NSF Funding Opportunity: Science and Technology Centers: Integrative Partnerships

Just got this from Amy Pruden, via Paula Olseiwski.   Seems like a potential opportunity to get some funding for the microbiology of the built environment from NSF.   The “Concept” of the program is described below: The Science and Technology Centers: Integrative Partnerships — Concept The Science and Technology Centers (STC): Integrative Partnerships program supports innovative research and education projects that require large-scale, long-term investments. STCs conduct world-class research through partnerships among academic institutions, national laboratories, industrial organizations, and/or other public/private entities, and via international collaborations, as appropriate. These partnerships build intellectual and physical infrastructure within or between disciplines and facilitate … Continue reading

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Swabs to Genome Workflow Part II: The Problems

You can check out David Coil’s introduction to the project here. The workflow pre-print is hosted by Peer J here. Feel free to check it out! We would love any comments or suggestions. I was first introduced to the swabs to genome workflow project a little over a year ago. I had just started in the Eisen lab and was looking for a project I could work on over the summer and finish up before I graduated in December. David described the extensive work that had gone into the undergraduate reference genome project, explaining that while it had been difficult to … Continue reading

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Diversify Your Microbiome by Rock Climbing Indoors

When a recently published paper entitled “Microbial Sequencing Analyses Suggest the Presence of a Fecal Veneer on Indoor Climbing Wall Holds” showed up in my NCBI digest, I got excited.  However, my excitement died a little when I actually read the paper. Most importantly, the title is slightly deceptive, as only 9% of all reads in the study classified as fecal-associated organisms.  The authors even state that their results indicate “dispersal of microorganisms from climbing shoes, hands, and environmental sources, with less input from human sources on climbing holds compared to other built environments.” The study authors swabbed hand holds … Continue reading

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Nice series of papers on microbial ecology and space travel

Well, here is another benefit of automated Google Scholar searches. I think it is unlikely I would have found these new papers without such searches but these are fascinating and directly relevant to many aspects of work we are doing on Project MERCCURI.  A series of papers on microbial ecolog and space travel in the journal “Microbes and Environment” Microbial Monitoring of Crewed Habitats in Space—Current Status and Future Perspectives Microbial Existence in Controlled Habitats and Their Resistance to Space Conditions Space Habitation and Microbiology: Status and Roadmap of Space Agencies And for each the Full Text is freely available. … Continue reading

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Antioxidants: Their role in Anaerobic Culturing

Back in May, I had the pleasure of attending a talk at ASM 2014 by Didier Raoult on the the importance of culturomics. At one point in the talk he mentioned that they just came out with a paper that showed that they could get anaerobes to grow in the presence of oxygen if you supplied antioxidants to the media. Different ways of culturing anaerobes came up in lab the other day reminding me to read the paper that had come out back in May. The 2014 preliminary report  showed that the addition of high concentrations of ascorbic acid and/or glutathione … Continue reading

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Swabs to Genome Workflow available as pre-print on PeerJ

Almost exactly a year ago we finally wrapped up our undergraduate project focusing on sequencing and assembling reference genomes from the built environment.  This project aimed to take undergrads through every step from starting with a swab to ending with a published genome announcement and data in NCBI. Over the course of the work, we discovered a number of unforeseen complications and snags in the process.  So we set out to try it again, document every step, and to produce a workflow allowing others to do the same thing.   Along the way we got a push from several people to … Continue reading

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Termite mounds: another kind of built environment

Recently I was doing field work in southern Africa and marveling at the enormous termite mounds that dot the landscape. Composed of soil, saliva and poop, termite mounds are amongst the most spectacular of the structures built by animals. These fascinating structures maintain the ventilation of termite nests that are actually subterranean. This PBS blog post has a nice diagram of the structure of a termite mound: http://www.pbs.org/wnet/nature/episodes/the-animal-house/the-incredible-termite-mound/7222/. Termites have been tending fungal gardens for about 30 million years. In northern Namibia, all of the termite mounds tilt to the north (or towards the equator). Do the building scientists have any explanations to offer … Continue reading

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Workshop on Animals in the Built Environment

We are organizing a workshop to catalyze the study of the microbiology of built environments where animals live. The workshop is scheduled for October 7th and 8th at UC Davis. Our aim is to bring together experts in animal health, building science and microbiology to discuss why these systems are worthy of study and how research in this area might improve both human and animal health.  I am writing this to (1) see who might be interested in participating and (2) look for ideas for topics for the workshop. We are not alone in living in built environments and the animals that live amongst us … Continue reading

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Are Green Building Materials Tastier for Fungi than Conventional Materials?

With the recent popularity of “green” buildings, we have to wonder how these new materials affect the microbes in the built environment. This 2010 paper from researchers at the University of Texas examines fungal growth in such materials. The study involved artificially and naturally inoculating four green building materials and their non-green counterparts with Aspergillus niger, as well as testing water capacity.  They found that a material’s capacity to hold water provided a great environment for the fungi to grow in, so materials with a high capacity tended to have more fungal growth. The high humidity in building components is what encourages A. niger and other fungi to … Continue reading

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Contaminated tap water in hospitals

Quick post here on a hospital water sampling study in Italy that found much higher levels of potentially pathogenic bacteria (e.g. Legionella) in aerators than in the rest of the plumbing system.   Reading this gives a really good sense of how complicated it is to maintain a sufficiently sterile water distribution system for immunocompromised patients in a hospital.  Abstract below: Objective.  Our aim was to evaluate the impact of aerators on water microbiological contamination in at-risk hospital departments, with a view to quantifying the possible risk of patient exposure to waterborne microorganisms. Design.  We analyzed the microbiological and chemical-physical characteristics … Continue reading

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