Antibiotic Alternatives

We write a fair bit about antibiotic resistance on this blog, but seldom about the alternatives. Obviously, medicine shouldn’t avoid using antibiotics altogether, but we do need better management and use of our current anti-microbial compounds. We also need new methods of treating infection. Nature News has a brief but informative list of antibiotic alternatives written by Sarah Reardon. It seems to be a fairly good summary of the state of antibiotic research right now.

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Project MERCCURI (#spacemicrobes) results… comparing earth to space

We’ve posted previously about the results of the microbial playoffs in space (microbenet post here, and project website here).  And while it’s fun to compare the growth of a microbe representing the Raiders to one representing the 49ers (Raiders won that one)… there’s a more serious question being asked here.

We wanted to know what would happen when we took normal, built environment associated microbes and grew them in microgravity on board the International Space Station.   Most previous work of this nature had focused on pathogens… which is understandable from NASA’s point of view.   But from the perspective of microbial ecology it’d be interesting to know how the “normal” and non-pathogenic members of the community might behave.

Here are the results, comparing growth on earth to growth in space for each of the 48 bugs.

2_JPL_MERTA8-2The punchline?  We have one microbe that appeared to grow much better in space (Bacillus safensis, collected from a Mars Rover before launch at JPL) and basically all the rest of them looked pretty similar between space and earth.  Good news for long-term manned spaceflight?

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Recent Built Environment Microbiology papers

Some recent scientific papers and popular science articles that I already included on my daily MicrobiomeDigest blog, but that I would like to share here as well. 

Feasibility study involving the search for natural strains of microorganisms capable of degrading graffiti from heritage materials – Patricia Sanmartín – International Biodeterioration & Biodegradation

A total of 54 different strains were obtained from various sources, recent and old graffiti, the bodywork of a car in a scrapyard and the soil beneath it, an acrylic wall painting and the interior of spray paint cans

Characterization of the relative importance of human- and infrastructure-associated bacteria in grey water: a case study – S.P. Keely – Journal of Applied Microbiology

The aim of this study was to characterize the bacterial composition from (i) various points throughout a grey water recycling system that collects shower and sink handwash water into an equalization tank prior to treatment and (ii) laundry water effluent of a commercial-scale washer.

Distribution and population structure characteristics of microorganisms in urban sewage system – Yanchen Liu – Applied Microbiology and Biotechnology

The study aims to investigate the microbial communities spatial distribution inside manholes and sewage pipes by using the massive parallel 454 pyrosequencing combined with denaturing gradient gel electrophoresis of V1–V3 regions of 16S rRNA.

Effects of Source- versus Household Contamination of Tubewell Water on Child Diarrhea in Rural Bangladesh: A Randomized Controlled Trial – Ayse Ercumen – PLOS ONE

We randomly assigned 1800 households with a child aged 6-18 months (index child) into one of three arms: chlorine plus safe storage, safe storage and control. We followed households with monthly visits for one year to promote the interventions, track their uptake, test participants’ source and stored water for fecal contamination, and record caregiver-reported child diarrhea prevalence (primary outcome).

Self-healing bio-concrete uses bacteria to repair itself – Anthony Cuthbertson – International Business Times

Microbiologists at Delft University of Technology (TU Delft) in the Netherlands embedded calcite-precipitating bacteria into a concrete mixture to give it self-healing properties under the right conditions.

How Germs Might Shape the Future of Architecture – Vicky Gan – City Lab

The study of indoor microbiology isn’t new, says UC Davis biologist Jonathan Eisen, but it is moving faster than ever thanks to recent advances in DNA sequencing technology.

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The White House wants input on the future of microbiome research (by June 15)

Well this is very promising. The Science and Technology Policy Office of the White House has posted a Request for Information on “Microbiome Research”.


Advanced sequencing technologies have illuminated vast networks of microorganisms that drive essential functions in all environments on Earth. The study of these communities of microorganisms, or microbiomes, is nascent, and the potential of microbiome research has only begun to be tapped. Primary to achieving this potential is a functional understanding of microbiomes, which would be greatly advanced by addressing fundamental questions common to all fields of microbiome research; developing platform technologies useful to all fields; and identifying gaps in training or fields of research that should be addressed. The Office of Science and Technology Policy (OSTP) is interested in developing an effort to unify and focus microbiome research across sectors. The views of stakeholders—academic and industry researchers, private companies, and charitable foundations—are important to inform an understanding of current and future needs in diverse fields.

Responses must be recieved by June 15, 2015

What are they asking specifically?  Here is the text:

The purpose of this RFI is to solicit feedback from industry, academia, research laboratories, and other stakeholder groups on both the overarching questions that unite all microbiome research and the tools, technologies, and training that are needed to answer these questions. OSTP is specifically interested in information that corresponds to the mission statements of multiple Federal agencies, private sector interests, and current White House Policy Initiatives. In particular, respondents may wish to address the following topics:

  • What are the most pressing, fundamental questions in microbiome research, common to most or all fields?

  • Over the next ten years, what are the most important research gaps that must be addressed to advance this field?

  • What tools, platform technologies, or technological advances would propel microbiome research from correlative to predictive?

  • What crucial types of scientific and technical training will be needed to take advantage of harnessing the microbiome’s potential?

  • What fields of microbiome research are currently underfunded or underrepresented?

  • What specific steps could be taken by the federal government, research institutes, universities, and philanthropies to encourage multi-disciplinary microbiome research?

  • Is there any additional information, not requested above, that you believe OSTP should consider in identifying crucial areas of microbiome research?

How do you send in comments:

You may submit comments by any of the following methods:

  • Fax: (202) 456-6027, Attn: Elizabeth Stulberg.
  • Mail: Attn: Elizabeth Stulberg, Office of Science and Technology Policy, Eisenhower Executive Office Building, 1650 Pennsylvania Ave., NW., Washington, DC 20504.

Instructions: Electronic responses must be provided as attachments to an email. It is recommended that attachments with file sizes exceeding 25MB be compressed (i.e., zipped) to ensure message delivery. Please identify your answers by responding to a specific question or topic if possible. Respondents may answer as many or as few questions as they wish. Comments of up to two pages or fewer (1,000 words) are requested; longer responses will not be considered. Any information obtained as a result of this RFI is intended to be used by the Government on a non-attribution basis for planning and strategy development. OSTP will not respond to individual submissions. A response to this RFI will not be viewed as a binding commitment to develop or pursue the project or ideas discussed. OSTP will not pay for information provided under this RFI. This RFI is not accepting applications for financial assistance or financial incentives. OSTP requests that no proprietary information, copyrighted information, or personally identifiable information be submitted in response to this RFI.

Update 5/23 – Jo Handelsman and Elizabeth Stulberg have a post about this here.

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Will Microbes Clean our Water?

A recent publication in Environmental Science & Technology and subsequent review on gave a lot of promise for the technology of using microbes to clean up waterways. The study suggested that harnessing microbes is an environmentally sustainable solution to breaking down pollutants in water.

I think ‘breakthrough’ is a bit strong of an accolade for this study. Bioremediation is not a new understanding, but perhaps the policies surrounding it are. For example, certain species of microbes flourished during the deepwater horizon oil spill because they harnessed the hydrocarbons in the oil as fuel. We did little to control this natural bioremediation; organic pollutants to us are simply macro-nutrients to microbes that will thrive when their environmental conditions are ideal.

So if these microbes naturally exist and we can now identify them, how much leeway will legislation allow us to alter natural microbial communities for the purpose of more efficient bioremediation? I can’t imagine too many folks will be on board with dumping a tank of some microbial cocktail into our storm drains and rivers. How would this idea overlap with invasive species legislation? Will we have cane toad situation on our hands? Even in controlled systems like manure anaerobic digesters, policies are struggling to create standards for the ins and outs these bioremediation tanks. I argue that the rate-limiting step into harnessing microbes for to clean up our water is not on the microbes, it is on government.

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Exposure to dust and dirt increases mouse gut microbial diversity

Appropriate song to play while reading this post: Farmhouse – Phish

Just a quick post today about a paper that was published in Environmental Microbiology this week. Not open access, alas, but it looks like a good study.

Exposure to soil, house dust, and decaying plants increases gut microbial diversity and decreases serum IgE levels in BALB/c mice – Dongrui Zhou et al.- Environmental Microbiology

Abstract: To assess the impact of sanitation of a living environment on gut microbiota and development of the immune system, we raised BALB/c mice under three distinct environmental conditions: a specific-pathogen-free animal room (SPF), general animal room (XZ), and farmhouse (JD). All other variables like diet, age, genetic background, physiological status, and original gut microbiota were controlled for in the three groups. Using high-throughput sequencing of the 16S rRNA gene, we found that each mouse group had a specific structure of the gut microbial community. Groups JD and XZ harbored a significantly more diverse and richer gut microbiota than did group SPF. Bacteroidetes were significantly more abundant in groups XZ and JD than in group SPF, whereas Firmicutes showed the inverse pattern. Total serum IgE levels were significantly lower in groups XZ and JD than in group SPF. There were no significant differences in gut microbiota diversity and serum IgE concentration between groups JD and XZ, but we found higher abundance of dominant genera in the gut microflora of group JD. We conclude that exposure to soil, house dust, and decaying plant material enhances gut microbial diversity and innate immunity. Our results seem to provide new evidence supporting the hygiene hypothesis.

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The kittybiome Project – background and some plans

A little update here.  Last week a group of us launched a new participatory science project on the microbiome of cats.  It is called “kittybiome” and we have launched a Kickstarter fundraiser for the project — more information about the project and how one can get involved can be found at the Kickstarter home page:

The main people involved in the project right now are myself, Jennifer Gardy, Jack Gilbert and Holly Ganz. Holly – a Project Scientist in my lab – has been the key developer of the project and the person who took it from discussions and ideas to an actual project. This project has a long and somewhat convoluted history and I will try to write about it another time. Basically the idea started in discussions at a Citizen Microbiology meeting run at UC Davis in 2012 and then re-started in discussions between myself, Jennifer Gardy and Jack Gilbert and then Jack and Jennifer explored possibilities for a year or so and finally Holly joined my lab and when I told her about this as a possible project she took the lead and turned it into this current project (with help from many many people).

Anyway – our hope with this project is to both engage the public in studies of microbiomes and of the microbiome of cats specifically and also to start to gather data to provide a better understanding of the variability in the cat microbiome and how it might be connected to cat biology.  We are interested primarily here in domestic cats but also in general in all cats (e.g., lions and tigers and, well not bears,but cheetahs and such).

I note we are also interested here in the connection between cat microbiomes and the built environment such as in animal shelters, homes and zoos.  So in the long run our hope is to connect cat microbiome studies to studies of the microbial ecology and building science of the places in which the cats reside or spend a lot of time. We recently ran a workshop on “microbiomes of animals in the built environment” and plan to discuss this topic much more here at microBEnet.

We are also hoping to partner with other “cat”-izen science projects such as the brilliant and wonderful CatTracker from Your Wildlife.  If you know of others which we may want to partner with please let us know.

As part of our work in this project we will also be ouytting together various resources about cats and their microbiomes and trying to make them as open and available as we are allowed to do.  For example, I have started an open reference collection via Zotero on kittybiomes that anyone can participate in.

The project has gotten a little bit of press and some blog coverage already:

The Kickstarter project launched last week and we rapidly passed our initial funding goal of $3000 thanks to help from many people.  If you are interested in participating there are a diversity of ways you can contribute – from small donations to sponsoring microbiome studies of a shelter cat to sponsoring microbiome studies of wild cats.  See the Kickstarter page for more info.

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Live/Dead Workshop Meeting Report

Schrodinger’s microbes inside?

From May 13-14 2015 we hosted a “Live/Dead Workshop” here at UC Davis where we basically discussed a number of issues related to the topic of figuring out which bacteria are alive/viable in a given microbial community.   This is particularly important in the built environment where we suspect that many (most?) microbes are dead and where DNA might persist for a long time.    The talks were mostly methodological but we did cover some interesting terrain related to semantics, Planetary Protection, quantification, and such.   The agenda of the meeting and list of participants is here.  On the second day we made good progress towards producing a paper summarizing the state of the field and some future directions we think this work should go.

Below I’ve listed the talks and given my brief thoughts on them.  As people (hopefully) upload their talks to Slideshare, I will link to them in this post.   And finally a huge thank you to everyone who came to this meeting and made it such a great success!

Parag Vaishampayan (JPL)
“New perspectives on viable microbial communities in low-biomass cleanroom environments”

This talk covered a lot of ground, focusing on Planetary Protection and the importance of live/dead determination in that context.  I learned that using PMA for live/dead also means finding low abundance OTUs who were otherwise masked by the high-abundance dead stuff in a sample.  Parag also discussed “Double-PMA” which basically involves treating PCR reagents with PMA in order to get rid of exogenous contaminating DNA.  Gotta try that!

Ivan G. Paulino-Lima (NASA-Ames)
“Use of cell staining techniques to study radiation resistance of uncultivated microorganisms.”

The title pretty much says it all here… Ivan talked about looking “beyond Deinococcus” at radiation-resistant organisms, mostly in the context of Astrobiology and Planetary Protection.  Covered a lot of really interesting material and mechanisms of radiation resistance.
Andreas Nocker (Cranfield University)
“Practical tips to improve viability PCR”

Andreas is the father of PMA and so his talk covered this pretty exhaustively, including the pros and cons and a lot of methodological tips.  He made a point to emphasize that membrane integrity is just a proxy for viability and not the end of the story.   He also mentioned that flow cytometry and PMA are applicable to different questions and should not be considered exclusive.
Nicolas Justice (LBNL)
“A high-throughput method for absolute quantification of microbial community dynamics using next generation sequencing”

This talk really focused on the importance of absolute quantification in microbial ecology.  One interesting idea I’d not heard of was spiking in a known concentration of a lab bug before doing DNA extraction in a 16S survey.  He discussed the many systematic biases in PCR and most depressingly showed data suggesting a PCR efficiency disparity with different barcodes in the primers.

Tiffany Hsu (Harvard School of Public Health)
 “Using PMA assays and sequencing to differentiate live/dead bacteria on a mass transit system.”

Tiffany’s talk covered their experience of trying to get PMA to work in their subway study.   She showed data suggesting that PMA bound DNA is not isolated in DNA extraction (as opposed to just not working in the PCR).

Erica Hartmann/Clarisse Betancourt Román (BioBE Center, University of Oregon)
 “Live/dead determination in dust with flow cytometry and PMA”

Erica and Clarisse gave a tag-team talk that could probably be summed as as “dust is really hard”.  They discussed their experience of trying to get both flow cytometry and PMA to work on dust samples… significant difficulties in both cases.

Joanne Emerson (University of Arizona)
 “Pros and cons of using flow cytometry and qPCR to count bacteria and fungi in air samples”

Joanne talked about her experience with flow cytometry and qPCR for absolute quantification in air samples.  Of the two, she expressed a strong preference for qPCR in this context.

Cinta Silvan (LBNL)
“RNA as a proxy for metabolic activity”

Cinta rounded out the day by talking about RNA.  This is a project not yet started, but she presented evidence from other work about the utility of RNA to determine metabolic activity.  This sparked a lot of discussion about the difference between “alive”, “viable”, and “metabolically active” which I think is important to think about.


Here is a Storify of the tweets from the meeting:

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Retirement Symposium for Norman Pace–a “Normposium”

A Retirement Symposium for Dr. Norman R. Pace from the Department of Molecular, Cellular and Developmental Biology at the University of Colorado, Boulder will be held on 4 – 5 June 2015.  The symposium is free and open to the public with generous support provided by the Alfred P. Sloan Foundation and the Agouron Institute.NormPace

This “Norm-posium” will be held at the Colorado School of Mines, Department of Civil and Environmental Engineering in Coolbaugh Hall (map), in Golden, Colorado.

Norm Pace has made enumerable contributions to science over the course of an incredible career.  Focused on two primary aspects relating to the biochemistry of RNaseP, a unique ribozyme that catalyzes the maturation of tRNA, and “The Search” for life, in all three domains, to better understand life on Earth.  Contributions to both areas of science from Norm and the many members of his laboratory over the years have greatly expanded what is know about both areas of science.  Without the early techniques developed in his lab for the sequencing and constructing of phylogenetic trees based upon ribosomal RNA gene sequencing, little would be known of “The Big Tree”–a ‘map’ of life that we rely upon for understanding life today.  Now, with next-generation DNA sequencing technology and larger, whole micro-biome projects, we can better understand the kinds of life and types of life that make both ourselves and our environment these amazing, living conglomerations of life-types.  None of us are ‘me’–we are all ‘we.’Big_Tree_Bold_Letters

None of this would have been possible with out the contributions that originated and have since stemmed from, Norm Pace’s laboratory.  The remarkable achievements in being able to better understand ourselves and our environments all trace back to Norm’s laboratory.  It is for this that Norm is a member of the National Academy of Sciences and recognized as a MacArthur Fellow.

To celebrate Norm’s retirement a collection of former postdocs and lab members are coming together in Golden on 4 – 5 June 2015.  The line-up includes:

Thursday, 4 June 2015, 5:00PM

Keynote:  Dr. Norman Pace

Friday, 5 June 2015, beginning at 8:30AM, Adjourn at 4:30PM:

Dr. Scott Dawson, University of California, Davis

Dr. Laura Baumgartner, Front Range Community College

Dr. Alex Burgin, Broad Institute

Dr. Daniel Frank, University of Colorado, Denver

Dr. Amy Buck, Edinburgh University

Dr. Gary Olsen, University of Illinois, Urbana Champaign

Dr. Tom Schmidt, University of Michigan

Dr. Anna-Louise Reysenbach, Portland State University

Dr. Mitchell Sogin, Marine Biological Laboratory

Dr. John Spear, Colorado School of Mines

For contact information and questions:

John Spear,


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