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Experiencing the culture and the climate at ASM- Day 1

Amy Cullinan
| Jun 17, 2012

ASM sizedIt's been a few years since I've attended, but the ASM General Meeting never fails to impress me with its size, organization, and the sheer number of interesting simultaneous sessions. This year I'm here to focus on how next-generation sequencing is being used, and specifically, how to make it more accessible to all researchers at all levels.

This sunny Sunday I attended some great talks on various microbiomes, advances in culture-independent microbial identification, and exciting work being done on metatranscriptomics. And one not for the squeamish on what's lurking on the light switch of my hotel room. Here are some of the highlights.

In the morning session, I jumped into the deep end of the ocean with Jonathan Zehr of the University of California Santa Cruz talking about metatransciptomic and genomic approaches to studying nitrogen fixation from free living, symbiotic, and microbial communities. Among several examples in this "Who's Doing What in Microbial Communities" session, he discussed analysis of a novel cyanobacterium using an interesting comination of qPCR, flow sorting, and paired-end high throughput sequencing, revealing its probable symbiont nature.

Jon Eisen from University of California at Davis spoke about MicroBEnet, an internet compendium on the microbiology of the built environment (BE), which is loosely defined as human-made structures and dwellings. The website is dedicated to creating and curating resources for building engineers, architects, and the general public, including some wonderfully simple guides that explain often intimidating microbiology & molecular biology terminology. Dr. Eisen also evangelized the use of social media and why scientists should be using it as a powerful communication channel. Sharing is more than caring, it's good science and good business.

Next up was Nicholas Be, from Lawrence Livermore examining the microbiome of aerosol environments using next-gen sequencing. To answer the question of what aerosolized microbes (both the ubiquitous and the potential pathogens) surround large, highly mobile human populations, aerosol material was collected from public facilities for an entire year. Using paired-end Illumina sequencing reads as a culture-independent technique, they mapped millions of unique sequence reads to taxonomic IDs, recording both abundance and composition shifts in the microbial population over time. In another experiment, a spore used as an environmental insecticide (Bacillus thuringensis serovar kurstaki) was easily identified using this aerosol sampling and sequencing method. Demonstrated success in picking out a single airborne biological agent is of keen interest to those interested in biodefense countermeasures.

Brett Baker from the University of Michigan gave a talk about sampling deep ocean vent communities and performing de novo assembly on transcripts sequenced with the Illumina HiSeq. This metatranscriptome work shows that highly active organisms are present at low genetic coverage, and pointed towards a new player in nitrate oxidation.

And finally, for those who felt like they couldn't wash their hands enough today was a talk from Katie Kirsch from the Conrad N. Hilton College of Hotel Management on microbial analysis of environmental surfaces in hotel rooms. This baseline study performed aerobic plate and coliform counts sampled on each of 19 surfaces from lightswitches and sink handles to the gloves, mop, and sponges from the cleaning carts of 9 different hotel rooms. The results were fairly predictable in that "high touch" areas had the most bacteria, while a high standard deviation suggests that items were not consistently cleaned to the same level. Larger studies adhering to strict Hazard Analysis & Critical Control Points guidelines are planned, and those of us in hotel rooms at this very moment are grateful for the recognition that cleaning standardization and testing in the hotel industry is being addressed!