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A summary of the recent topics posted on microBE.net  


As usual, our blog posts spanned a wide range of topics relevant to the microbiology of the built environment, ranging from kitchens to space stations.






Recent interesting papers:




Microbes in the popular press:




Podcasts and videos:


Methods and Tools:



New and ongoing studies:


Soliciting community feedback:


Project Highlight:
Project MERCCURI (aka Microbes in Space)


This month we're highlighting our own Project MERCCURI, since the rocket carrying our built environment microbes into space will be launching this Sunday, March 16th.


This is a 3-part project, aimed at engaging with the public and increasing awareness about microbes, and in particular microbes in the built environment.   Our outreach goal is simple... to convey to as many people as possible the simple two concepts "Microbes are everywhere around us, and the vast majority of them are harmless or beneficial".


The three parts of the project are as follows:


  1. Collect samples from the International Space Station (ISS).  We're sending a bunch of swabs and the astronauts are going to swab various surfaces around the station... a unique sort of built environment since it's a closed system.
  2. Collect 4000 cell phone/shoe samples from public events around the country.   While the primary goal of this portion of the project is public engagement, these results will be compared to the swabs on the space station and to previous work on cell phones and shoes by Jack Gilbert's group through the Earth Microbiome Project.
  3. Grow bacteria isolated from built environments on earth up on the space station.  We have selected 48 strains of bacteria collected from a variety of built environments on earth.  These will be grown on the ISS and their growth compared to control plates here at UC Davis.


To learn more about the project and see the data once we have it, check out the project website:




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By Rachel Adams

Well, I have always told people that we need more mixing of art and science.  In recent years we have seen lots of attempts to do some sort of art inspired by - or even incorporating - microbes.  But this is perhaps the other side of the coin.

You could say that I'm milking this one study design - one in which we surveyed the airborne microbial communities and surfaces around different units of a university housing complex - and you'd be right. But for good reason: it's a powerful study design. We have replication of residential units of a common design across buildings; we took simultaneous outdoor and indoor samples; and the samples collected aerosols in a non-invasive way over a discrete, one-month time period.  


We've published previously on the airborne fungi and the fungi on surfaces, and now our analysis of the airborne bacteria has just been published.


We found that bacterial bioaerosols were influenced by which unit the sample came from and the room type in which it was sampled. On the other hand, our earlier study showed that fungal bioaerosols showed influence of season, unit, and to a small extent, the room in which the dust was collected.


This is one of the first published studies that consider fungi and bacteria from the same samples, and it suggests that the processes the influence these two microorganisms have some commonalities but key differences. In common, both the composition of fungi and bacteria in samples decrease as the samples move farther away in space  - the distance-decay effect. In contrast, there is an abundance of human-associated bacteria indoors, and this isn't matched with fungi. There were many human-associated bacterial that were abundant indoors, and rare or absent outdoors. Fungal taxa that were abundant indoors were also abundant outdoors.


Lest you worry, we've used up many of our samples, so there will be no more publications from this one study. Bacteria on households surfaces have been tackled already, anyway (here and  here). As with most studies, it will be interesting to compare these results to other studies in the pipeline that further characterize the microbes - both bacteria and fungi - in homes.




by Holly Ganz

We've been hearing a lot about  Microbes in Space. But what about Microbes in Smog?


Here in California, we know a thing or two about smog. To avoid it during the drought, we have been having a lot of Spare the Air Days lately to try to protect our air quality and reduce the amount of particulate matter in the air. Indeed small particulates have been linked to asthma,  respiratory disease, emphysema,  lung cancer.

With more than 20 million people living in Beijing, air quality has declined dramatically. You can find daily air quality forecasts for Beijing here and you can follow Beijing air quality on Twitter @BeijingAir. Poor air quality has become such a problem in Beijing that in 2013 tourism dropped significantly compared to 2012.


In a recent article, Cao et al. 2014 (sorry! paywall) used metagenomics to examine what microbes were found in smog before, during and after a massive, severe smog event that occurred from January 10-14, 2013 in Beijing. At the height of the smog event, particulate matter (PM) 2.5 measured 20 times higher than the WHO guideline value. They collected samples at a air quality monitoring site based at Tsinghua University, an area without nearby pollution sources. Particulate matter was separated by size into ≤ 2.5 um and ≤ 10 um. In all samples, Cao et al. detected 1315 bacterial and archaeal species; most species were terrestrial or fecal in origin and are harmless. A genus containing nitrogen fixing, filamentous bacteria, Frankia was the most abundant genus and the soil bacterium, Geodermatophilus obscurus was also abundant.


Several species increased dramatically during the smog event. Thermobifida fusca, a bacterial degrader found in decaying organic matter, showed a five-fold increase. The cause of community-acquired pneumonia, Streptococcus pneumonia showed a two-fold increase. A major fungal allergen, Aspergillus fumigatus increased by about four-fold. Human adenovirus also increased.


It's unclear that these microbes are of as much concern to our health as the particulates themselves. Still most research on air quality focuses on particulates and neglects microbes. Researchers in the built environment are also starting to look at microbes in air, including this study by Robertson et al. 2013 that looked at bacteria in bioaerosols in the New York City subway.


We know that human babies born through vaginal birth are colonized by their mother's microbes but what about the case of premature infants?

A paper published by Jill Banfield and colleagues as part of a Sloan-funded project investigates the connection between microbial communities of the neonatal intensive care unit (NICU) and those of the premature infant gut.

 Premature infants are heavily treated with antibiotics and this study found that after the administration of antibiotics, infant guts are colonized by NICU bacterial reservoirs, particularly those found on the feeding and breathing tubes. The study also found a large host of antibiotic-resistance genes in the reconstructed genomes of the gut colonizers.

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