugs.

Those involved in the effort argued that such findings underscore the importance of developing partnerships with Native American communities and other populations that could benefit from the future translation of microbiome research.

"[I]t is essential that the scientific community actively engage in and recruit these vulnerable populations in basic research through a strategy that promotes mutual trust and understanding," the study's authors wrote.

For their part, the researchers are gearing up to publish findings on samples not included in the current study. They are also in discussions with Cheyenne-Arapaho members in Oklahoma about the possibility of doing additional research with the tribes and are interested in establishing relationships with other Native American populations.

In particular, Lewis explained, it may be particularly helpful to delve into the roles that diet, access to high-quality foods, and other socioeconomic factors play in gut microbiome features from various populations across Oklahoma.

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