The microbial aura of our pets

In Dirty Dog: Do Pets Track Bacteria in Your Home? on the Popular Science blog, science journalist Brooke Borel describes her recent experience contributing to the citizen science experiment called The Wild Life of Our Homes run by Rob Dunn and Holly Menninger at North Carolina State University. Here she presents a beautiful graphic depicting how the samples that she collected from her house, herself and her dog compared with some of the other participants in the study. This graphic was published as a sidebar to a longer article on the Wild Life of Our Homes project by Joel Warner in the April issue of Popular Science. One of the interesting things Brooke learned from participating in the study is that apparently she has dog microbes on her tongue and other parts of her body. She wants to know what we all think about sharing our houses, beds, couches and microbes with our pets.

Yuki picking up some soil microbes to bring back home

Yuki picking up some soil microbes to bring back home. Photo by Holly Ganz.

Personally I’m all for microbial sharing with our pets. I even think that we should allow dogs in restaurants, trains, buses and other public places like they do in Europe. I was going to posit that maybe Europeans are better at picking up after their dogs than we are but then I remembered that when I stepped in dog poop last year while visiting Marseille, my friend Marie said “Welcome to France!”

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Manipulating the Unseen Microbial Ecosystem—The Future of Hospitals? (NOVA Online)

Great article from Brooke Borel writing for NOVA Online, “Manipulating the Unseen Microbial Ecosystem—The Future of Hospitals?”.

This covers some of the background of microbiology in hospitals, discusses work by both the BioBE Center and microBEnet… and of course the Hospital Microbiome Project as well as the NICU study from Jill Banfield’s lab.  The article doesn’t explicitly go into the topic of building probiotics (a favorite of ours) but does discuss possible implications of these kinds of studies for building design.

A very good introduction to the topic…

US Navy 030415-N-1056B-001 A Navy Hospital Corpsman prepares the operating room at Fleet Hospital Eight (FH-8), located at Naval Station Rota, in preparation for the arrival of 39 wounded Marines and Soldiers from Operation Ir

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Potentially useful tool for culture collection: LIIS

Quick post here.  This seems like a potentially useful tools for labs to keep track of their culture collections.  We definitely need something like this in my lab.

LIIS: A web-based system for culture collections and sample annotation | Forster | Journal of Open Research Software.


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Microbes and the design of animal shelters

Animal shelters provide an essential and beneficial social service, caring for an estimated 9 million pets each year in the United States. Many animals entering a shelter are highly stressed and lack the benefits of standard veterinary care, including vaccinations. Moreover animal shelters are an intensive housing situation that amplifies the transmission of infectious diseases (Pesavento and Murphy 2014). Consequently shelter staff devote a lot of time and resources to cleaning and disinfection, in addition to providing animal care.

Architect George Miers of Swatt Miers Architects has designed and built many animal shelters on the West Coast. In this video, he discusses some of the considerations that go into designing a new animal shelter. If you are like me, you will be amazed by the amount of attention paid to drain design and power washing.

Is there a better way to disinfect animal housing areas? Would UV be a better alternative to chemical disinfectants? Animal shelters are built environments with an important and under-appreciated microbiology and there are many unanswered questions. As part of a very preliminary study, we sampled the air in a walkway adjacent to the dog kennels in a local shelter using a Petri dish air sampler to provide a pretty picture of the diverse and abundant bacteria and fungi found inside animal shelters.

Sample from kennel walkway, 100 L air sampled, 44 hour incubation.

Sample from kennel walkway, 100 L air sampled, 44 hour incubation.


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‘Frozen’ Microbial Ecology

This past Saturday, my wife picked ‘Frozen’ for movie night (no, we don’t have kids). In the movie, one of the main characters was born with the power to freeze her surroundings, which she struggles to control. By the time, ‘Let It Go’ was playing, I couldn’t help but wonder how the repeated freezing of the castle was impacting the indoor microbiology, which led to Google Scholar (I am a terrible movie watcher) to investigate what we know about the microbial ecology of refrigerators and freezers.

The amount of cold storage we use is staggering (at least to me) – the USDA reports that the US has ~4 billion cubic feet of refrigerated storage. Searching for information on the microbial ecology of refrigerators is difficult – imagine how many studies use some formation of the word ‘refrigerated’ or ‘frozen’ when referring to sample storage and processing.  However, The microbiology of psychrophiles (cold-loving microorganisms) dates back to at least 1902, when Schmidt-Nelson coined the term ‘psychrophile’. Psychrophiles include members of the genera Pseudomonas, Psychrobacter, Staphylococcus, Photobacterium, and Halomonas, among others. The biology behind these microbes is fascinating (anti-freeze proteins!) and they are widely distributed in the environment. Almost all psychrophile ecology research that I was able to identify investigated the impact on food storage and spoilage – however I can’t help but wonder about the microbial ecology of the refrigerated spaces themselves. I’m starting the search in the back of the grad student lunchroom fridge.


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A Hospital Door Handle That Sanitizes Hands With a Touch (

Not sure how I feel about this one so I’m going to just throw it out there for discussion.  It’s a hand sanitizer built into a hospital door, on the theory that since compliance is apparently problem in hospitals they should make it part of a motion that people are doing anyway (e.g. opening doors).

I’m definitely against sanitizing things for no reason, but it does seem like a pretty good idea in hospitals.  So maybe this is more than a gimmick.

Pull Clean

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ASM Symposium #241: Microbial Revelations of the Built Environment

Looks like there will be a great symposium on the Microbiology of the Built Environment this year.  The symposium is organized by Filipa Godoy-Vitorino and Sarah Preheim.   Speakers include several Sloan-funded labs  (including Maria Dominguez-Bello, James Meadow, and Mark Hernandez) and it looks to cover a wide range of cool topics.   Check out the video below:

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So about those #spacemicrobes from the built environment?

Yesterday was to have been the day that our collection of 48 microbes, collected from built environments around the country, were to blast off into space and try growing in microgravity.  This would be followed by swabbing of the space station performed by the astronauts.  We plan to analyze these swabs using bacterial, archaeal, and fungal primers.  These results will also be compared to the 4000 earth-based samples that we’re collecting and analyzing with the help of Jack Gilbert and the Earth Microbiome Project.

Alas, rocket science appears to be hard and the launch was cancelled for what I believe is the 7th time.  Except this time it was only an hour before launch and we were all in Florida ready to watch it.   Next launch window is Friday afternoon so we’ll see what happens then.   Jenna Lang has made a storify from the #spacemicrobes hashtag yesterday:

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Dreaming that the Clinton Global Initiative @Clintonglobal will start looking at microbes in the built enviornment

Well this is interesting. Holly Bik pointed me to the fact that the Clinton Global Initiative has a track on the Built Environment:About Us: The Built Environment | Clinton Global Initiative.

Not sure exactly what they do in this track but seems like a good way to get exposure for the field of microbiology of the built environment would be to get the CGI people to include discussions of microbes in their next meetings.

Their next US meeting is in June in Denver (see  Wonder if there is a way to get some microbiology included …

(Also see the 2014 working group they have on Sustainable Buildings)


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Harvard Magazine covers Sloan grantee Curtis Huttenhower’s research: microbes in transportation systems

Curtis Huttenhower

In November, 2012, Curtis Huttenhower began work (with funding from the Sloan Foundation) to examine the transmission of human-associated microbes by public transportation surfaces.

An article on “Big Data” in the current issue of Harvard Magazine includes a description of Huttenhower’s work in the lead article “Why “Big Data” Is a Big Deal.”

After very briefly describing Huttenhower’s Sloan Foundation funded work, it quotes him saying: “Just think about the number of things that have changed in the past 50 years that affect microbes,” Commercial antibiotics didn’t exist until about 50 years ago; our locations have changed; and over a longer period, we have gone from 75 percent of the population working in agriculture to 2 percent; our exposure to animals has changed; our exposure to the environment; our use of agricultural antibiotics has changed; what we eat has changed; the availability of drugs has changed. There are so many things that are different over that timescale that would specifically affect microbes. That is why there is some weight given to the microbiome link to the hygiene hypothesis.”

The Harvard Magazine article goes on to discuss “Discerning Patterns in Complexity. Making sense of the relationships between distinct kinds of information is another challenge facing researchers. What insights can be gleaned from connecting gene sequences, health records, and environmental influences? And how can humans understand the results?”

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