Tagged: microbiome

The concept of hygiene and the human microbiome.

Reblogged from MicrobeBE.net.


(This post was written by Roo Vandegrift, at the University of Oregon)

I was recently asked to spearhead the writing of a review centered around the interaction between the concept of hygiene and our increasingly nuanced understanding of the human skin microbiome for the Biology and the Built Environment (BioBE) Center at the University of Oregon.

This review began with an invitation from Dyson to conduct an impartial review of hand drying studies, which have been mired in competing interests and faulty methods. We saw an opportunity to not only provide an unbiased review of the literature, but also to ask a more fundamental question: how should hygiene be defined in light of our evolving perspective of the human and indoor microbiome?  We delivered a brief summary to Dyson (here) and then built upon that work to develop this question.  

As we started digging into the body of literature on hand hygiene, two things struck us as peculiar: the first was that in the hundreds of studies explicitly examining hygiene, the concept was never explicitly defined; the second was that there seemed to be a clear division between skin microbiological investigations coming from clinically and ecologically informed perspectives, with clinical research generally relying on older cultivation-dependent techniques. These two issues became the drivers for our review, and our goal was to provide an explicit definition of hygiene that would help to bridge the gap between the clinical skin microbiology literature and the newer human-associated microbial ecology literature. We were then able to use the body of literature on hand drying as a case-study to examine the implications of using a microbial ecology-based approach to defining hygiene.

You can read the full review as a preprint on bioRxiv now: http://biorxiv.org/content/early/2016/12/20/0957450

You can read the shorter, white page summary of the review on the BioBE blog: https://biobe.uoregon.edu/2016/11/04/cleanliness-in-context

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Cleanliness in Context

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The BioBE Center just published a white paper, titled “Hand Hygiene in the 21st Century: Cleanliness in Context” that examines the history and current literature on hygiene. Specifically, the paper focuses on the role of hand drying and the debate in the literature surrounding paper towels and electric hand dryers. We posit that the conception of hygiene as a unilateral reduction or removal of microorganisms has outlived its usefulness, and propose a definition that is quantitative, uses modern molecular biology tools, and is focused on disease reduction.  20170102_BioBE_Hygiene_Dyson_summary

Edit 2017.01.11: updated white paper to reflect most recent version, added image.

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

Hickey_LabRoots_160907

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.

 

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.

BioBE hosts Microbiome Science Youth Outreach event

The BioBE Center hosted its inaugural Microbiome Science Youth Outreach workshop this past Saturday, March 12. The event featured hands-on activities covering microbiology, bioinformatics and architecture led by volunteers from the Green lab and Energy Studies in Buildings Laboratory. It was attended by 21 middle-school and high-school students and mentors from the Youth Mentoring Program of the Centro Latino Americano (CLA). CLA is a multicultural nonprofit organization in Eugene dedicated to the empowerment of the local Latino community. The Youth Mentoring Program offers one on one mentoring relationships, group mentoring, and facilitates educational and enriching activities for students in Lane County.

Photo Mar 13, 8 46 24 AM

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BioBE in GEO Magazine

 

Image courtesy of Lori Nix, www.lorinix.net
Image courtesy of Lori Nix, www.lorinix.net

 

BioBE research is featured in a new article in GEO Magazine. Titled “Die Wildnis im Wohnzimmer” (“The Wilderness in the Living Room”) and written by Ute Eberle, the article discusses the human and built environment microbiome experiments that use ESBL’s climate chamber, and quotes James Meadow.

Check out the cool video at the end of the article!