The microBEnet blog

What kind of DNA lingers on ATM keypads? Your food, your skin microbes…and (maybe) parasites

Amidst the November/December holiday chaos, myself and co-authors were proud to witness the publication of a neat new paper focused on ATM keypads in New York City. Yes, just like all other surfaces in the Built Environment, those ATM keypads are harboring lots of microbes and bits of orphaned DNA!

This ATM keypad study was work that I carried out during my previous position in Jane Carlton’s lab in the Center for Genomics & Systems Biology at New York University. The project was a collaboration between the Carlton lab and the lab of Maria Gloria Dominguez-Bello (an associate professor in New York University School of Medicine’s Human Microbiome Program). The research was partially funded by a New York University Grand Challenge project called “Microbes, Sewage, Health and Disease: Mapping the New York City Metagenome” and a grant from the Alfred P. Sloan Foundation.

This study aimed to carry out a baseline assessment of the microbes found on ATM keypads, looking at both prokaryotic (bacteria/archaea) and eukaryotic microbes using 16S rRNA and 18S rRNA amplicon sequencing, respectively. Call it “exploratory research”  – we weren’t looking at any patterns in particular, because we weren’t sure what we were going to find. However, ATM keypads are an interesting micro-habitat, since they can be considered a highly trafficked surface in the Built Environment (think of how many thousands of people are probably using an average bank ATM every day in Manhattan – lots of fingers pressing those keys at all hours of the day!).

With that goal in mind, during June and July 2014 we used cotton swabs to sample microbes from 66 ATM keypads in eight neighborhoods across three New York City boroughs (Manhattan, Queens, and Brooklyn).

NYC neighborhoods sampled during this ATM study, with associated demographic information obtained from the NYC Open Data portal

What did we find? NOTHING. That is to say – we didn’t find that microbial communities lumped together in any obvious way according to NYC geography (neighborhood or borough). We also tried to correlate microbial community patterns with population demographics obtained from the NYC Open data portal – things like age group, predominant ethnicity, etc. in each neighborhood – but again, no strong patterns there.

Microbial communities in NYC did not cluster according to neighborhood, borough, site type, or any other metadata category. Patterns were consistent across 16S and 18S data

The most interesting things were the expected patterns and associations that were neat to actually see in our dataset. First, many microbes on ATM keypads seemed to be derived from the human skin microbiome – ATM microbes were similar to those found on household surfaces such as pillowcases, and TVs (surfaces which probably amalgamate an “average” of skin microbes from everyone living in the house). Other microbes on ATM keypads were similar to outdoor air (perhaps representing dust/pollen/airborne microbes settling on ATM keypads), and restroom surfaces (don’t think about that one too much…)

“Sources” of ATM microbes – household surfaces, outdoor air, and restrooms

Second, in some neighborhoods we found traces of food species (chicken and seafood DNA), indicating a “microbial echo” of a person’s last meal. You might not think about it much, but when you handle food bits of DNA and cells are most likely sloughing off and sticking to your hands – so people in busy NYC may eat their meals on the go (perhaps without washing their hands) and then use an ATM keypad and transfer the food DNA onto the buttons.

Microbial taxa that were enriched (read: more abundant) on some ATM keypads: chicken, seafood, and an “extreme” mold species. Figure generated using LDA Effect Size (LEfSE) analysis.

Finally we also found subtle patterns and exciting taxa in our ATM dataset, all of which are interesting topics for further research. Some ATMs showed higher abundances of specific microbial species, such as the “extreme” mold Xeromyces bisporus (the “enrichment” of this microbe was statistically significant in certain neighborhhoods – see above figure), which could potentially be used as a biomarker for fungal species associated with baked goods. X. bisporus seems to be able to tolerate low water availability and live in comparatively harsh habitats such as sugary/processed foods, hence why we can consider it an extremophile. On other ATMs we also found microbial species representing putatively parasitic taxa – Trichomonas, a sexually transmitted disease in humans, and Toxoplasmosa, the infamous parasite found in cats. While we can’t 100% confirm that these parasites linger on ATM keypads (the rRNA gene region we used does not allow us to definitely separate these parasites from other closely related protist species), these tantalizing data set the stage for future (more focused) studies of the “urban microbiome”.

If you want to hear more about this study (and more about urban microbes in general), have a listen to this radio interview I did for The Innovation Hub (a WGBH/PRI show), as part of an episode focused on “The Future of Cities”.


Bik HM, Maritz JM, Luong A, Shin H, Dominguez-Bello MG, Carlton JM (2016)
Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City mSphere, 1(6) e00226-16; DOI: 10.1128/mSphere.00226-16

Wrap up of #PSB17 – Pacific Symposium in Biocomputing

Just got back from the Pacific Symposium in Biocomputing. The meeting had some aspects that may be of interest to various folks.

Electronic proceedings of the meeting are here.

I talked in a session on functional predictions.  I was asked to do this at the last minute so I made my slides by hand. Here they are.


I also recorded audio of my talk. Have not synched it to the slides but this may be of interest to some.


And I made a Storify of Tweets related to the meeting:


Multiple Positions Open at University of Oregon BioBE Center

Kevin Van Den Wymelenberg and Jessica Green, of the Biology and the Built Environment Center (BioBE), are currently seeking a microbial ecology Research Associate / Research Assistant Professor / Research Associate Professor (non-tenure track faculty) to investigate fundamental questions surrounding the role of microorganisms (bacteria, archaea, fungi, protists, and viruses) in the built environment and in relation to human health outcomes. Applicants must have a Ph.D. in biology, bioinformatics, or a related discipline.

The ideal candidate will have a combination of domain expertise and leadership potential. With regards to domain expertise, candidates should possess a demonstrated ability to generate and interpret microbiome data. Deep knowledge in data analytics, bioinformatics, and/or clinical microbiology is highly desirable. From a leadership perspective, we are seeking candidates that: are comfortable working on multiple concurrent projects with interdisciplinary scientists comprising a diverse range of experience (undergraduate through postdoc); have demonstrated a record of scientific writing and scholarly productivity; have a record of, or evidence of potential for, obtaining external research funding.

The successful candidate will have the ability to work with faculty, students, and industry partners from a variety of diverse backgrounds and the opportunity to creatively and independently engage in research at the BioBE Center (, funded by the Alfred P. Sloan Foundation, federal agencies, and members of industry.

The BioBE Center is training a new generation of innovators to study the built environment microbiome, including the diversity of microorganisms interacting with each other and with the indoor environment. The vision of this national research center is to understand buildings and urban environments as complex systems and to explore how urban, architectural, and building system (passive and active) design work to shape the microbiome, with the ultimate goal of designing healthy and sustainable buildings and cities.

For more information or to apply, see the full job post.

The concept of hygiene and the human microbiome.

(This post was written by Roo Vandegrift at the University of Oregon)

I was recently asked to spearhead the writing of a review centered around the interaction between the concept of hygiene and our increasingly nuanced understanding of the human skin microbiome for the Biology and the Built Environment (BioBE) Center at the University of Oregon.

This review began with an invitation from Dyson to conduct an impartial review of hand drying studies, which have been mired in competing interests and faulty methods. We saw an opportunity to not only provide an unbiased review of the literature, but also to ask a more fundamental question: how should hygiene be defined in light of our evolving perspective of the human and indoor microbiome?  We delivered a brief summary to Dyson (here) and then built upon that work to develop this question.  

As we started digging into the body of literature on hand hygiene, two things struck us as peculiar: the first was that in the hundreds of studies explicitly examining hygiene, the concept was never explicitly defined; the second was that there seemed to be a clear division between skin microbiological investigations coming from clinically and ecologically informed perspectives, with clinical research generally relying on older cultivation-dependent techniques. These two issues became the drivers for our review, and our goal was to provide an explicit definition of hygiene that would help to bridge the gap between the clinical skin microbiology literature and the newer human-associated microbial ecology literature. We were then able to use the body of literature on hand drying as a case-study to examine the implications of using a microbial ecology-based approach to defining hygiene.

You can read the full review as a preprint on bioRxiv now:

You can read the shorter, white page summary of the review on the BioBE blog:

Our review is broadly split into three sections: one section summarizing previous work on hygiene, one section briefly outlining previous work on human-associated microbial communities (including those found on the skin and in the built environment), and one section attempting to synthesize the two.

In the first section, we start seeing some of the limitations of cultivation-dependent methods, and how those limitations combine with implicit assumptions about the concept of hygiene. One thing that stands out to me from a thorough reading of clinical literature on hand hygiene is how often the idea of sterilization is used as a stand-in for the idea of hygiene — one result of the complete adoption of the germ theory of disease is the common misconception that “all microbes are germs”. This is apparent in the majority of studies of hygiene, particularly reflected in the focus on bulk reduction in microbial load, regardless of the identities of those microbes. I would, however, like to acknowledge Allison Aiello and Elaine Larson’s careful 2002 review, “What is the evidence for a causal link between hygiene and infections?“, which goes considerably beyond thinking of all microbes as germs and examines hundreds of studies, pulling out those that actually examine health outcomes as a dependent variable. Their review lays the conceptual foundations for what we are trying to do in our review.

In bridging into the second section, which outlines human-associated microbial ecology, we wanted to clearly illustrate the advances in techniques that the field utilizes. We put together this simple, but hopefully informative, conceptual figure to help:

Figure 1: Cultivation-dependent methods (A) are commonly used to study aspects of hand hygiene; many microbes are not detectable using this methodology (represented in grey). Handwashing reduces bulk microbial load, and cultivation yields data showing changes in the numbers of colony-forming units (counts); some studies identify colonies using morphological or molecular methods, yielding limited taxonomic information. Cultivation-independent methods (B), including high-throughput DNA sequencing, are commonly used to study the microbial ecology of the skin. Using these methods, it is possible to quantify alterations in relative abundance of bacterial populations with treatment (such as handwashing), obtain deep, comprehensive taxonomic diversity estimates; depending on technique, it may be possible to also obtain information on functional metabolic pathways (using metagenomics), assessment of proportion of the community that is active (using rRNA / rDNA comparisons, or live/dead cell assays), among other things.

It is clear that hygienic practices may interact significantly with human-associated microbial ecology. We highlight and summarize some of the important ecological factors that may interact with hygienic practice in a second conceptual figure:

Figure 2: Conceptual illustration of important ecological factors impacted by hygienic practice. Dispersal (a) is the movement of organisms across space; a patch of habitat is continuously sampling the pool of available colonists, which vary across a variety of traits (dispersal efficiency, rate of establishment, ex host survivability, etc.) (Vellend 2010); high dispersal rates due to human behaviors (e.g., microbial resuspension due to drying hands with an air dryer) have the potential to disperse both beneficial and harmful bacteria alike. Protective mutualisms (b) function through the occupation of niche space; harmful microorganisms are excluded from colonization via saturation of available habitat by benign, non-harmful microbes (Poisot et al. 2014). Host/microbe feedbacks (c) occur via the microbiota’s ability to activate host immune response, and the host immune system’s ability to modulate the skin microbiota (Chehoud et al, 2013; Garcia-Garcera et al, 2012; Oh et al, 2013) — multiple pathways, including IL-1 signalling (Naik et al 2012) and differential T-cell activation (Seneschal et al 2012), are involved — such feedbacks between host immune response and the skin microbiota are thought to be important to the maintenance of a healthy microbiota and the exclusion of invasive pathogenic microbes (Zhang et al 2015). Environmental filtering (d) works on the traits of dispersed colonists — microbes that can survive in a given set of environmental conditions are filtered from the pool of potential colonists (Vellend 2010): the resources and conditions found there permit the survival/growth of some organisms but not others. The importance of diversity of the microbiota to each of these ecological factors should not be underestimated; interactions between taxa may modulate their ecological roles, and community variation across a range of ecological traits may be altered by changes in community membership or structure (HMPC, 2012).

Coming to the third and final section, it should be clear to the reader that future work on hygiene would benefit from integrating modern techniques and an ecological perspective from recent human microbiome research. To facilitate that, we believe that it would be helpful to have a clear, concise definition of hygiene from which to work. This is probably the most important moment from our paper:

The evidence that microbes are essential for maintaining a healthy skin microbiota supports the idea that hygienic practices aimed at the simple removal of microbes may not be the best approach. Rather, hygienic practices should aim to reduce pathogenic microorganisms and simultaneously increase and maintain the presence of beneficial microorganisms essential for host protection. It is clear that microbial colonization of the skin is not deleterious, per se. Humans are covered in an imperceptible skim of microbial life at all times, with which we interact constantly. We posit that the conception of hygiene as a unilateral reduction or removal of microbial load has outlived its usefulness and that a definition of hygiene that is quantitative, uses modern molecular biology tools, and is focused on disease reduction is needed. As such, we explicitly define hygiene as ‘those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease’.

Let me repeat that last part: we explicitly define hygiene as ‘those actions and practices that reduce the spread or transmission of pathogenic microorganisms, and thus reduce the incidence of disease’. We feel that it is incredibly important to define hygiene in terms of health outcomes, not just in terms of reduction in number of microbes. This allows for research (consider, for example, probiotics research) to address the root of hygienic practice: cleanliness in pursuit of improved health.

From the hand drying example, it is clear that a standard definition of hygiene would be helpful: it turns out the vast majority of research on the hygienic aspects of hand drying has been funded by either the paper towel industry or the blow drier industry as advertising tools. There appears to be something of a feud going on between these two competing industries. Sadly, there is much about the current state of hand drying literature that is clearly partisan, and it is difficult to evaluate claims from either side because they define hygiene differently.

The hand drying literature can be separated into two opposing divisions: one attempting to demonstrate that the newer air dryers are as hygienically efficacious as paper towels, and the other attempting to discredit the newer technology in favor of paper towels. While both divisions utilize bulk reduction in microbial load as a proxy for hand hygiene, research from the first division largely focuses on the potential of wet hands to transfer microbes and the ability of air dryers (whether warm or jet) to effectively dry hands: the hypothesis in this case is drying is hygienically efficacious if hands are dry and new microbes are not acquired through the process. Research from the second division tends to focus on the risk of air dryers to spread microbes throughout the environment by aerosolizing moisture from the hands: the hypothesis in this case is drying is hygienically efficacious if new microbes are not acquired through the process and if production of aerosols are minimized. It is difficult to compare the two divisions because many of these studies include methodological issues (e.g., variation in protocols, lack of appropriate controls or statistical analyses) that make it difficult to compare results across studies.

Despite there being an obvious interplay between these two divisions, many of the concerns on either side remain unaddressed. Utilizing a definition of hygiene that explicitly relies on reduction in disease spread would address concerns on both sides of the debate: there is currently no evidence linking aerosolization of residual moisture (and associated microbes) with the actual spread of disease. Likewise, despite demonstrations that wet hands allow for increased bacterial transmission, there does not seem to be evidence linking wet hands after washing to deleterious health outcomes. The complex ecological context of the hand microbiota may modulate effects of both aerosolization and prolonged moistening. Additionally, the majority of hand drying research largely ignores the relative hygienic contribution of the hand washing step; understanding the relative contribution of washing to hygienic efficacy is necessary to put the hand drying literature in proper context.

The experience of working on this review has been incredibly positive: I’ve gotten to read deeply in corners of the scientific literature that I would not have expected I would be delving into even six months ago, I’ve learned a number of beautiful and startling things, and I believe that we have been able to contribute something necessary and worthwhile to the scientific discussion of hygiene. There is a gradual paradigm shift occurring right now in the clinical sciences, with germ theory being gently replaced by a more nuanced theory of disease that takes into account the beneficial role that our symbiotic microbiome plays; this review, I hope, will be a helpful building block for that new paradigm.

Koala Poop Microbiome Class: Summary and Class Materials

In class

As introduced a few months ago, our lab (with indispensable help again from Ashley Vater) taught a new research-based freshman seminar course.  The impetus for this course was one that we ran last year, testing if Swabs to Genomes was possible in a 10-week quarter.  Given the complexity and expense of the genome sequencing, we wanted to design a course that would avoid that portion but still get at most of the important topics and techniques.  Our chosen model system was the koala poop microbiome, as discussed in our introductory post.  Student blogs from the quarter can be found here, describing each week of the course.   As with last time, we have made all the course materials available online… everything from the lab notebooks (names removed) to the syllabus and protocols.

A few things were different this quarter, instead of two instructors we had three instructors and two TAs… for only 15 students!  Having run a similar course before, and having removed the genome sequencing component we figured that we would have smooth sailing.  Like that ever happens in research.  Having so many hands on deck was actually a mixed blessing, on the one hand it was awesome to divide up the work so many ways but on the other hand there was a problem with diffusion of responsibility.  This resulted in more last minute “what are we doing tomorrow?” meetings than with fewer instructors.

Koala fecal microbes

In the end, this class was much much cheaper than the Swabs to Genomes class… but was not as much less work as we had hoped.  Partly that’s because we scaled up the number of isolates, we started with around 100 isolates.   But also the usual problems reared their head… contaminated cultures, problem with PCR, lack of appropriate equipment (we literally had a gel box fire out lightning and then die).   We were able to power through all of those problems and still keep on track… but only through a lot of work behind the scenes.  I think this is not ideal and doesn’t convey the way typical lab research goes.   I think a class like this would be much better if it met more often and for longer (allowing the students to actually do all the work)  and/or to have an “open lab” where students could come in at other times and repeat experiments.

I think the students had a good time and learned a lot, I know the instructors did!  We’ll keep plugging away at this model and will keep posting our course materials hoping that they will be of use to someone out there.

New papers on Microbiology of the Built Environment, January 7, 2017

Microbes around the house

EditorialAn emerging paradox: Toward a better understanding of the potential benefits and adversity of microbe exposures in the indoor environment – J. Mensah-Attipoe – Indoor Air (OA)

Alfred P. Sloan Foundation logo

In order to further explore indoor microbial exposures and their associated health effects, and to help establish research agenda priorities, a two-day workshop to discuss the key challenges in recognizing and resolving the emerging paradox of indoor microbe exposures, sponsored by the Alfred P. Sloan Foundation, was held in Kuopio, Finland. The workshop brought together 50 researchers/experts in the field of indoor microbiology, environmental engineering, asthma and allergy research, toxicology, and epidemiology, from North America and Europe. The workshop consisted of podium presentations from invited speakers and a breakout group discussion session, with the outcomes from these groups being reported to the general assembly in the course of a final discussion. We highlight here the key recommendations that stemmed from the group discussions and the final discussion, structured based on a set of questions (in italics) that were provided to guide the process.

Sandpits as a reservoir of potentially pathogenic fungi for children – Anna Wójcik – Annals of Agricultural and Environmental Medicine (OA)

Children playing in sandbox. Source: Artaxerxes, Wikipedia.

Fungi belonging to various physiological and morphological groups present in the environment are potential human pathogens. Some of them are considered as emerging pathogens. Therefore, their presence in children’s playgrounds should be regarded as health risk factor. Sixty-eight samples of sand collected from 17 sandpits of different localities in Łódź, Poland, in autumn 2010 and 2011, and in spring 2011 and 2012 were evaluated. The fungi were isolated with classical mycological methods and identified on the basis of morphological and biochemical features. The prevalence of fungi in spring was 94.1% of sandpits in both layers of sand (depth 0–3 cm and 10–15 cm) and in one kindergarten sandpit, but only in a deeper layer. In autumn, fungi occurred in both layers in all sandpits (100%). (…). There were important causes of allergies, among them Cladosporium herbarum and Alternaria alternata, as well as of opportunistic mycoses: Cryptococcus neoformans, Aspergillus fumigatus and new and ‘emerging’ fungal pathogens e.g., Trichosporon, Rhodotorula, Fusarium and Scedosporium species.

Mold and dampness exposure and allergic outcomes from birth to adolescence: data from the BAMSE cohort – J. D. Thacher – Allergy (OA)

Association between exposure to mold or dampness indicators during infancy and the overall risk of asthma, rhinitis, or sensitization

Exposure to moldy or damp indoor environments is associated with allergic disease in young children, but it is unclear whether the effects persist to adolescence. Our objective was to assess whether exposure to mold or dampness during infancy increases the risk of asthma, rhinitis, or IgE sensitization in children followed from birth to 16 years of age. We collected questionnaire derived reports of mold or dampness indicators and allergic outcomes from 3798 children in a Swedish birth cohort (BAMSE). Sensitization was assessed from blood samples in 3293 children. Longitudinal associations between prevalent asthma, rhinitis, and IgE sensitization and mold or dampness indicators were assessed using generalized estimating equations. (…) Exposure to mold or dampness during infancy increased the risk of asthma and rhinitis up to 16 years of age, particularly for nonallergic disease. Early exposure to mold or dampness appeared particularly associated with persistent asthma through adolescence.

Using soil microbial inoculations to enhance substrate performance on extensive green roofs – Chloe J. Molineux – Science of the Total Environment ($41.95)

Graphical abstract

(…)  Extensive green roofs are lightweight systems generally constructed with a specialised growing medium that tends to be biologically limited and as such can be a harsh habitat for plants to thrive in. Thus, this investigation aimed to enhance the soil functioning with inoculations of soil microbes to increase plant diversity, improve vegetation health/performance and maximise access to soil nutrients. Manipulations included the addition of mycorrhizal fungi and a microbial mixture (‘compost tea’) to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs, with complex relationships between depth and type of substrate and the type of microbial inoculant applied, with no clear pattern being observed. (…)

Microbes in public places

Indoor fungal contamination of traditional public baths (Hammams) – Leyla Benammar – International Biodeterioration & Biodegradation ($35.95)

Graphical abstract

This study was carried out to provide an overview of the fungal load in Algerian traditional baths (Hammams) as well as to isolate and identify the main pathogenic fungi. Over a period of four months, ten baths were examined and screened for fungal contamination from several parts of the hot steamy rooms (floor, wall, door, air and marble massage platform). In total, 7157 fungi isolates were recovered from the surveyed Hammams and the most abundant molds were Penicillium spp. (45.12%) followed by Aspergillus spp. (28.80%). (…) ANCOVA revealed a significant increase in fungal loads related to the average number of customers and mean opening year of the Hammams, in contrast with locality (favored or popular district). This study indicates that Hammams present a potential source of pathogenic fungi which may impose a real threat on public health.

Resistance of Aerosolized Bacterial Viruses to Four Germicidal Products – Nathalie Turgeon – PLOS ONE (OA)

Effect of Pledge®, Eugenol, MiST®, and H2O2 on the infectivity of airborne phage ϕ6.

Viral diseases can spread through a variety of routes including aerosols. Yet, limited data are available on the efficacy of aerosolized chemicals to reduce viral loads in the air. Bacteriophages (phages) are often used as surrogates for hazardous viruses in aerosol studies because they are inexpensive, easy to handle, and safe for laboratory workers.  (…)  The resistance levels of the four phages varied depending on the relative humidity (RH) and germicidal products tested. Phage MS2 was the most stable airborne virus under the environmental conditions tested while phage PR772 was the least stable. Pledge® and Eugenol reduced the infectivity of all airborne phages tested. At 25% RH, Pledge® and Eugenol were more effective at reducing infectivity of RNA phages ϕ6 and MS2. At 50% RH, Pledge® was the most effective agent against phage MS2. These findings illustrate that various airborne viruses should be tested to demonstrate the effectiveness of germicidal treatments. This research also provides a set of parameters for testing germicidal products in large-scale settings to reduce the risk of virus transmission.

Microbes and city birds

Plumage micro-organisms and preen gland size in an urbanizing context – Mathieu Giraudeau – Science of The Total Environment ($41.95)

Graphical abstract

(…) Birds carry a large variety of microorganisms on their plumage and some of them have the capacity to degrade feather keratin and alter plumage integrity. To limit the negative effects of these feather-degrading bacteria, birds coat their feathers with preen gland secretions containing antibacterial substances. Here we examined urban-rural variation in feather microbial abundance and preen gland size in house finches (Haemorhous mexicanus). We found that, although urban and rural finches carry similar total-cultivable microbial loads on their plumage, the abundance of feather-degrading bacteria was on average three times higher on the plumage of urban birds. We also found an increase in preen gland size along the gradient of urbanization, suggesting that urban birds may coat their feathers with more preen oil to limit the growth or activity of feather-degrading microbes. (…)

Microbes on ships

Molecular methods resolve the bacterial composition of natural marine biofilms on galvanically coupled stainless steel cathodes – Athenia L. Oldham – Journal of Industrial Microbiology & Biotechnology ($39.95)

Navy vessel. Source: Wikipedia.

Navy vessels consist of various metal alloys and biofilm accumulation at the metal surface is thought to play a role in influencing metal deterioration. To develop better strategies to monitor and control metallic biofilms, it is necessary to resolve the bacterial composition within the biofilm. This study aimed to determine if differences in electrochemical current could influence the composition of dominant bacteria in a metallic biofilm, and if so, determine the level of resolution using metagenomic amplicon sequencing. (…) Following 3 months of exposure, the bacterial composition of biofilms collected from the SSCs was determined and compared. Dominant bacterial taxa from the two higher current SSCs were different from that of the low-current SSC as determined by DGGE and verified by Illumina DNA-seq analysis. These results demonstrate that electrochemical current could influence the composition of dominant bacteria in metallic biofilms and that amplicon sequencing is sufficient to complement current methods used to study metallic biofilms in marine environments.

Microbes in drinking water

Biofilm composition and threshold concentration for growth of Legionella pneumophila on surfaces exposed to flowing warm tap water without disinfectant – Applied and Environmental Microbiology ($25 for 1 day)

Legionella bacterium (green) caught by a Vermamoeba amoeba (orange). Source: Wikipedia.

Legionella pneumophila in potable-water installations poses a potential health risk, but quantitative information about its replication in biofilms in relation to water quality is scarce. Therefore, biofilm formation on surfaces of glass and chlorinated polyvinyl chloride (CPVC) in contact with tap water at 34-39°C was investigated under controlled hydraulic conditions in a model system inoculated with biofilm-grown L. pneumophila. (…) An elevated biofilm concentration and growth of L. pneumophila were also observed with tap water at the laboratory. The Betaproteobacteria Piscinibacter and Methyloversatilis and amoeba-resisting Alphaproteobacteria predominated in the clones and isolates retrieved from the biofilms. In the biofilm, the Legionella colony counts correlated significantly with total cell count (TCC), heterotrophic plate count, ATP concentration and Vermamoeba vermiformis. (…)

PressDutch scientists discover favorable conditions for growth of Legionella bacteria – News Medical

“Drinking water prepared from aerobic groundwater with a low concentration of dissolved natural organic matter induced a very low biofilm concentration that did not support growth of L. pneumophila,” said van der Kooij. “Drinking water from two other sources with higher concentrations of organic matter induced higher biofilm concentrations that supported Legionella growth.” Legionella bacteria grew exponentially in relation to biofilm concentration, said van der Kooij. Below a threshold concentration of biofilm, Legionella did not multiply.

Spatial and temporal analogies in microbial communities in natural drinking water biofilms – I. Douterelo – Science of The Total Environment (OA)

Graphical abstract

Biofilms are ubiquitous throughout drinking water distribution systems (DWDS), playing central roles in system performance and delivery of safe clean drinking water. However, little is known about how the interaction of abiotic and biotic factors influence the microbial communities of these biofilms in real systems. Results are presented here from a one-year study using in situ sampling devices installed in two operational systems supplied with different source waters. Independently of the characteristics of the incoming water and marked differences in hydraulic conditions between sites and over time, a core bacterial community was observed in all samples suggesting that internal factors (autogenic) are central in shaping biofilm formation and composition. From this it is apparent that future research and management strategies need to consider the specific microorganisms found to be able to colonise pipe surfaces and form biofilms, such that it might be possible to exclude these and hence protect the supply of safe clean drinking water.

Microbes and food production

Microbial Quality, Safety, and Pathogen Detection by Using Quantitative PCR of Raw Salad Vegetables Sold in Dhanbad City, India – Sujeet K. Mritunjay – Journal of Food Protection (restricted access, no price listed)

Tossed salad. Source: Wikipedia.

Consumption of ready-to-eat fresh vegetables has increased worldwide, with a consequent increase in outbreaks caused by foodborne pathogens. In the Indian subcontinent, raw fresh vegetables are usually consumed without washing or other decontamination procedures, thereby leading to new food safety threats. In this study, the microbiological quality and pathogenic profile of raw salad vegetables was evaluated through standard protocols. In total, 480 samples (60 each of eight different salad vegetables) of cucumber, tomato, carrot, coriander, cabbage, beetroot, radish, and spinach were collected (…). The samples were analyzed for total plate count, total coliforms, Escherichia coli, E. coli O157:H7, Listeria monocytogenes, and Salmonella spp. Incidences of pathogens were detected through quantitative PCR subsequent to isolation. Results showed that 46.7% (for total plate counts) and 30% (for total coliforms) of samples were unacceptable for consumption per the Food Safety and Standards Authority of India.(…)

Microbes and cultural heritage objects

About a Sloth: Survey of the state of conservation of the Mylodon listai (Xenarthra-Mylodontidae) skin fragment from the Pleistocene of Argentina kept at the Museum of La Plata (Argentina) – Daniela Silvana Nitiu – Ge-conservación (OA)

Showcase in the La Plata Museum where the skin fragment is kept

The aim of the present study was to assess the state of conservation of the fossilized skin fragment assigned to Mylodon listai preserved in a showcase of the Paleontology Hall of the Museum of La Plata. To this end, we conducted a volumetric aerobiological sampling both inside the showcase and in the hall to detect the presence of fungal load that could alter its preservation. We also determined the environmental parameters both inside and outside the showcase. The aerobiological sampling inside the showcase showed 3061.50 spores/m3 corresponding to 22 fungal types, while in the hall, 2283.20 spores/m3 corresponding to 14 fungal types where detected. Cladosporium was the most important type in all the sampling points. The temperatures recorded were lower than those recommended for the conservation of leather and the relative humidity values were acceptable in 70% of the record for this material.

New paper of possible interest: High diversity of airborne fungi in the hospital environment 

Invasive fungal infections acquired in the hospital have progressively emerged as an important cause of life-threatening infection. In particular, airborne fungi in hospitals are considered critical pathogens of hospital-associated infections.

Just a quick post – this may be of interest. 

Source: High diversity of airborne fungi in the hospital environment as revealed by meta-sequencing-based microbiome analysis



Invasive fungal infections acquired in the hospital have progressively emerged as an important cause of life-threatening infection. In particular, airborne fungi in hospitals are considered critical pathogens of hospital-associated infections. To identify the causative airborne microorganisms, high-volume air samplers were utilized for collection, and species identification was performed using a culture-based method and DNA sequencing analysis with the Illumina MiSeq and HiSeq 2000 sequencing systems. Few bacteria were grown after cultivation in blood agar. However, using microbiome sequencing, the relative abundance of fungi, Archaea species, bacteria and viruses was determined. The distribution characteristics of fungi were investigated using heat map analysis of four departments, including the Respiratory Intensive Care Unit, Intensive Care Unit, Emergency Room and Outpatient Department. The prevalence of Aspergillus among fungi was the highest at the species level, approximately 17% to 61%, and the prevalence of Aspergillus fumigatus among Aspergillus species was from 34% to 50% in the four departments. Draft genomes of microorganisms isolated from the hospital environment were obtained by sequence analysis, indicating that investigation into the diversity of airborne fungi may provide reliable results for hospital infection control and surveillance.

Upcoming National Academies Study on Legionella in Drinking Water Systems

Just got this from the a representative of the National Academy of Sciences who asked me to post here.

Scope of work: An ad hoc committee of The National Academies will review the state of science with respect to Legionella contamination of water systems and issue a report that addresses the following: ecology and diagnosis; transmission via water systems; review of outbreak and environmental data; prevention and control; policy and training issues; as well as the gaps in science and how to address them. Partial funding has been secured through the Alfred P. Sloan Foundation. Additional funding is still sought before the study will officially begin. A draft statement of task is available upon request. Please contact Dr. Laura Ehlers ( for more information about the study.


Paper of interest: Environmental Viral Metagenomics Analyses in Aquaculture

Just a quick post here.  Studies of the microbiology of built environments that house animals (e.g., aquaria, farms, animal shelters, zoos, etc) are of growing interest for multiple reasons.  In that regard this paper might be of interest to some – because it covers some topics that are sometimes neglected in this general area – viral diversity and aquaculture.  Here is a link to the paper

Source: Environmental Viral Metagenomics Analyses in Aquaculture: Applications in Epidemiology and Disease Control

A must read from Reuters on the closed access world of superbug infections #terrifying

Vague rules give healthcare providers leeway in deciding when, or even whether, to report clusters of infections. And when they do, the public rarely knows.

This is a really really big deal. We desperately need to be more open about antibiotic resistant bugs and any outbreaks of them.  Kudos to Reuters and Deborah J. Nelson, David Rohde, Benjamin Lesser and Ryan McNeill for this report.  It should put a chill in your spine.  Antibiotic resistant infections is one of the biggest health threats of modern times and it is getting worse.


Source: How hospitals, nursing homes keep deadly ‘superbug’ outbreaks secret

Update 4pm

Note it is worth checking out the other articles in this series from Reuters: