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Nasal Microbiome Study Examines Influence of Host Genetics, Types of Bacterial Communities

NEW YORK (GenomeWeb) – The contents of a person's nasal microbiome appear to be swayed more by the environment than by host genetics, according to a team of researchers from the US and Denmark.

A team led by Paal Skytt Andersen from the Translational Genomics Research Institute and the University of Copenhagen examined the nasal microbiomes of 46 identical and 43 fraternal twin pairs, finding little influence of host genetics on the composition of the microbiome. Still, Andersen and his team noted broad nasal community types that did affect whether an individual was colonized by the pathogen Staphylcoccus aureus, as they reported in Science Advances today.

"This study … suggests that the bacteria in the nose are not defined by our genes and that we may be able to introduce good bacteria to knock out bad bugs like staph," co-author Lance Price, the director of the Center for Microbiomics and Human Health at TGen, said in a statement. "Using probiotics to promote gut health has become common in our culture. Now we're looking to use these same strategies to prevent the spread of superbugs."

People colonized by S. aureus, the researchers noted, are at increased risk for developing an infection due to the bacterium, the drug-resistant version of which has been responsible for more than 18,000 deaths a year in the US.

After 16S rRNA sequencing and classification of the nasal microbiome samples the researchers collected from the cohort of Danish twins, they were able to divvy the samples into seven types based on the prevalence and proportion of bacteria present.

For instance, the nasal microbiome community state type dubbed CST4 — which was the most common type — was defined by the presence of Propionibacterium species, while CST2 was marked by the presence of Enterobacteriaceae like Escherichia, Proteus, and Klebsiella species.

Only about a quarter of monozygotic twins shared the same nasal CST and roughly the same percentage of dizygotic twins shared nasal CSTs, indicating host genetics doesn't have much of an influence on the make-up of the nasal microbiome, the researchers said.

However, they found that that there was a significant link between host genetics and nasal bacteria density. About 30 percent of variation in nasal bacteria density was heritable, they noted.

Women, they added, tended to have lower levels of bacterial density than men.

At the same time, bacterial density was associated with the types of bacteria present, the researchers said. Bacterial density was highest in the two least common CSTs and lowest in the two most common CSTs.

Nasal colonization by S. aureus varies among CSTs. Some taxa, the researchers said, could predict the presence or absence of S. aureus, while others could predict its absolute abundance in a threshold-dependent manner.

Dolosigranulum, the researchers reported, was the best at indicating whether S. aureus would be present. The rate of S. aureus nasal colonization among individuals at or above the Dolosigranulum threshold was 16 percent, as compared to 56 percent in a simulated population.

In addition, P. granulosum was negatively correlated with the presence of S. aureus, while S. epidermidis was positively correlated with its presence.

There also appeared to be no difference in S. aureus nasal colonization rates of men and women. This, the researchers said, contradicts previous culture-based reports. They argued, though, that previous reports didn't take the higher bacterial density levels that men have into account.

From this study, the researchers concluded the nasal microbiome is environmentally derived and what taxa are present can influence whether S. aureus is able colonize.

"We believe this study provides the early evidence that the introduction of probiotics could work to prevent or knock out Staph from the nose," first author Cindy Liu from Johns Hopkins School of Medicine said.