Tagged: microBEnet

ESBL/BioBE welcomes new Associate Director of Outreach

ESBL and BioBE are thrilled to announce that Mark Fretz has joined the team as the new Associate Director of Outreach, based out of the Portland location.  Mark brings a unique combination of experience in architecture and public health service, and will help further our goal of promoting health in the built environment through research, outreach, and knowledge exchange.

Mark has a history of successful collaboration with the lab- several years ago he was a research assistant with ESBL.  He helped to develop the idea and grant for our ongoing project on the effect of weatherization on indoor air quality, human health, and the indoor microbiome.  He was also involved developing field materials and pilot studies for our study on the effect of daylight on dust communities, currently in review.

Mark helping set up data collection boxes for the home weatherization project.
Installing “lightboxes” onto the roof of Pacific Hall for a bacterial community study.

In addition to developing future research, and teaching, Mark will primarily be developing the Institute for Health & the Built Environment consortium that ESBL and BioBE initiated in May 2017 with their inaugural meeting.  The Consortium aims to dramatically reduce energy consumption and maximize human health by conducting research that transforms the design, construction and operation of built environments. Mark will help foster collaboration between innovative industry professionals and academic researchers in the disciplines of architecture, biology, chemistry, engineering, and urban design,  provide sharp focus to our research agenda, and accelerate the impact of our scientific discoveries.

Welcome to the team!

National Academies of Science MoBE meeting

In mid-October, The Alfred P. Sloan Foundation and The National Academies of Sciences, Engineering and Medicine co-hosted the MoBE 2017 (Microbiology of the Built Environment) Research and Applications Symposium, in Washington, D.C.  The meeting brings together researchers, industry professionals, and funders to discuss the state of MoBE research and how to bridge the gap between research and application.  Some of the opening remarks to the meeting were given by Paula Olsiewki, Program Director at the Alfred P. Sloan Foundation, who gave a retrospective on the history of MoBE and the process of growing research fields.

A number of BioBE members and collaborators were in attendance and gave presentations, including Jess Green, Co-Director of BioBE, who gave a brief history on the research of BioBE, followed by more detailed narratives on how ventilation and bioaerosols, daylighting, and antimicrobial compounds are driving community structure of the indoor microbiome.  Jonathan Eisen, Professor at the University of California, Davis, gave some background on microBEnet and the massive effort to promote microbiology on social media and in education to give our work as much impact as possible.  Richard Corsi, Professor at the University of Texas, Austin, who just spent two weeks visiting BioBE, spoke about indoor chemistry and how building design, materials, and the indoor microbiome can all affect the types and concentrations of chemicals indoor- often to the detriment of our health.  Kent Duffy, architect at SRG, spoke about how microbial research has impacted architectural design, and how this information can be used to change the way we design spaces.

In addition to presentations on their recent work, a number of meeting participants also sat on several panels to discuss broader issues.  For example, “The Myth and Reality of MoBE Manipulation” panel, moderated by Rob Knight, University of California San Diego and featuring Rita Colwell, Jeffrey Siegel, Ilana Brito, and Jessica Green as panelists, discussed the challenges to improving MoBE research and outreach.  The panel discussed the need for more basic science and evidence-based applied studies, in order to make more informed decisions on when and how to make interventions.

The full list of speaker and panel videos can be found on the microBE.net YouTube Channel, the presentation slides can be found here, and photos here.

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!

3rd Annual Microbiology of the Built Environment Conference

original-cropped-microbenet6

Last week several members of the BioBE Center visited Boulder, CO for the 3rd annual Microbiology of the Built Environment Conference hosted by the Alfred P. Sloan Foundation. James Meadow presented our recent work on building-scale microbial patterns, the phone-hand connection, and the human microbial cloud. Adam Altrichter presented a poster (see it here) on our ongoing work with the Light Box experiments that Kyla Martichuski put together for a recent symposium at the U of O. Gwynne Mhuireach also presented a poster with an update on the analyses from her study looking at the bacteria in air from parks vs parking lots throughout Eugene. Check out the Storify put together from tweets during the conference to see what folks were talking about all week.