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Team Tracks Airborne Microbes Using Household Dust Samples Collected by US Volunteers

NEW YORK (GenomeWeb) – A study published online this week in the Proceedings of the National Academy of Sciences considered the composition of microbial communities in dust samples from households across the US, providing a glimpse at airborne microbial communities and factors that can influence them.

"This study provides the first glimpse of the continental-scale distributions of microorganisms in the atmosphere, giving us the baseline data to ask all sorts of interesting questions," the University of Colorado at Boulder's Noah Fierer, senior author on the study, said in a statement.

Fierer and colleagues from the US and Denmark used targeted sequencing to identify the bacterial and fungal members of dust samples from some 1,200 American households, spanning all 50 states. All told, the samples housed roughly 112,000 bacterial phylotypes and around 57,000 fungal phylotypes, though the composition of the communities varied by location and with shifting climate and soil conditions.

It's estimated that the average person inhales thousands of airborne microbes for every hour spent outside, the study's authors explained. And such exposure is suspected of contributing to everything from human conditions such as allergic asthma to fungal infections in crop plants.

Still, efforts to fully characterize the collections of microbes swirling around us remain incomplete. The current study centered on bacteria and fungi circulating in the near-surface atmosphere at sites around the country.

To scrutinize these microbial communities, the team did targeted sequencing on samples obtained through a North Carolina State University-organized citizen-scientist effort called the "Wild Life of Our Homes" project. Using a kit supplied by the center, participants recruited between early 2012 and spring 2013 took swab samples from the upper trim of exterior doors — a site suspected of serving as a rarely cleaned landing site for dust aerosols.

Investigators sequenced 16S rRNA genes in the samples with Illumina HiSeq or MiSeq instruments to get a look at the bacteria and archaea they contained. They also sequenced the internal transcribed spacer genes ITS1 and ITS2 to glean information on fungal species in the communities.

From this data, the team saw around 4,700 bacterial phylotypes and 1,400 fungal phylotypes in each dust sample, on average. Alphaproteobacteria bacteria and Ascomycota fungi turned up most frequently, though many of bacterial or fungal phylotypes were picked up in just a smattering of samples.

Bacterial and fungal representatives varied by geographical region, researchers reported, especially when comparing coastal and central sites. Comparable microbial community compositions were detected at sites near the East and West Coasts, for example, while central sites had distinct microbial mixtures.

The team didn't see any clear-cut differences in microbial community membership between urban and rural sites in the same geographic regions. But it did detect somewhat more homogeneous dust microbiomes in samples from urban centers.

"If I go from a rural area near Raleigh, North Carolina, to downtown Raleigh, I don't see a big difference in airborne microbial life between the two places," co-author Dunn, a biological sciences researcher affiliated with North Carolina State University and the University of Copenhagen, said in a statement. "But if I go from Raleigh to New York City, the microbial life is even more similar. So there are subtle differences here."

Some of the dust microbes patterns appear to be linked to environmental factors such as climate and soil composition, the study's authors explained. Additional research will be needed to tease apart impacts that airborne microbes found in various locales have on human health and the environment.