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Mouth Microbiomes Diverse the World Over

NEW YORK (GenomeWeb News) – A varied array of bacteria live in human saliva — and this salivary microbiome may eventually provide a new, easily-accessible tool for evaluating human population patterns, according to a paper appearing online last night in Genome Research.

Scientists from the Max Planck Institute for Evolutionary Anthropology, the Shanghai Institutes for Biological Sciences, and the China Pharmaceutical University used partial 16S rRNA sequencing to assess the human saliva microbiome in 120 individuals from half a dozen spots around the world. The researchers discovered bacterial diversity both within and between individuals. But the team is still trying to hone in on key spittle bacteria that might help them track human history and migration.

"We found there was pretty high diversity within individuals and between individuals," senior author Mark Stoneking, an evolutionary geneticist at the Max Planck Institute for Evolutionary Anthropology, told GenomeWeb Daily News.

Beyond their health effects, microbes can also be used to help interpret human history. For instance, in a recent Science paper, an international research team used genetic information from Helicobacter pylori, a species of bacteria found in the gut, to resolve previously unrecognized details about human migration in the Pacific.

In an effort to turn up mouth microbes that might be similarly informative, Stoneking and his team used Sanger sequencing to assess 16S rRNA from saliva samples taken from 120 individuals around the world, sampling two individuals each from North America, South America, Western Europe, Eastern Europe, Africa, and Eastern Asia.

The research is one of several ongoing projects that are characterizing the microbes in and on the human body and attempting to understand their role in human health and disease, including the National Institutes of Health's Human Microbiome Project, launched in December 2007, and the International Human Microbiome Consortium officially launched last October. In addition, scientists from Forsyth Institute and Kings College, London, announced last spring that they were developing a Human Oral Microbiome Database.

Although complementary, the research was done independent of the other ongoing, large-scale microbiome projects. The work sprung from the team's previous molecular anthropology studies. For several years, the team collected human DNA samples using cheek swabs. But while that approach works well, it's a bit invasive, Stoneking explained. Then he heard that researchers were getting usable amounts of human DNA from saliva and decided to give it a try.

Indeed, they found lots of DNA in the slobber samples. But most of it was bacterial. That got Stoneking thinking that it might be possible to use this microbial DNA for anthropological studies too.

"[S]ince saliva is increasingly preferred in sampling humans as a source of DNA for epidemiologic and population genetic studies, it would be useful to identify bacterial taxa in saliva that may be able to provide insights into human population structure and migrations," he and his co-workers wrote.

For this study, they evaluated roughly 120 different clones for each individual and compared the 16S rRNA sequences with those in GenBank and the Ribosomal Database Project II. The team identified 101 known bacterial genera, including many found in the mouth before. The most commonly genus: Streptococcus, which represented nearly 23 percent of sequences detected.

They also found 196 sequences that didn't match any in the database. When the researchers did a phylogenetic analysis of the unknown sequences, they found that they fell into about 64 clusters. Altogether, the researchers estimated about 103 genera they detected had not been reported in human saliva before.

"Overall, we saw a lot of diversity," Stoneking said.

Even so, the geographic structure of the bacterial populations was surprisingly low given differences in diet, culture, environment, and other factors in different parts of the world, he noted. In fact, there seemed to be as much or more variation between individuals from the same place as between individuals from different places. Even so, Stoneking noted, the researchers may see clearer patterns if they go to the species level or deeper.

"[T]his conclusion of an overall lack of geographic structure extends only to the pool of 16S rRNA sequences and the bacterial genera identified from them," the authors noted. "Sequence variation within particular bacterial taxa may very well exhibit geographic structure that would provide insight into human population structure, relationships, and migrations, as has been observed for H. pylori."

To that end, the researchers noted, the most useful bacterial taxa will likely be those found in many places and individuals. In the new study, for example, more than 70 percent of the sequences found represented eight genera — Streptococcus, Prevotella, Veillonella, Neisseria, Haemophilus, Rothia, Porphyromonas, and Fusobacterium. As such, the authors noted, these may warrant further investigation as potential population markers.

"Our results provide a framework for further investigations of the ecological and cultural factors that may influence the composition of the human salivary microbiome, and identify promising taxa for further characterization that may provide novel insights into human population structure, migration, and contact," the authors wrote.

Still, "this is just a first sort of glimpse" of the mouth microbiome from different parts of the world, Stoneking said. He and his team are continuing to characterize samples collected so far, looking for informative species and using multi-locus sequence typing — sequencing a handful of standard, protein-coding genes — to try to dig up useful geographic and anthropological markers.

Stoneking said they are also thinking of throwing the samples into a next-generation sequencer to see what they can find.

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