UC District Court rules on whether bacteria are a pollutant

Well, I am no lawyer but this certainly seems interesting from a microbial point of view: Court’s Reasoning That “Bacteria” Is Not A “Pollutant” Favorable For Policyholders In Other Cases – Insurance – United States.  From the article:

That court found that “under Louisiana law, Legionella and Pseudomonas aeruginosa bacteria” – the bacteria which cause Legionnaire’s disease – “do not qualify as ‘pollutants’ within the meaning of [pollution] exclusions.”

The article also quotes the ruling:

[T]he Court concludes that the bacteria Legionella and Pseudomonas aeruginosa do not qualify as pollutants. The nature of these microbial agents are bacteria, not pollutants as is “generally understood.” These bacteria are significantly different than a typical environmental pollutant and are also distinguishable from other common “pollutants” such as asbestos, carbon monoxide, gasoline, and lead paint. Nor are these bacteria “typically used” in the same manner with which the previously discussed pollutants are used by a “polluter.” Rather, these bacteria are simply microorganisms existing in a natural environment. Finally, they do not discharge, dispersal [sic], seepage [sic], migration [sic] in the manner that a typical pollutant does. For these reasons, Legionella and Pseudomonas aeruginosa do not qualify as pollutants ..


I am certainly out of my normal comfort zone here but I thought some of the microbiology of the built environment folks might find this interesting.


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Fox 25 germophobia report on “Hidden hospital germs” actually is a bit of a hidden gem

When I first saw this headline: Fox 25 Investigates: Hidden hospital germs  I geared up for YASS – yet another swab story (this is a bit of a play on the “swab story” complaint Mark Martin uses for stories that report on microbes found by swabbing.

But despite my instinct, this story is in a way a hidden gem.  First, they based what they did on a new published paper and they even link to and discuss the paper itself.  The paper is “Elevator buttons as unrecognized sources of bacterial colonization in hospitals” published in Open Medicine, which I am happy to say is an open access journal.

The abstract for the paper is below:

Background: Elevators are ubiquitous and active inside hospitals, potentially facilitating bacterial transmission. The objective of this study was to estimate the prevalence of bacterial colonization on elevator buttons in large urban teaching hospitals.

Methods: A total of 120 elevator buttons and 96 toilet surfaces were swabbed over separate intervals at 3 tertiary care hospitals on weekdays and weekends in Toronto, Ontario. For the elevators, swabs were taken from 2 interior buttons (buttons for the ground floor and one randomly selected upper-level floor) and 2 exterior buttons (the “up” button from the ground floor and the “down” button from the upper-level floor). For the toilet surfaces, swabs were taken from the exterior and interior handles of the entry door, the privacy latch, and the toilet flusher. Samples were obtained using standard bacterial collection techniques, followed by plating, culture, and species identification by a technician blind to sample source.

Results: The prevalence of colonization of elevator buttons was 61% (95% confidence interval 52%–70%). No significant differences in colonization prevalence were apparent in relation to location of the buttons, day of the week, or panel position within the elevator. Coagulase-negative staphylococci were the most common organisms cultured, whereas Enterococcus and Pseudomonas species were infrequent. Elevator buttons had a higher prevalence of colonization than toilet surfaces (61% v. 43%, p = 0.008).

Conclusion: Hospital elevator buttons were commonly colonized by bacteria, although most pathogens were not clinically relevant. The risk of pathogen transmission might be reduced by simple countermeasures.


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Not all that surprising: New Study Shows Restroom Hand Dryers Spread More Germs Than Paper Towel

Well, there is clearly some germophobia behind all of the coverage for this new study published in the Journal of Hospital Infection: Microbiological comparison of hand-drying methods: the potential for contamination of the environment, user, and bystander. by E.L. Best, P. Parnell, M.H. Wilcox.  I have pasted their abstract below:


To compare the propensity of three common hand-drying methods (jet air, warm air dryers, and paper towels) to contaminate the environment, users, and bystanders.


Hands were coated in lactobacilli to simulate poorly washed, contaminated hands, and dried. The investigation comprised 120 air-sampling tests (60 tests and 60 controls), divided into close and 1m proximity from the drying process. Separate tests used hands coated in paint to visualize droplet dispersal.


Air bacterial counts in close proximity to hand drying were 4.5-fold higher for the jet air dryer (70.7cfu) compared with the warm air dryer (15.7cfu) (P = 0.001), and 27-fold higher compared with use of paper towels (2.6cfu) (P < 0.001). Airborne counts were also significantly different during use of towel drying versus warm air dryer (P = 0.001). A similar pattern was seen for bacterial counts at 1m away. Visualization experiments demonstrated that the jet air dryer caused the most droplet dispersal.


Jet air and warm air dryers result in increased bacterial aerosolization when drying hands. These results suggest that air dryers may be unsuitable for use in healthcare settings, as they may facilitate microbial cross-contamination via airborne dissemination to the environment or bathroom visitors.

Anyway – the article has now been picked up by a variety of news sources.  See below for some links:

Love the picture in the NY Magazine article:

Restroom Hand Dryers Spread More Germs Than Paper Towels, Study Finds – WebMD


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Pre-order Rob Knight’s Microbiome TED Book on Amazon

Rob Knight, together with science journalist Brendan Buhler, has written a witty synopsis (entitled “Follow Your Gut: The Enormous Impact of Tiny Microbes”) about the human microbiome and how it affects human life in the form of a TED book, now available for pre-order on Amazon.com.

The description from Amazon’s webpage is below:

“Allergies, asthma, obesity, stomachaches, acne: these are just a few of the conditions that may be caused—and cured—by the microscopic life inside us. Understand how to use groundbreaking science to improve your health, mood, and more.

In just the last few years, scientists have shown how the microscopic ecosystem within our bodies—particularly within our intestines—has an astonishing impact on our lives. Pioneering scientist Rob Knight and award-winning science journalist Brendan Buhler explain—with humor and witty metaphors—why these new findings matters to everyone.

You are mostly not you. The human gut is host to trillions of microbes, and evidence shows that small changes in these microbes present (altered by antibiotics, diet, geographic region, and so on) may affect weight, likelihood of disease, and even psychological factors like risk-taking behavior. The evidence for their influence is astonishing. Rob Knight is one of the key figures driving forward this new science. His work demonstrates the startling connection between the presence of certain harmless bacteria and the health benefits we all seek—for ourselves and our children.

In Follow Your Gut, Knight pairs with Brendan Buhler, an award-winning science writer, to explore the previously unseen world inside our bodies. With a practical eye toward deeper knowledge and better decisions, they lead a detailed tour of our “microbiome” as well as an exploration of the known effects of antibiotics, probiotics, diet choices, birth method, and access to livestock on our children’s lifelong health. Ultimately, this pioneering book explains how to learn about your own “microbiome” and take steps toward understanding and improving your health, using the latest research as a guide.”


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Toilet Ecology

Photo Credit: Kat Gilbert

Today, humans spend ~90% of their lives roaming the ‘great indoors’, which is very different from the of outdoor environments where we co-evolved with our commensal microbiota (Kelley and Gilbert, 2013). We are just beginning to understand how the design of built environments (BEs) influences our microbiome, and how these interactions, in turn, might affect human health. An improved understanding of the BE-microbe-host feedback loop is important for protecting public health in an increasingly urbanized world.

Restrooms are a shared public space with clear disease transmission potential. Pioneering work by Flores et al. (2011) demonstrated how microbial communities, sourced predominantly from the human microbiome, are geographically distributed in a public restroom, showing gender- and surface-specific signatures. Recent work from our group has corroborated these results, showing how BE surfaces are coated with mostly human-associated microbes (Lax et al., 2014). In addition, we found that individuals leave behind distinct microbial fingerprints on BE surfaces, which has implications for forensics and for disease transmission.

In our most recent BE paper, we expand upon the Flores et al. (2011) work with a series of longitudinal studies (Gibbons et al., 2014). We characterize the reproducibility of microbial succession on public restroom surfaces and demonstrate the viability of host-associated microbes deposited on these surfaces. Specifically, we show that thorough decontamination of restroom surfaces with bleach results in the transient dominance of fecal-associated microbes, but that these fecal taxa are rapidly displaced by skin-associated microbes after ~5 hours. This skin-dominated community persists stably for months, even in the presence of normal soap-and-water cleaning regimes.

To our surprise, several Staphylococcus species represented a majority of the culturable floor community, even after many hours of human-exclusion. Staphylococcus aureus is responsible for a large fraction of hospital-related infections, and is a relatively common constituent of the human skin microbiome. Our results show that these potential pathogens remain viable on BE surfaces for long periods of time in the absence of their hosts. Methicillin resistant S. aureus (MRSA) is increasingly common outside the hospital environment, and represents a significant public health risk. We found evidence for methicillin resistance genes in the shotgun metagenomes from the late-successional communities, but we did not find any MRSA-related genes within assembled Staphylococcus sp. pan-genomes from our culture work.

In addition to bacteria, we were able to look at the viral community. We found a strong positive correlation between bacterial and viral abundances, and a dominance of the viral community by enterrophages (viruses that prey upon gut bacteria). We also found a large number of Human Papilloma and Herpes viruses on restroom surfaces. The unexpectedly low virus-to-bacterial ratio suggests that viral activity is minimal in this system. This fact, combined with low bacterial biomass on BE surfaces, reflects the ecological mismatch between the BE and host environments. Most host-associated taxa are coming from a warm, moist, and sometimes anaerobic ecosystem, with plenty of substrate for growth. Restroom surfaces are relatively dry, cold, aerobic and barren (inert), when compared to the host system. Thus, most bacteria are probably dormant, dying, or dead in these microbial deserts.

In summary, we found that the restroom microbiota show reproducible ecological succession from fecal-associated organisms toward a stable community state dominated by skin-associated taxa. This transition was rapid, occurring within a few hours. This was likely due to the dispersal of fecal taxa due to aerosolization from toilet flushing, followed by the enhanced ability of skin taxa to persist on dry, aerobic surfaces. Many human-associated organisms, including known pathogens, remained viable on BE surfaces for hours in the absence of humans. Overall, microbial communities residing on restroom surfaces are a reflection of the humans that inhabit the space; they are the slowly decaying remnants of the vibrant ecosystems found across the human body. As such, the health state of BEs may simply be a reflection of the health state of the humans that reside in them.



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Tutorial video on making a microBEnet blog post

As people have probably noticed, we have an increasing number of guests posts here on microBEnet, which is awesome.   This is intended to be a community resource, and we’ve been actively reaching out and recruiting people to post about their work here.  To that end, I’ve just made a tutorial video that walks you through the steps of creating a blog post… it’s really easy.

If you have a guest account but haven’t posted, this would be a great place to start.

If you don’t have an account and are intimidated by the whole idea, this should put you at ease.

This 5-minute video covers:

  • Logging into microBEnet
  • Creating a post
  • Using links, block quotes, and inserting images
  • Using tags/categories for your post

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Sloan foundation funds Symposium at Healthy Buildings 2015 – Europe

(Note:  This post is by Hal Levin)

isiaq logo-KDDesign300dpi smallThe Alfred P. Sloan foundation has approved a grant to ISIAQ, the International Society of Indoor Air Quality and Climate, to organize a symposium at the Healthy Buildings 2015-Europe conference in Eindhoven, Netherlands, May 18- 20, 2015. The Symposium organization project will be led by Hal Levin of the Building Ecology Research Group, and co-P.I. Martin Täubel of the Finnish National Institute of Health and Welfare.

The goal of the proposed symposium is to identify key results from the Sloan Microbiology of the Built Environment program, which are complimentary to leading edge European work. The Symposium’s forums will be designed to promote interactive dialogue and collaboration between researchers, practitioners, and students.    The purpose of this forum is to advance the use of the culture independent methods by developing a framework for their use by practitioners and identifying the scientific challenges that need to be addressed to achieve this goal.

The Sloan Symposium at Healthy Buildings 2015 Europe will feature a  high profile lecture at the conference’s plenary session highlighting themes of the this Sloan sponsored Symposium. The lecture will be given by Miia Pitkaranta of the
Organization of two technical session(s) focused on practical uses of indoor microbiome surveys in the built environment. Invited speakers include Sloan grantees and European leaders in microbiology of the indoor environment.
Organization of a workshop to explore the most important issues for translating cutting edge science into best practices available for the indoor environmental science and engineering community
Organize Sloan Symposium Annex Workshop immediately following the conference:  invited scientists will discuss the scientific challenges facing the building science and indoor air quality community to improve the availability and utility of molecular methods. A key content of this activity is the formulation of research questions and potential project concepts that respond to the needs of practitioners (environment and health) in the field.

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Studies in Mycology 78: Species diversity in Aspergillus, Penicillium and Talaromyces

A new volume of Studies in Mycology was published recently and is dedicated to the diversity in the fungal genera Aspergillus, Penicillium and Talaromyces, all of which play a significant role indoors. The issue includes 6 papers related to our Indoor Mycota Barcode of Life (IM-BOL) project funded by the Alfred P. Sloan Foundation Program on the Microbiology of the Built Environment. Our goal is to bridge the knowledge gap between uncultured and cultured fungi in indoor environments by providing authoritative taxonomic and DNA barcode data to be used for metagenomic studies. House dust was collected from all over the world. Half the dust was used for isolations using a dilution-to-extinction (d2e) method, while the remaining dust was used for a 454-pyrosequencing analysis (published in Amend et al. 2010).

The first paper deals with the identification of the 2717 d2e isolates belonging to Aspergillus, Penicillium and Talaromyces. The usual view of indoor moulds recognizes about 40 common species of these genera, but we found 126 species of which 18 were described as new (Aspergillus 1160 isolates, 59 spp., 8 new; Penicillium 1459 isolates, 49 spp., 7 new; Talaromyces 98 isolates, 18 spp., 3 new). For each species, ITS barcodes and the secondary barcodes Calmodulin (Aspergillus) and β-tubulin (Penicillium & Talaromyces) were generated, adding to the reference sequences. Reference sequences obtained were not only from the commonly found indoor species, but also rare ones such as A. taichungensis, P. incoloratum and P. hispanicum for which only singleton sequences were available previously.

Among the interesting new species were an Aspergillus and Penicillium, which we found remarkable enough to name them after Alfred P. Sloan. Aspergillus has long been known to contain xerophilic species (previously also associated with the teleomorphic genus Eurotium), but the discovery of a species that is not able to grow on any of the media generally used for Aspergillus identifications was remarkable. The species only grew on low water activity media and then produced a eurotium-like sexual state and conidiophores with very large spiny conidia. This was our favorite Aspergillus isolated in the study and named it Aspergillus sloanii. The interesting Penicillium species was described as P. alfredii and was phylogenetically so distinct that it could not be placed into any of the 25 taxonomic sections of Penicillium. Unfortunately we could not introduce a new section for P. alfredii, because its phylogenetic position makes two other sections polyphyletic. This issue will be resolved in future, but additional data and sampling is needed to accomplish this.


Fig. 1. Aspergillus sloanii (left), an obligately xerophilic species only growing on low water activity media such as DG18. Penicillium alfredii (right) also displays slow growth on general media.


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To all of the microbial researchers out there, be careful about contaminants in your cultures, reagents, and equipment! Yes, we all are careful about good techniques and having proper controls. However, this article suggested that perhaps contaminants are surfacing much more in microbial related literature than we thought. This concept isn’t new, and the aforementioned article provides a good summary of the common culprits. Also, this article had a shoutout to Jonathan at the very end: “Apologies in advance to Jonathan Eisen for “contaminomics”. Don’t hit me.”

Katie Dahlhausen (@PhDKD) is a PhD student in Jonathan Eisen’s lab and is interested in the biogeography and mechanisms of antibiotic resistance

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