Antibiotic Resistance Can Spread Through the Air

There is an abundance of literature on how microbes can obtain antibiotic resistance, but not as much about how antibiotic resistance can spread. Jonathan drew my attention to this article today, which highlights the fact that antibiotic resistance can be spread through the air. While I didn’t find the conclusions all that surprising, I was a little bit terrified to know that antibiotic resistance can spread miles, if not hundreds of miles, from where the antibiotics were used. Where there is DNA, there can be antibiotic resistance. What other vehicles does DNA have to spread around our world (wind, water, soil, people, animals, etc)? As someone who lives in very close proximity to many farms, I am regrettably ignorant about antibiotic use around me and what ramifications it can or will have on my health. Does anyone else have similar concerns?

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Submit data to NCBI’s Short Read Archive

I was recently contacted by a SRA curator to submit the raw pacbio datasets that go with genomes that were deposited to NCBI. I did go through with the submission and will share what I did and my experience doing so.

Be prepared to answer a lot of questions regarding your project as well as write short paragraphs about the project or specific samples. The more information you add the better for the community.

When submitting reads to the archive, you will need to reference BioSample that is itself linked to a BioProject. In my case those were already created because the genome were already on NCBI. I just added the identifiers when prompted.

How to submit to SRA will take you to the SRA’s tutorial.

Log in to the SRA website using your NCBI account. If you do not have one, create one.

Create a new submission. All your data that is grouped under the same submission will have the same release date. You can set your data to be released at a particular date. The earliest you can do is the following day at midnight. I am not sure how long you can keep your data private but the refilled release date is set for 1 year from the day you start the submission.

Once your submission is create, you can create a new experiment. The experiments are linked to a sample. You can have multiple experiments link to the same BioSample. For this step you will need:

The name of the platform, alias, title and a BioProject identifier, BioSample identifier. You will also need to specify a name for the library construction, a strategy (from a list of predefined terms), Source and Selection method used.

Optionally you can add links to other Dbs or websites for the particular experiment. A pipeline information can also be entered but is not required. Once you have entered the required data, you can save and your experiment will now show up in the submission table.

Add a run to the experiment by clicking “new run”, give it an alias so you can remember which dataset you are uploading. Select the data type (in my case PacBio_HDF5).

For HDF5 submission, you need to submit 4 files. 3 bax.h5 file and 1 bas.h5. I compressed the files using gzip but it did not reduce the file size that much (maybe I will skip this next time). You can find the h5 files in the Analysis_Results folder in the PacBio data that I downloaded from the sequencing center.

I have not submitted any other file format so far. There are descriptions on the SRA website for what they are expecting for each format or platform.

Before you upload the files to the SRA ftp, you will need to enter the file name as well as the MD5 checksum for the file. This is used to make sure the file that they received is the same as the file you are intending on sending. It allows the sra people to make sure the file is complete and not corrupted incase of interrupted connections or other things that can happen when transferring 1 or 2 Gb files. The description and help text on the new run page is fairly clear.

On my mac, the command to get the checksum is

> MD5 <filename>

Once the 4 filenames have been added with their corresponding checksums, I needed to actually send the files over to the SRA. This is what gave me the most trouble. My ftp/sftp setting must be set up in such a way that it was not allowing me to use the command line tool. I ended up using FileZilla with the appropriate credentials using port 21 (the port number can change depending on your settings but it worked for me). I created a directory with my BioProject ID so I wouldn’t just dump data in a top level directory. I pushed my 4 files over and waited. The transfer rate was very fast (1.5Mb/s) most of the time but dropped to a 100Kb/s for a little while. I would recommend letting this happen over night or on the weekend. Make sure your computer does not go to sleep after long periods of inactivity and that your internet connection stays alive.

Repeat for the other runs and samples you may have. I had 6 samples with 12 runs (about 40Gb of data) took 4-5 hours of upload time and a couple of hours to learn the submission form, gather and enter the required data.

Once the data is uploaded the SRA system will link the files to the runs you just added to your experiment. You can check the status of the file links here

The following websites/papers were very helpful.

Section 12 (Data Submission) of the Swab to Genome paper describes the Biosample and Bioproject creation.


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Tangible Interactive Microbiology for Informal Science Education

Crosspsting from my Tree of Life blog

This is so cool: Tangible Interactive Microbiology for Informal Science Education.


We present an interactive platform that enables human users to interface with microbiological living cells through a touch-screen, thereby generating a tangible interactive experience with the microscopic world that is hidden to most people. Euglena gracilis, single-celled phototactic microorganisms, are imaged and optically stimulated via a microscope setup equipped with a projector and a touch- screen display. Users can directly interact with these organisms by drawing patterns onto the screen, which displays the real-time magnified view of the microfluidic chamber with the motile euglena cells. The drawings are directly projected onto the chamber, thereby influencing the swimming motion of the cells. We discuss the architecture of the system and provide exploratory user testing results in a facilitated setting, which shows engaging nature of our system for children and the general public. In conclusion, our tangible interactive microscope allows artistic expression and scientific exploration with the ease of “child’s play.”

And check out this video.

I would post a picture here but they discourage it.  So you will just have to go look for yourself.  The PDF is free, at least for now.

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Moving from commensalism to mutualism: not microbes, but the people who study them

Nice editorial in Indoor Air from Brent Stephen, Rachel Adams, Seema Bhangar, Kyle Bibby and Michael Waring: From commensalism to mutualism: integrating the microbial ecology, building science, and indoor air communities to advance research on the indoor microbiome.

In it they present what they view as key findings from recent studies of microbiology of the buiolt / indoor environment.  And they also discuss findings from a workshop that was help in 2014 on “Building science to advance research in the microbiology of the built environment“.

They have separately summarized the workshop and here present some key findings including key goals for the community:

  • Increase the use and/or development quantitative metrics
  • “Conduct longitudinal intervention and controlled environment studies that focus on fundamental processes familiar to those in the indoor air sciences”
  • “Engage a broader funding base.”

They also emphasize the following needs:

  • “Continue and enhance efforts to communicate and transfer knowledge between microbiology and building science communities, and begin integrating health scientists into the research agenda.”
  • “Continue efforts to improve standardization and evaluation of sampling methods.”
  • “Explore connections between indoor microbiology and chemistry.”


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Today in microbes and art: Bioart and Bacteria – The Artwork of Anna Dumitriu

Crossposting this from my Tree of Life blog.

I could spend a lot of time on this website: Bioart and Bacteria – The Artwork of Anna Dumitriu.  I found out about it from a Tweet from Dumutriu:

And it is right up my alley (being interested in the interface between art and science, especially in relation to microbes).  Lots of interesting sections here including:

And many more.  I do not know much about the artist but really glad she pointed me to this.

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Evolution in urban environments

Nice story worth reading in New York Magazine by Ferris Jabr: Uptown Mice Are Different From Downtown Mice — NYMag.  It discusses some work on evolution in urban environments, including a little bit about work starting to be done on gut microbes of rodents and how they might be affected by urban life.

Other things of note on this topic

And I am sure many others (not trying to be comprehensive here).

There are many reasons to be interested in this topic.  One aspect of this I find of potential importance is in how microbes are evolving in respose to urban environments.  Of course we know a lot about this in regard to some pathogens, but less in terms of the rest of the microbes out there.  Now I note – this is a different angle than the normal work on microbial communities which has focused on the ecology of the such communities (e.g., comparing the types of microbes found in cities vs. other locations).  The key questions here relate to what evolutionary changes have occurred in microbes (well, non pathogenic ones) in response to living in urban environments.  I have very little work on this topic — and would love to know examples if people know of any.

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How Cosmetic Use Changes the Microbiome

Almost everyone in developed countries uses cosmetics, from body washes to make-up. In the US, the cosmetics industry makes over $56 billion dollars in revenue. As a society, we use a lot of personal care products. And in order for those products to have a useful shelf-life, they contain antimicrobials – no one wants to open their hair gel and find a fuzzy patch in there.

But just like how antibiotics have had a huge impact on human microbiota, especially in terms of resistance, I wondered how antimicrobial use in cosmetics affect our skin microbiota. It has an effect, no doubt, but is it significant and can we say anything about positive or negative effects on human health? Should it be as huge a concern as antibiotic use? And how prevalent is antimicrobial use in everyday products or even food?

The most recent antimicrobial to get attention from the public was Triclosan, which is used in a variety of everyday products, including personal care items. Triclosan has been correlated with allergies and has raised worries of antibiotic resistance. However, there are other antimicrobials in products we regularly use on our skin. For instance, titanium dioxide is widely used in food and personal care items primarily as an anti-fungal. There are a few studies researching the effect of using products containing titanium dioxide, but even fewer of these examine the effect on the skin microbiome. In fact, a lot of skin microbiome research can be summarized as follows:

The human skin microbiota can be affected by many environmental factors, such as temperature, humidity, pH, exposure to air and light, and host factors, such as genetic background, body locations, gender, immune response, hygiene habit, use of antibiotics and antimicrobial detergent, and cosmetic use.

Unsurprisingly, fungi (like yeast), have started developing resistance to common anti-fungals used in cosmetics.

It shouldn’t be surprising by now that antimicrobial resistance is so prolific in our human environment. It is always surprising to become aware of where these antimicrobial compounds exist.

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Sloan Foundation at Healthy Buildings 2015 America

Greetings from the Healthy Buildings Conference Committee! We are excited to be hosting Healthy Buildings 2015 America in Boulder, Colorado, at the University of Colorado Boulder. Healthy Buildings is a unique forum for built environment researchers and professionals to engage with innovative projects, products, and services and to meet and collaborate with colleagues working on the pressing global challenge of making buildings healthy, energy efficient, and sustainable.

Healthy Buildings 2015_B.jpg


This years conference theme is Innovation in a Time of Energy Uncertainty and Climate Adaptation. Topics that will be presented include sustainable buildings, health building issues, mission critical environments, and indoor environmental factors and human health.  Conference papers are being accepted through Jan 22, 2015.

The Sloan Foundation will be sponsoring a series of events at the conference.  A plenary speaker will present on the microbiology of the building environment. Sloan-funded researchers will present their research in a workshop so that the results can be utilized to promote, design, and operate healthy buildings. A panel of practitioners and researchers that will demonstrate key methods related to assessing Healthy Buildings and the Microbiology of the Built Environment. One social and one career event will be planned to promote collaboration between researchers, practitioners, and students.

A workshop will be organized that bring together a group of 8 MoBE grantees from both the microbiology and building science fields to present their work in the context of dissemination and implementation. Speakers will be invited from the Sloan list of grantees who are more applied in their research programs or have disseminated their work through papers that interpreted the science in a practical way. They will also be a combination of microbiologists and engineers, and also a mix of male and female researchers. The talks be short and focused on what is translatable in the research findings. Time for a question and answer period would follow each presentation, and detailed notes would be available for all participants in the session, including contact information. This workshop will be held in the morning of Day 2 of the conference, Monday Jul 20.

A panel will be convened of both practitioners and researchers to address how the microbiology of the built environment is currently being assessed with a demonstration of techniques that can be used by practitioners. This session is designed to be much more interactive and hands on. Methods will be demonstrated for collecting microbial samples including swab sampling and open plate sampling. Instrumentation will be demonstrated that is used to make equilibrium humidity, particulate matter, and CO2 measurements. Once microbial samples are collected, they must be analyzed. Pros and cons of culturing, microscopy, and DNA/RNA sequencing will be discussed. Suggestions for meta-data interpretations and how to analyze these data will be included. Protocols will be provided for all techniques presented to collect microbiological samples and building meta-data. How to interpret the data will be presented. This panel will take place in the afternoon of Day 2 of the conference, Monday Jul 20.

One social and one professional event will be organized for Tuesday Day 3 of the conference, after the Panel and Workshop that take place on Monday Day 2 of the conference, with the goal of meeting each other and finding common interests. Input from students will be explicitly incorporated into the planning of these events to ensure that they are engaged. The social event will be a breakfast on Day 3 of the conference, held at the engineering center before the plenary (8-9am). The professional event is a career lunch discussion, which includes academics, practitioners, consultants, engineers, and scientists, to talk about their career paths and answer questions from students. This career discussion will take place during the lunchtime of Day 3, in a special room at the C4C (this is the location on campus for conference lunches). Specific individuals selected by the students will be invited to this event.

 We encourage you to submit papers and plan on attending our conference!
On behalf of the Conference Committee, Shelly Miller, Conference President.

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How We View Air

Whenever I got sick as a young child, my mom insisted upon opening my windows in the mornings to let fresh air in. She claimed it would help me get better if we let clean air in to flush out the dirty air. To me, it was a nuisance. I had the chills and resented the loss of warm, comfortable air from the room.

Over the past few years, I’ve been thinking more about indoor air. The number of posts on the subject on this blog alone could probably make up a small novel. And research on indoor air and the microbes that dwell in it is on the rise. A recent article on Popular Science touches upon the subject of microbes in indoor air and ventilation systems. The article seems a bit sensationalist at times, but it brings up some good points. For instance, research on air-dwelling microbes dropped after the discovery of antibiotics because doctors thought they didn’t need to study how pathogens were spread if they had the “cure” to so many of them.

A large part of the article talks about influenza transmission through ventilation systems and the air shared by sick and healthy people alike. It also addresses how our collective views on air and ventilation affect the virus’ movement. For instance, influenza is transmitted better in dry air, but winter months call for heavy heater usage in most building, effectively creating an optimal environment for the virus to spread.

I think part of the reason why ventilation and indoor air in general is so worrisome is because there is a culture of ignorance surrounding it. No one will be able to convince me that the clearly dusty and dirty ducts in most buildings I enter are doing anything good for indoor air. I’m also surprised at how many windows don’t open. Although there is little evidence to support the hypothesis that opening windows benefits the occupants of an indoor space, there is something to be said of simply circulating the air in a room, among other things.

So, for the umpteenth time in my life, my mom might have actually been right.

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Dairy genomes: Good example of the power of reference genomes for particular environments

Quick post here.  Just got alerted to this paper by automated searches from PubchaseConstruction of a dairy microbial genome catalog opens new perspect… – PubMed – NCBI.  This paper provides a really good example of how researchers interested in microbial ecology of a particular system (in this case, dairies and cheese) can use culturing and genome sequencing of select taxa to then help inform microbial ecology studies of that system.  It would be great to do this from more ecosystems, including, especially in my mind, built environments where we right now have only a limited number of reference genomes for cultured isolates.  This is one of the reasons we started on “Built Environment Reference Genomes” project at microBEnet as an undergraduate research activity.  Stay tuned for more information about this as we are also developing tools and methods and course materials to hopefully have anyone (and,well, everyone) do things like this.  (For example see our Swabs to Genomes workflow preprint).


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The Importance of Microbial Eukaryotes in Premise Plumbing Systems

The environmental engineering research community now recognizes that it is important to understand the bacterial ecology of premise (building) plumbing systems to control opportunistic pathogens (OP). Many investigations, including those supported by the Sloan Foundation MoBE program, have begun to shed light on the factors driving bacterial ecology in drinking water systems. While the bacterial ecology story is far from complete, the ecology of microbial eukaryotes is even less well understood. Microbial eukaryotes are  important members of premise plumbing microbial ecology, both for their influence on bacterial ecology and as OP. Some free-living amoeba (FLA), such as Acanthamoeba, are OP. FLA also control biofilms through bacterial grazing, and may protect bacterial OP, such as Legionella and Mycobacterium, from disinfection. In fact, bacterial OP infecting FLA are known to be more virulent than they would otherwise be. Additionally, fungi may be relevant OP in the water system, especially for immune-compromised persons.

These points take on greater importance in light of the proposed ASHRAE standard 188p for control of legionellosis. In all likelihood, the final version of this standard will recommend on-site disinfection for control of Legionella spp. This topic is of concern to property owners due to liability for infections caused by the drinking water system. It is rare for facilities to design or operate disinfection systems to control more than Legionella or some other indicator bacteria, but these same facilities operate under the assumption that because they are utilizing secondary disinfection, their premise plumbing is “safe” from all and any microbial threats. A much more elegant approach, as put forth by Dr. Amy Pruden, would be to design and operate the system in a ‘probiotic’ way such that a more desirable microbial ecology is naturally selected and outcompetes OP. A probiotic approach would require an understanding of all microbial ecology drivers, including microbial eukaryotes.

In our recent paper published in Water Research, we examined the fungal ecology of samples that were previously analyzed for bacterial ecology. These samples were from a hospital hot water system both before and after the installation and operation of an on-site monochloramine disinfection system. As shown in the attached figure, we saw an immediately detectable shift in the bacterial community, but no discernable shift in the fungal community, after the introduction of on-site monochloramine. The apparent fungal diversity of the system was also low, with only five core genera; however, there were a high diversity of fungi ‘passing-through’, likely from the surface water being treated and an inability to discern viable fungal cells.


To me, this work raises questions about not only fungal ecology in premise plumbing systems, but microbial eukaryotes in general. What are the factors driving the abundance and diversity of microbial eukaryotes? If our overall goal is to control premise plumbing OP, should we be targeting microbial eukaryotes as a ‘keystone species’? What is the interplay between microbial eukaryotes and the overall microbial ecology – not just OP? As we have often heard throughout the Sloan MoBE program, gaining a comprehensive view of the microbial ecology of the built environment will require a holistic view, and in the case of premise plumbing, must include microbial eukaryotes.

Ma, X.; Baron, J. L.; Vikram, A.; Stout, J. E.; Bibby, K., Fungal Diversity and Presence of Potentially Pathogenic Fungi in a Hospital Hot Water System Treated with On-Site Monochloramine. Water Research. doi:10.1016/j.watres.2014.12.052

Baron, J. L.; Vikram, A.; Duda, S.; Stout, J. E.; Bibby, K., Shift in the Microbial Ecology of a Hospital Hot Water System following the Introduction of an On-Site Monochloramine Disinfection System. PLoS ONE 2014, 9, (7), e102679.


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Looking back at 2014 under the microscope

Agricultural sludge, by Eberhardt Josué Friedrich Kernahan and Enrique Rodríguez Cañas
Agricultural sludge, by Eberhardt Josué Friedrich Kernahan and Enrique Rodríguez Cañas

For those folks who spend most of our time looking at code, charts and graphs, it’s always fun to look at what folks are doing with imaging and microscopy. Advances in sequencing technology have changed the way we think about the microbial world, but the way we see the microbial world is also changing as technology improves.

To cap off 2014, there are a number of wonderful competitions that showcase particularly striking or important examples in scientific imaging and microscopy. Here are a few of them :

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Extended Abstract Deadline for Healthy Buildings America is Jan 15.

Just a quick reminder that the Abstract Deadline for Healthy Buildings America is January 15th.  This conference will take place July 19-22 in Boulder CO… just following the Sloan Microbiology of The Built Environment Conference, also in Boulder from July 15-18.    Here’s a description of the Healthy Buildings Conference:

Healthy Buildings is a unique forum for built environment researchers and professionals to engage with innovative projects, products, and services and to meet and collaborate with colleagues working on the pressing global challenge of making buildings healthy, energy efficient, and sustainable.

Healthy Buildings attracts researchers and other professionals from the fields of indoor air quality, built environments, HVAC, health sciences, public health policy, urban planning, mechanical engineering, architecture, building design and management, and more.

Healthy Buildings sustains ISIAQ’s mission to support the creation of healthy, comfortable, and productive indoor environments. ISIAQ believes this is achievable by advancing the science and technology of indoor air quality and climate as it relates to indoor environment design, construction, operation, maintenance, air quality measurement, and health sciences.

ISIAQ’s major role is to facilitate international and interdisciplinary communication and information exchange, as well as develop, adapt, and maintain codes, standards, and guidelines for the improvements of indoor air quality and climate.

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Teixobactin has been getting a lot of press since it’s debut in the most recent publication of Nature. And rightfully so: The authors claim that the mechanisms by which Teixobactin works will make it very hard for resistance development. Surely this discovery couldn’t have come at a better time, in a period where we have more antibiotic resistant bacteria than ever before. To think we may be able to fend of MRSA, Tuberculosis, Streptococcus, and a plethora of other antibiotic resistant diseases is downright amazing.
However, I can’t help but approach Teixobactin with skepticism. It is my belief that if you put a selective pressure on microbes, they will find a way to overcome it. Take peroxides for example. They are extremely effective antimicrobial agents, but there are now dozens of genes that code for resistance to them. Furthermore, the authors of this paper make no mention of Teixobactions efficacy on spore forming bacteria, such as Anthrax. I am not arguing that this discovery doesn’t come with weight, but Lewis’s claim that “this for all practical purposes may be a largely resistance-free compound” may be spoken too soon. What are your thoughts?

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BioBE Selected for AIA Design + Health Research Consortium


The University of Oregon’s Biology and the Built Environment Center has been chosen by the American Institute of Architects (AIA), the AIA Foundation, and the Association of Collegiate Schools of Architecture to be a charter member of the AIA Design & Health Research Consortium. The eleven Consortium members are university-led teams of architecture and public health experts seeking to advance revolutionary research at the intersection of design and health. According to the AIA, the Consortium’s primary goals are to:

  1. Strengthen and expand the knowledge base that informs the connection between design and health through peer-reviewed quantitative and qualitative research projects, documenting and disseminating outcomes.
  2. Develop evidence-based tools for practicing professionals informed by current research.
  3. Translate the outcomes of research about the connection between design and health for policymakers and the general public.

In order to achieve these goals, the AIA Foundation and its partners will promote transdisciplinary collaboration and research activities that provide evidence-based support for the design of healthier built environments. Six different approaches (environmental quality, natural systems, physical activity, safety, sensory environments, and social connectedness) will be addressed. Recognition of social equity issues underpins the Consortium’s mission.

More information can be found at

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The Initiative for the Critical Assessment of Metagenome Interpretation (CAMI)

cami-logo_smIn just over a decade, metagenomics has developed into a powerful and productive method in microbiology and microbial ecology. The ability to retrieve and organize bits and pieces of genomic DNA from any natural context has opened a window into the vast universe of uncultivated microbes. Tremendous progress has been made in computational approaches to interpret this sequence data but none can completely recover the complex information encoded in metagenomes.

A number of challenges stand in the way. Simplifying assumptions are needed and lead to strong limitations and potential inaccuracies in practice. Critically, methodological improvements are difficult to gauge due to the lack of a general standard for comparison. Developers face a substantial burden to individually evaluate existing approaches, which consumes time and computational resources, and may introduce unintended biases.

The Critical Assessment of Metagenome Interpretation (CAMI) is a new community-led initiative designed to help tackle these problems by aiming for an independent, comprehensive and bias-free evaluation of methods. We are making extensive high-quality unpublished metagenomic data sets available for developers to test their short read assembly, binning and taxonomic profiling methods. The results of CAMI will provide exhaustive quantitative measurements of tool performance to serve as a guide to users under different scenarios, and to help developers identify promising directions for future work.

The competition is tentatively scheduled to open in the beginning of 2015. Key data sets are being generated, and CAMI is currently seeking additional data contributors to provide genomes of deep-branching lineages for data set generation. Contest participants can already register on the submission website, download test data sets, and upload their predictions for these.

To facilitate future benchmarking endeavours and the assessment of novel or altered software, reproducibility of the results is an important point on the agenda of CAMI Contest participants are therefore encouraged to additionally submit the software that has been used to generate their results in a Docker container. Among participants submitting reproducible results, CAMI will award a prize of 1000 Euros to three randomly chosen contestants with a submission performing better than a baseline. The results will be presented and discussed in a workshop a few month after the competition. For all reproducible contributions with permissions provided, a joint publication of the generated insights together with all CAMI contest participants and data contributors is planned.

If you are interested in participating, subscribe to the newsletter on the CAMI homepage and we keep you updated. Also, please take our survey so that we get a better idea of your needs in terms of compute resources and reference databases.


Alice McHardy*, Tanja Woyke, Eddy Rubin, Nikos Kyrpides, Paul Schulze-Lefert, Julia Vorholt, Nicole Shapiro, Hans-Peter Klenk, Stephan Majda, Johannes Droege, Ivan Gregor, Peter Hofmann, Eik Dahms, Jessika Fiedler, Ruben Garrido-Oter, Yang Bai, Girish Srinivas, Phil Blood, Mihai Pop, Aaron Darling, Matthew DeMaere, Dmitri Turaev, Chris Hill, Peter Belmann, Andreas Bremges, Liren Huang, Thomas Rattei*, Alexander Sczyrba*
*Steering Committtee




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“Inactivation of Norovirus on Dry Copper Alloy Surfaces”

Just a quick post here to highlight an article I was reading over the break, “Inactivation of Norovirus on Dry Copper Alloy Surfaces”.   We’ve posted a number of times in the past about the use of copper in the built environment as an antimicrobial (e.g. here, here, here, here, and here).   It’s a somewhat charged topic since opinions on the use of copper for this purpose seem to range from “it’s snake oil” to “it’s a panacea for the built environment”.  Into a discussion like this, data is always welcome and here’s some showing the effect of copper surfaces on Norovirus… which is a microbe of particular interest to the built environment.   Abstract below:

Noroviruses (family Caliciviridae) are the primary cause of viral gastroenteritis worldwide. The virus is highly infectious and touching contaminated surfaces can contribute to infection spread. Although the virus was identified over 40 years ago the lack of methods to assess infectivity has hampered the study of the human pathogen. Recently the murine virus, MNV-1, has successfully been used as a close surrogate. Copper alloys have previously been shown to be effective antimicrobial surfaces against a range of bacteria and fungi. We now report rapid inactivation of murine norovirus on alloys, containing over 60% copper, at room temperature but no reduction of infectivity on stainless steel dry surfaces in simulated wet fomite and dry touch contamination. The rate of inactivation was initially very rapid and proportional to copper content of alloy tested. Viral inactivation was not as rapid on brass as previously observed for bacteria but copper-nickel alloy was very effective. The use of chelators and quenchers of reactive oxygen species (ROS) determined that Cu(II) and especially Cu(I) ions are still the primary effectors of toxicity but quenching superoxide and hydroxyl radicals did not confer protection. This suggests Fenton generation of ROS is not important for the inactivation mechanism. One of the targets of copper toxicity was the viral genome and a reduced copy number of the gene for a viral encoded protein, VPg (viral-protein-genome-linked), which is essential for infectivity, was observed following contact with copper and brass dry surfaces. The use of antimicrobial surfaces containing copper in high risk closed environments such as cruise ships and care facilities could help to reduce the spread of this highly infectious and costly pathogen.

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Chickens and eggs: changes to look forward to in 2015

After eight years, California’s Proposition 2 goes into effect in 2015. NPR’s Forum did a program on this today. Prop. 2 is the California law to allow egg-laying chickens enough space to stand up, turn around and stretch their legs. Opponents of the law claim that the eggs will get pooped on with the new space guidelines. On the other hand, proponents claim these changes will benefit food safety and that industrial chicken farms are responsible for major Salmonella outbreaks, like one in Iowa in 2010 where 550 million eggs were recalled. Earlier this year, Russell wrote in how Denmark eradicated Salmonella about different approaches to managing Salmonella in chicken housing. Implementation of Prop. 2 provides the opportunity to understand how changes in chicken housing affects its microbiology. At the Animals in the Built Environment Workshop held earlier this year, we learned about studies already underway to characterize effects of new approaches to housing egg laying hens in response to this new law.


egg carton


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11+ things everyone needs to know about microbes

Well, I made a list.  I had written up text justifying everything on this list but I think it is better to just publish the list and then discuss.  Any additional suggestions or comments would be welcome.

1. Microbes are small, mostly

2. Microbes are not simple

3. No microbe alive today is ancient

4. There are no good or bad microbes.

4b. Microbes are not here to help us or to hurt us, they are here for themselves

5. We know very little about microbial diversity

5b. We still do not know how many domains, kingdoms, phyla, classes, orders, families, genera, or species of microbes there are.

5c. There are likely hundreds of millions of microbial species on the planet.

6.  Microbes can move (using their own power)

7. Attempts to make our world more sterile have massive negative consequences

8. The importance of microbes is both underappreciated and oversold

9. Microbes evolve

10. Microbes are everywhere (mostly) but no one kind of microbe is everywhere (i.e., each microbe has its own range).

11. Microbes are critical to our past, present and future.


Update 1/2/2015 – adding notes for each item

1. Microbes are small, mostly

Yes, I know.  Smallness is implied in their name.  And there are two things I want to point out here that many people may not be aware of.  First, the smallness of microorganisms is a critical part of their biology and, well, why we don’t know a lot about their biology.  We know lots about birds and trees and other multicellular creatures because people can see them and observe their biology and biogeography and other properties directly.  For microbes, well, that just does not work well.

A second point to make about microbes being small is that, if you group organisms by their evolutionary relatedness (which is the ideal way to group them) we see that there are some organisms that are closely related to microbes, that are in fact not microscopic.  This is interesting and important too.  For example, consider kelp.  They can get very very big.  But they are actually not closely related to plants (which they resemble in some ways) but instead are in a group generally known as the “brown algae” and this group is related to diatoms. So – they are certainly NOT microbes, but they are not plants or animals or fungi (the groups people normally think of as having multicellular representatives).  Perhaps more confusing, and also more interesting, there are some reasonably big members of groups where virtually all the other members are small (i.e., microscopic).  For example, consider Thiomargarita namibiensis a quite big bacterium.  This species is in all aspects of its biology a bacterium, but it’s larger size does mean that some of the forces that affect it are slightly different than those that affect most single celled bacteria.

I note that some people use the term “microbe” to refer to all taxa that are not plants, animals, or fungi.  This seems awkward at best since some of these taxa (e.g. kelp) are not microscopic.  I prefer to use microbe to refer to organisms based on their size and then to use the formal group names to refer to evolutionary groupings (e.g., bacteria, archaea, eukaryotes, viruses, etc).

2. Microbes are not simple

Yes, they are small (see above).  But many have quite complex processes, structures, behaviors and other features and in general one should never assume things are simple simply because they are small.  Consider for example, the relatively recent discovery of a type of adaptive immune system in bacteria and archaea – the CRISPR system.  Definitely not simple.  Or quorum sensing.  Or the sociobiology of Dictyostelium.

3. No microbe alive today is ancient

One sees many many reports of organisms alive today being referred to as “ancient” in relation to their placement in evolutionary trees.  Generally, this is done when an organism is in a “deep branching” lineage.  That is, if you drew an evolutionary tree of a group of species, this organism’s ancestors would have separated from the ancestors of other species a long time ago.  Many people for some reason assume that this means that the species on such deep branches have no evolved since they separated off in the evolutionary tree of their group and thus can be viewed as some “relic” or “ancient” taxon.  This is just completely wrong.  No matter if a taxon is on a deep branch or a recent branch, it continues to evolve and change just as other taxa do.

4. There are no good or bad microbes.

4b. Microbes are not here to help us or to hurt us, they are here for themselves

Not much to add to this other than that the terminology used by humans to refer to microbes frequently includes references to whether they are good or bad.  This is bad terminology for a few reasons.  First, some organisms may be “bad” to some humans (i.e., they make them sick) while they may be innocuous or even beneficial to others.  That is, badness is contingent upon other factors.  Second, this terminology is usually used to refer to “species” of microbes as though the whole species is good or bad.  And this is almost always a bad idea.  Each microbial species comes in many forms – also known as strains.  For each species that includes a lot of strains that can make people sick (e.g., Staphylococcus aureus), there are strains that are basically harmless.   The same is generally true for microbes referred to as “good”.  One strain might provide a benefit to a host (e.g., as a probiotic) while it might make other people sick.

5. We know very little about microbial diversity

5b. We still do not know how many domains, kingdoms, phyla, classes, orders, families, genera, or species of microbes there are.

5c. There are likely hundreds of millions of microbial species on the planet.

Overall, we have just not sampled the full diversity of microbes on the planet at even a remotely deep level.  Basically, the best method we have right now to characterize the diversity of types of microbes present in a particular environment is through DNA sequencing.  And we have just sampled very few places overall in terms of DNA sequencing technology.  For the places we have sampled, we have never, or almost never, saturated the sampling such that we feel like we have characterize all the microbes even in those single samples, let alone across the planet.  And then if we add to this how little we know about the biology of different microbes, the absence of knowledge is massive.  For example, in 2009 we published a paper on a 1st attempt at building a genomic encyclopedia of bacteria and archaea – to fill in the tree of life with genome sequences (something that stemmed from an NSF Tree of Life grant I had).  And though we felt like we were beginning to gain traction on getting genomes of cultured organisms sampled across a decent amount of diversity, most of the lineages of bacteria and archaea on the planet are still as of yet uncultured.  And most of the genomic diversity of life is in these lineages.  This is why we (well, Tanja Woyke at DOE-JGI with me as a cheerleader) started a project to sequence genomes of novel uncultured lineages – which she called “microbial dark matter” and why a group of us applied for and got a new NSF Geneology of Life grant on the same topic.

What our studies and those of others show is that we know even less about the functional diversity present across the diversity of microbes and that basically, we know only a tiny fraction of a percent of anything about microbial life on the planet.

6.  Microbes can move (using their own power)

Many people view microbes as being completely at the whim of their environment in terms of moving around.  But this is not so.  Microbes swim, crawl, glide, use controlled floating, and do other fascinating types of movements.

7. Attempts to make our world more sterile have massive negative consequences

Not much to say here other than that the obsessive germophobia and overuse of antibiotics is creating some serious problems around the globe.  And we really need to stop trying to kill all microbes all the time.

8. The importance of microbes is both underappreciated and oversold

I wrote often about overselling the microbiome and it is a big program (I call it microbiomania).  But there is also not enough attention given to the importance of microbes and microbial diversity in many other situations.

9. Microbes evolve

I know.  It is obvious to some people.  But not to others.  And it is critical to appreciate.  This relates to the “microbes are not ancient” point above.  An appreciation of the rates and patterns of evolution in microbes has big impacts on things like the use of antibiotics and in thinking about microbial ecology an functions in any situation.

10. Microbes are everywhere (mostly) but no one kind of microbe is everywhere (i.e., each microbe has its own range).

Yes, we find microbes in all sorts of places.  But it is important to realize that microbes have their geographical patterns and preferences and we do not find all microbes in every place.  This is important for issues like conservation biology, agriculture, and human and animal health.

11. Microbes are critical to our past, present and future.



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Genomic data sharing via BitTorrent, part 2 – BioTorrents to BitTorious

As someone who uses sequence data for most of my research,  I am continually happy with the fact that sequencing continues to get cheaper and easier and faster and bigger and better and more and more and more.  Along with such continued advances, sharing the data produced by such sequencing has become somewhat challenging at times.  A few years ago, Morgan Langille, who was a post doc in my lab at the time, proposed the use of BitTorrent file sharing tools for sharing biological data, such as sequence data.  He called the system for this “Biotorrents” and built some tools associated with the idea.  For more about this, see:

But alas, Morgan got one of those faculty job things, and, well, keeping up with the idea and the service was not easy.

Thus I am glad someone else has picked up the BitTorrent for Biology torch: BMC Bioinformatics | Abstract | BitTorious: global controlled genomics data publication, research and archiving via BitTorrent extensions.  Not sure how well this will work or how many people will use it, but it seems to me that there are many possible benefits from BitTorrent that still could be explored for biology.

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