Housing characteristics and microbial communities in homes of asthmatic children

Appropriate song to play while reading this post: Harder To Breathe – Maroon 5

Asthma severity can be affected by several indoor and outdoor conditions, including dust and microbes. In a paper that came out last week in Indoor Air, researchers from Yale University applied NextGen DNA sequencing to characterize the bacterial and fungal communities in house-dust sampled from nearly 200 homes of asthmatic children in southern New England.

Dust was collected from couch and floor surfaces in the main living area using a special vacuum cleaner. After DNA extraction, fungi and bacterial communities were amplified and sequenced (454 Titanium technology for the fungal amplicons and Ion Torrent for the bacterial fragments).

Figure S1. Principal coordinate analysis bacteria for occupancy, housing characteristics, and dust composition. doi:10.1111/ina.12205
Figure S1. Principal coordinate analysis bacteria for occupancy, housing characteristics, and dust composition. doi:10.1111/ina.12205

The most abundant fungal species found in these dust samples were Leptosphaerulina chartarum, Epicoccum nigrum, and Wallemia sebi. Not surprisingly, the most abundant bacterial families were Staphylococcaceae, Streptococcaceae, and Corynebacteriaceae, taxa commonly found on human skin.

Higher concentrations of human cells in the dust were associated with higher abundance of human human-associated fungi, such as Malassezia spp., and human-associated bacteria such as Rothia mucilaginosa, Streptococcus, Corynebacterium, and Staphylococcus.

More fungal species were found in houses with pets, and higher humidity (water leaks, less use of AC unit). Bacterial richness was higher in houses with pets and in suburban areas. In addition, bacterial composition was associated with high human occupancy and presence of pets.

So no major surprises here, but it was nice to see correlations between household characteristics and microbial communities. A major limitation is that the study only included households with a child with asthma, so there was no comparison possible to homes with healthy children. In addition, as noted by the authors, a high fungal richness might be protective against the development of asthma development, so the number of fungal species in these houses might actually be lower than those without asthmatic children. I would also have liked to see a correlation between the severity of asthma and dust microbial composition, which would have been a great addition. Finally, I would have preferred to see the PCoA plots that are currently in the supplemental materials in the main text, instead of the current tables and bar graphs. But that is maybe just my personal preference.

All in all, a nice study to add to our knowledge of fungi and bacterial communities in indoor air, that would have been stronger if it had included homes from children without asthma.

Influence of housing characteristics on bacterial and fungal communities in homes of asthmatic children – K. C. Dannemiller, J. F. Gent, B. P. Leaderer, and J. Peccia – Indoor Air – doi:10.1111/ina.12205

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Bleach and Its Association with Respiratory Infections

A 2015 paper from Casas et al investigated the effect of bleach on respiratory infections in young school-children. They analyzed information from Spain, the Netherlands, and Finland. Spain had the most instance of bleach use, which corresponded with a higher respiratory and related infections. On the other end of the spectrum, Finland had very little bleach use, which correlated with lower infection rates.

The researchers hypothesized that aerosolized bleach has the same potential mechanisms of affecting health as second-hand smoke or air pollution. Irritation caused by inhaled bleach causes inflammation, which makes it easier for infections to start.

From another perspective, this can also be another case of the hygiene hypothesis. If things are overly clean, our bodies’ microflora suffers and falls into dysbiosis.

By Scott Ingram via https://www.flickr.com/photos/scingram/69472343/in/photolist-794H2-754HV-754CK-8LLyg-a7Syo-qufMRX-7wWeR-9C8tZ-754Je-754J4-7ocbYg-a7TpP-754J8-7wWeN-8BmmrX-8LLPn-8LLGb-pJZLQn-a7TpU-7wVGF-7dEhXa-9VQXTM-8LLgL-9C8CJ-65goXX-9C8u4-9C8tQ-7wVD2-6bcKZc-b2uo5-b2uo6-9C8tW-754CM-dP7X8C-8LLGc-7wVGH-7wVD6-oSun6H-7kTPF-7wWeP-6h8WmT-zu7CM-4VdEBm-8pzQHS-69vhYN-ebpJ9f-7cLorH-8HyiU-oh2WMa-94jpev
via Scott Ingram on Flickr


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Session on “The Microbiome” at the AHCJ (Association of Health Care Journalists) annual meeting

There will be a session on “The Microbiome” at the AHCJ Association of Health Care Journalists annual meeting in Santa Clara, CA that may be of interest.

Session Participants:

  • Jonathan Eisen, Ph.D., professor, School of Medicine and College of Biological Sciences, University of California
  • Susan Lynch, Ph.D., associate professor of medicine, University of California, San Francisco
  • Justin Sonnenburg, Ph.D., assistant professor, Department of Microbiology and Immunology, Stanford University School of Medicine
  • Neil Stollman, M.D., physician, East Bay Center for Digestive Health
  • Moderator: Kathleen McGowan, independent journalist, Berkeley, Calif.

Friday April 24 – 4:20 – 5:40 PM .

More information about the meeting:


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Fascinating “personal memoir about Hurricane Katrina and fungal volatiles” by Joan Bennett

There is a new paper out in Frontiers in Microbiology by fungal geneticist Joan Bennett that is fascinating: Frontiers | Silver linings: a personal memoir about Hurricane Katrina and fungal volatile.

Here is how it starts:

In August 2005 I was about to start a sabbatical leave during which I planned to work on the annotation of the genome of Aspergillus flavus, an aflatoxigenic species that had just been sequenced with funding by the U. S. Department of Agriculture. My sabbatical plans were permanently altered on August 29, 2005 when Hurricane Katrina crossed the Gulf of Mexico. The day before the hurricane, my husband and I evacuated to a small town in eastern Louisiana so we were not in New Orleans when the hurricane hit and the levees failed. About 80% of the city flooded, including our house. The National Guard barred residents from returning home. Therefore, we drove to New Jersey, where my husband had friends, and found temporary housing. The weeks after Hurricane Katrina were not easy. At first, I watched a lot of TV, getting increasingly angry at the negative media slant put on New Orleans and its residents.

When they finally returned to their house, it was a mess:

FIGURE 1. (A) The living room of the author’s New Orleans home on October 6, 2005 in the aftermath of Hurricane Katrina. (B) Closer view of moldy books on flooded book shelf.
FIGURE 1. (A) The living room of the author’s New Orleans home on October 6, 2005 in the aftermath of Hurricane Katrina. (B) Closer view of moldy books on flooded book shelf.



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“Making a microbe subway map” for Eureka! Lab by Bethany Brookshire

There is an article about the NY Subway Microbiome study by Bethany Brookshire that is worth checking out: Making a microbe subway map | Student Science.

It discusses how high school students helped in the subway microbiome study that came out recently (see the post by Chris Mason about this here: The long road from Data to Wisdom, and from DNA to Pathogen).

Some of the quotes are fun – I like in particular: “An old man said we were the strangest thing he’d ever seen on the subway. And he’d lived in New York City for 50 years,” notes Anya Dunaif, 17.

Definitely worth checking out.

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Small World Initiative – Who We Are and How to Get Involved

by Simon A. Hernandez & Nichole A. Broderick

Students in the Yale 2015 SWI course (Microbes to Molecules)

Since its launch in summer 2013, the Small World Initiative (SWI) has expanded from a small “Microbes to Molecules” course at Yale University to a multi-institutional (60 institutions in 5 countries) organization with more than 2000 students and alumni. Professor Jo Handelsman and colleagues at Yale pioneered this ambitious organization with an innovative approach to STEM education in response to a worldwide health crisis. The SWI seeks to harness the collective power of student researchers across the globe to discover new antibiotics from soil microorganisms, living up to its motto “crowdsourcing antibiotic discovery”. The program offers undergraduate students an authentic research experience, built into first- and second-year life science courses, where they explore the biological and chemical diversity of local soil environments. While antibiotic discovery and development take longer than a semester, the collective effort of many students increases the chance of identifying potential candidates for new drugs.

Professor Handelsman, who is currently on leave from her faculty position at Yale, has become a strong voice for the antibiotic crisis and the need for new strategies to combat resistance. Her current position as Associate Director of Science at the White House Office of Science and Technology Policy aligns with the SWI’s commitment to STEM education, scientific research, and science diplomacy. Funding for the first two years of the SWI was provided by the Leona and Harry B. Helmsley Charitable Trust.


Upcoming Events

  • This spring 2015, the SWI will be holding its second annual symposium and conference at the American Society for Microbiology Conference for Undergraduate Educators (ASM-CUE) in Austin, TX from May 28 to 31. Pilot Partner and head of the Symposium Committee Jean Schmidt from the University of Pittsburg organized the event. Partner Instructors from the U.S. and Canada will each bring one or two undergraduate students to share research findings, promote ongoing curriculum development, and make plans for 2015-2016.
  • Just after ASM-CUE, the SWI will hold the 2015 Training Workshop. This event will take place at National University in Costa Mesa, CA from June 2 to 6. Contact Pilot Partner and SWI regional leader Dr. Ana Barral (abarral@nu.edu) to request an application (the deadline is May 1). The hands-on workshop will train participants in the experimental setup of SWI as well as promote discussions on course design and assessments. Research scientists and educators with an interest in microbiology and undergraduate STEM education are encouraged to apply.
  • In March 2015, the Society for General Microbiology (SGM; UK-Ireland) announced the launch of their Small World Initiative at their annual conference. The SGM-SWI will expand the current focus on undergraduate classrooms to include high school partnerships and the general public with a Citizen Science component. Further details for interested parties in the UK and Ireland can be found at the SGM website.
  • Finally, the SWI is partnering with the American Society for Microbiology (ASM) to offer a workshop for Iraqi educators that will be held at the Jordan University of Science and Technology from June 7 to 11.
swi at ASM GM 2014 group
SWI partners and students at ASM General Meeting 2014 in Boston

Website and Social Media

Summer 2015 marks the third year that SWI has been in operation. The SWI Committees, led by the Pilot Partners and collaborators, have taken great strides in the past year to create curriculum packages, curate research and teaching materials, evaluate student outcomes, organize outreach events, and now, focus on training the second generation of Partner Instructors. Last year, the SWI welcomed 36 new instructors, expanding the network to Puerto Rico, Canada, the U.K., Belize, and Malaysia.

The SWI website is the best starting point for those interested in joining the community and participating in the SWI. On the website, registered users can access manuals, protocols, and implementation resources, as well as contact information of other partners and collaborators. Users will be able to upload data into the SWI’s online repository and view other participants’ results. In addition, the website will connect users to the SWI Facebook group, which provides an interactive and “in the moment” forum for instructors and students as they perform the research workflow each semester.

We look forward the next generation of SWI Partner Instructors and collaborators who will pledge to join our mission to transform STEM education and promote antibiotic discovery using curiosity and creativity of young scientists across the world.


Simon A. Hernandez is a Postgraduate Associate in Jo Handelsman’s Lab and the Center for Teaching and Learning at Yale University, and Communications Manager of the Small World Initiative. Contact him at simon.hernandez@yale.edu.

Nichole A. Broderick, Ph.D., is a Co-Lead Research Scientist in Jo Handelsman’s Lab and lecturer of Small World Initiative course at Yale University.

For more information about the getting involved, please contact Program Coordinator Todd Kelson (kelsont@byui.edu) or Regional Leader and host of the 2015 SWI Training Workshop Ana Barral (abarral@nu.edu). To meet us at the ASMCUE 2015 Meeting, please contact Pilot Partner and Symposium Coordinator Jean Schmidt (schmidtj@imap.pitt.edu).


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Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air

Appropriate song to play while reading this post: Mat Kearney – Breathe In, Breathe Out

This paper came out last month, and I thought it would be nice to briefly mention it here, even though many other papers have looked at the concentrations of airborne bacteria and viruses as well.

In this study, done by Aaron Prussin et al. from the Department of Civil and Environmental Engineering at Virginia Tech, air samples were collected in triplicate at 9 locations in Blacksburg, VA. The sample sites were: a classroom, a daycare center, a dining facility, a health center, three single-family houses, an office, and an outdoors at an unspecified university campus.

For each sample, about 100 liter of air was pumped through a 0.2 μm pore size filter, and nucleic acids on the filters were stained with a fluorescent dye and counted. Pinprick sized particles (between 0.02 and 0.50 μm) were counted as virus-like particles (VLPs), while the larger signals (between 0.50 and 5.00 μm) were counted as bacteria-like particles (BLPs).

Both BLP as well as VLP concentrations were found to be between 105 and 106 per cubic meter, and not significantly different between the indoors and outdoors locations, although there was a trend for higher concentrations outdoors. Notably, the lowest concentration of both particle types was in the health center, and the highest concentration indoors was found in the classroom and homes. Overall, the differences between the locations were very small.

The authors state that not many other studies have looked at virus concentrations in air. Unfortunately, filtering through a 0.2 μm filter is not the best choice to catch viruses (Update: see below). Many viruses will be able to pass that filter, and recent work from the Banfield lab has shown that even some very small bacteria will pass through these filters (Luef et al., Diverse uncultivated ultra-small bacterial cells in groundwater, Nature Communications 6: 6372, 2015). So it is likely that the actual virus concentration both indoors and outdoors is much higher.

Total Concentrations of Virus and Bacteria in Indoor and Outdoor Air – Aaron J. Prussin, II, Ellen B. Garcia, and Linsey C. Marr – Environmental Science & Technology Letters 2015, 2, 84−88. Work founded by the Alfred P. Sloan Foundation, the National Science Foundation, and the National Institutes of Health.

Update: I stand corrected. Filtering air and water are two very different processes, and in the conditions used in the paper, filtering air over a 0.2 μm filter will actually retain most of the viruses. For a detailed explanation, see the comments section below.


Virus and Bacteria in Indoor and Outdoor Air, DOI: 10.1021/acs.estlett.5b00050, or 7-legged spiders invading a cute house?
Virus and Bacteria in Indoor and Outdoor Air, DOI: 10.1021/acs.estlett.5b00050

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Synthetic Cheese and the Microbiome

Counter Culture Labs is a company that stemmed from an MIT iGEM team that made synthetic cheese. Their goal is to make vegan cheese that tastes just like the real thing with the single important difference being it is not derived from a cow, but rather a lab bench. Synthetic food is starting to trend. Already, we have seen synthetic beef, which could come in handy in saving non-renewable resources that we currently use for common food products.

A valid point was raised in the synthetic cheese article about the effect on the human microbiome. Even if something is chemically the same as the food in seeks to mimic, will it interact with our microbiome the same way? If those interactions are different, how do we measure them or go about determining whether they are good or bad changes? How far away are we from inoculating our synthetic cheese with say, a “model cheese microbiome” that would still input the same food-associated biota to our bodies? Does it matter?

Synthetic biology is an interesting field, but as with all new technology (especially biotech), there are many unaccounted for interactions that researchers may or may not be create from scratch or even quantify. Hopefully, the researchers creating this synthetic cheese take the microbiome into account now and realize how important these biological interactions can be.

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Mycodo : A homebrew automated cultivation setup for fungiculture

One of my favorite blogs, Hackaday, recently covered a brilliantly detailed build of a mushroom cultivation control system by Kyle Gabriel. Kyle is a microbiology graduate student at Georgia State University studying the interactions of bacteria and pathogenic fungi for his research, and cultivates edible fungi for fun. The gadget monitors temperature and humidity in a sealed room under positive pressure, and controls these parameters through the use of household space heaters and humidifiers on regular 110VAC sockets switched by relays. CO2 concentration is controlled by actuating exhaust fans placed at different heights in the room (manipulating the CO2 level is important for developing fruiting bodies, if I understand correctly). All of this is orchestrated by a RaspberryPi running Linux, a web server and Kyle’s Automated Mushroom Cultivator software (available on GitHub).

Kyle’s step-by-step instructions for his latest Mycodo build can be found on his blog, but for the very impatient, he recorded a time-lapse video of himself assembling the controller.

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US Program Seeks Comments on Connections Between Climate Change & Human Health

Screen Shot 2015-04-12 at 7.48.13 AM

There are many possible ways in which climate change could impact human health.  The U. S. Global Change Research Program has issued a new draft report on this topic and is soliciting public comments about this report (see USGCRP Climate for more information).

The report is The Impacts of Climate Change on Human Health in the United States: A Scientific Assessment.  Public comments will be taken until June 8.

To read the report see these links:

I have looked through the report and there are many areas in there with connections of microbiology.  Especially the sections on Air Quality Impacts and Water-Related Illness and Food Safety, Nutrition, and Distribution.  If you have ideas about climate change and health, such as in these areas, it would be worth looking at the report and submitting comments.

One area that is covered in the report is how as temperature rises in places this will lead to changes in building infrastructure and design which will in turn impact indoor air quality.  The report references some work that may be familiar to some readers here including

  • Fisk, W. J., 2015: Review of some effects of climate change on indoor environmental quality and health and associated no-regrets mitigation measures. Building and Environment, 86, 70-80, doi:10.1016/j.buildenv.2014.12.024.
  • Stephens, B., and J. A. Siegel, 2012: Penetration of ambient submicron particles into single- family residences and associations with building characteristics. Indoor Air, 22, 501-513, doi:10.1111/j.1600-0668.2012.00779.x.

One related area that is not covered that seems like it should be is how as we make more and more buildings “green” in terms of energy, we also greatly chage the microbial ecology in those buildings.  The more we seal up buildings, it seems likely that the microbial ecology will start to look a lot like the residents of the building rather than the outdoors.  This is suggested by work from Jessica Green and Jack Gilbert and others.  This topic certainly seems like it should be in the report — so I will be making that suggestion.

To make comments one has to go to this link and register.

Thanks to Paula Olsiewski for pointing me to this report and call for comments.

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