Lake Arrowhead Microbial Genomics

Lake Arrowhead

Postdoc Roxana Hickey presented “Microbial interactions between humans and the built environment” at the 21st Lake Arrowhead Microbial Genomics meeting held in Lake Arrowhead, California on September 18-22, 2016 (slide deck below). The biannual conference hosted more than 100 scientists and featured a variety of speakers (58% of whom were female!) highlighting research on the human microbiome, disease pathogenesis, population and evolutionary genomics, and cutting-edge omics techniques. Jonathan Eisen (UC Davis), a long-time attendee and promoter of the meeting, chaired a session on the built environment microbiome (Storify here) in which Dr. Hickey presented past and present BioBE research. Other talks in the session included microbial community assembly in cheese manufacturing (Rachel Dutton, UC San Diego), a citizen science study of the highly polluted Gowanus Canal in New York City (Elizabeth Hénaff, Mason lab @ Weill Cornell Medicine), community engagement through microbiome research aboard the International Space Station (David Coil, Eisen lab @ UC Davis), and evolution of biofilm formation in response to rising marine temperature (Alyssa Kent, Adam Martiny lab @ UC Irvine).

 

David Coil summarized each day of talks at the meeting on the microBEnet blog (day 1, 2, 3 and 4), and Jonathan Eisen created several Storify recaps of #LAGM16 tweets (here, here and here). The meeting was the most Twitter-active I (Roxana Hickey) have attended and contributed to yet, which facilitated active discussions with members both at and away from the meeting.


Here are my main three main takeaways from the meeting:

  1. Metagenomics (and other ‘omic’ techniques) is gaining strength and popularity for a variety of applications. These include genome reconstruction across whole communities of microorganisms, strain-level diversity and population genomics, functional analyses, and development of targeted therapeutics and rational probiotics. There were very few amplicon-based studies at this meeting (I noticed a similar trend at the International Symposium on Microbial Ecology #ISME16 last month in Montreal). In addition, the tools used to analyze omics data are plentiful and sophisticated. I was especially impressed by work featured from the labs of Eric Alm (MIT), Jill Banfield (UC Berkeley), Kostas Konstantinidis (Georgia Tech), and Adam Phillippy (NIH).
  2. Many are beating the drum for more reference genomes and cultured isolates. Human-associated bacteria are fairly well-represented in the databases, thanks in large part to the Human Microbiome Project, but for most other environments we have relatively low representation of the resident microbes. This dearth of reference genomes limits our ability to make inferences about the function and ecology of the vast majority of microbes on earth, as was highlighted in a recent update to the tree of life (Hug et al. Nature 2016). More and more scientists are shifting some of their efforts toward cultivation and sequencing of isolates from diverse environments.
  3. Citizen science and community outreach are increasingly popular and wildly successful approaches to microbiome research. I was really excited to learn about the BKBioreactor Project on the Gowanus Canal (which made use of a community biohacker lab in Brooklyn), Project MERCCURI (which relied on crowdsourcing efforts to send microbes to space), and FijiCOMP (a really cool study looking at microbial transmission among members of a community in Fiji). All of these projects promote open access to data and publications. It got me very excited and thinking about ways to incorporate more public outreach in my own research.

Finally, I would be remiss not to mention the stunning fluorescence microscopy images of dental plaque presented by Jessica Mark Welch (Marine Biological Laboratory) illustrating genus-specific bacterial assemblages in the finest of detail (recently published in PNAS). These images are not only beautiful, but they also provide direct insights into physical interactions between populations of bacteria and inform hypotheses about their possible ecological roles in assembly and succession. Would love to see this technique employed in other microbial habitats!

BioBe research highlighted in LabRoots webinar

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BioBE postdoc Roxana Hickey presented a live webinar highlighting past and ongoing BioBE research in the LabRoots Microbiology and Immunology Virtual Event held on September 7-8, 2016. Her talk, titled “Exploring the Great Indoors: The Built Environment and Human Health”, was featured alongside 16 other presentations covering a variety of topics in microbiology and biomedical research. Two other speakers, Jack Gilbert (University of Chicago) and Scott Kelley (San Diego State University), also presented built environment microbiome research to the broad audience of researchers and clinicians. All presentations from the event are available for on-demand viewing at LabRoots until the end of the year (free registration required).

Dr. Hickey’s slides can also be viewed at SlideShare.

 

Linking antimicrobials and antibiotic resistance genes in indoor dust

Previous BioBE postdoc Erica Hartmann (now Assistant Professor at Northwestern University!), along with several BioBE researchers and members of Curtis Huttenhower’s (Harvard) and Rolf Halden’s (Arizona State) research groups, recently published a paper establishing a link between antimicrobials and antibiotic resistance genes in indoor dust. Dr. Hartmann published a post summarizing the main findings at microBEnet. The paper is freely available in the journal Environmental Science & Technology.

OSU & The Corvallis Art Center: “Microbiomes: To See the Unseen”

Klari Reis petri dish art (https://www.google.com/url?sa=i&rct=j&q=&esrc=s&source=images&cd=&cad=rja&uact=8&ved=0ahUKEwjspNmOlefOAhUY52MKHWJGCgkQjRwIBw&url=https%3A%2F%2Fwww.pinterest.com%2Fpin%2F574771971167874557%2F&bvm=bv.131286987,d.cGc&psig=AFQjCNFaZz7_KZ2NSeBdt7Nb1ihd2rQT6w&ust=1472578615934970)
Klari Reis petri dish art

Graduate student Ashley Bateman recently contributed to the workshop portion of the The Microbiome Art Project, a collaboration between OSU and the Corvallis Arts Center. Artist workshops like the one she attended, bring graduate researchers and artists together to communicate & discuss current microbiome research while inspiring fantastic microbiome art! The art exhibition, “Microbiomes: To See the Unseen“, is scheduled for April 13-May 27, 2017 and will include visual artists, musicians, and poets.

2016 Pacific Northwest Women in Science Retreat

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I (Ashley Bateman) recently won a scholarship from the Women in Graduate Sciences organization at the University of Oregon, to attend the 2016 Pacific Northwest Women in Science Retreat. The event was held at Camp Magruder in Rockaway Beach, OR from July 8th-10th. The attendees and workshop leaders featured over 100 women from across the STEM career spectrum, from graduate students, technicians, and post-docs to government and industrial early and late career scientists. The focus of this retreat is on professional skill development and professional networking, especially for and with other women scientists in the region. The retreat featured 3 main workshops: A COACh workshop on the Performing Art of Science Presentations, a Rehearsals for Life: workshop, and a Bragging workshop led by the enthusiastic Judy Giordan. We also heard from and asked questions of a diverse group of women on academic, industrial, and alternative career panels.

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Understanding the microbiome of the Boston subway

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BioBE members Jessica Green and Erica Hartmann contributed to a study looking at the microbiome of the Boston transit system, the MBTA. The paper, published in mSystems is out here. The first author on the paper, Tiffany Hsu, also wrote a post on microBEnet.

Erica Hartmann also travelled to Shanghai, China, to represent the Boston subway study team at the second annual Metagenomics & Metadesign of Subways and Urban Biomes (MetaSUB) meeting. Researchers from around the world participated in the first ever world sampling day to collect microbes in subways and shared their experience and progress at this meeting. For more information, check out the project website.

“Microbiology of Built Environments” FAQ

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The American Academy of Microbiology has published a FAQ report on the microbiology of the built environment colloquium convened in September 2015. The report is “based on the deliberations of experts who gathered for a full day to discuss a series of questions developed by the steering committee regarding the role of complex microbial ecosystems found in built environments.” The BioBE Center was represented during the event by Jeff Kline.