Wednesday, October 19, 2016

My Talk and Interview on Microbes and Speciation from Germany

I returned last month from Kiel University for the 109th German Zoological Society Meeting. A Zoological Society Meeting alone is impressive these days, not to mention its 109 year history. Thomas Bosch invited me out for the keynote lecture. Thomas has been at the forefront of advancing a better appreciation of the natural world, namely the intricate interactions between a simple model system of the non-senescent cnidarian Hydra and its microbial community. Hydra represent an early key transition in the evolution of animals and therefore are critical to studying the origins of developmental mechanisms. Thomas is a CIFAR fellow and directs the Metaorganisms Collaborative Research Center, which is a beacon for systems biology thinking about the animal-microbiome assemblage.

Anyway, I presented our long-term studies on the role of bacteria in reproductive isolation and the origin of species. I presented old and new work, most recently by @ABrooksy19, @KevinDKohl, @liveinsymbiosis and @teddy1387 on phylosymbiosis across various animals. This work is currently in press.  Here's the talk and interview that the Collaborative Research Center clearly put a lot of work into - many thanks to the team.


Saturday, October 15, 2016

Phage WO: Guest Blog Post by Sarah Bordenstein

The latest craze over phage WO, the bacterial virus that infects Wolbachia, has been both exciting and overwhelming. The press is great at communicating the science in a digestible format, but it can sometimes become sensationalized and misleading. When one press release builds upon the hype of a previous release, the end result is much like the game of telephone. As an author of “Eukaryotic association module in phage WO genomes from Wolbachia”, I want to make sure that the science in the public's eye is not over-represented and that we are providing a realistic view of the data.

Let’s first talk about what the paper is not, though headlines have claimed otherwise.
·      Phage WO does not encode the entire black widow venom (latrotoxin) gene. In fact, as we present in the paper, it contains DNA that is similar to just the C-terminal domain. This particular region of the gene is associated with the protoxin that is hypothesized to be involved in lysis of the spider’s secretion cells.
·      The phage did not necessarily “steal” the DNA from the spider. Yes, viruses hijack DNA from their hosts and this has been shown in both bacterial viruses and animal viruses. Viruses are incredible, rapidly evolving entities. Due to the level of divergence between the sequences in this particular study, the genetic transfer, if it did happen, occurred long, long ago. We can’t definitively say if the spider transferred to phage or phage to spider, but in our opinion both would be equally exciting. The current data leans towards spider to virus, possibly via a yet-to-be-discovered intermediary (see the paper for more discussion). We also can’t definitively say that it was even a legitimate transfer event. It could have been the result of convergent evolution. This is when different organisms independently evolve similar traits. Given the fact that widow spiders are often infected with Wolbachia, and Wolbachia are often infected with phage WO, there is an ecological niche that would provide opportunity for genetic transfer. Plus, we present other examples in the paper that support genetic transfer from animal to virus. Beyond that, many other research groups have reported the transfer of DNA between Wolbachia and their animal hosts, so the transfer between the phages and the animal is not a huge stretch.

With that said, this is what the paper is:
·      To our knowledge, this is the first report of animal-like DNA found in a bacterial virus. Is this a completely absurd, mind-blowing discovery? Not really. Bacterial viruses are known to exchange DNA with their bacterial hosts and animal viruses with animals. However, we don’t really know much about how viruses of bacteria might interact with animals. This field is really in its infancy.
·      Phage WO harbors a eukaryotic association module. About half of WO’s genome is devoted to structural genes (such as capsid, tail, baseplate) and other common phage elements. However, it also devotes a large percentage of its genome to unique genes that putatively encode functions relevant to animal interaction. Like some other viruses, phage WO appears to take different chunks of DNA from different sources and mix and match the chunks to create unique genes. What do these genes do? Do they retain the same functions as they did in the original donor? These are all still mysteries to be solved; so many questions left to be answered! I can tell you that some of the genes in the eukaryotic association module quickly grabbed our attention and we look forward to expanding the story of phage WO and Wolbachia in the months to come. Stay tuned…
·      Phage WO integrates into the Wolbachia genome via specific attachment (att) sites. Why does this matter? Wolbachia is an obligate intracellular endosymbiont. That means, it is dependent on its animal host for survival and cannot be cultured outside of the animal cell (as you would with standard free-living microbes such as E. coli). This makes it very hard for scientists to test functions of specific genes and fully understand its biology. We are particularly interested in Wolbachia because it infects over 40% of all arthropods as well as some nematodes of human health relevance and crustaceans. The identification of WO’s att sites offers a potential method of accessing the Wolbachia chromosome in order to unlock its secrets. Using the phage may or may not work, but it’s the best chance we have to-date. 
On a personal note, I want to thank journalists such as Ed Yong (The Atlantic - link) and Jacqueline Howard (CNN - link) for directly reaching out to us, the scientists, and making sure that they understood the complexity of the system rather than simply promoting catchy phrases. When it comes to science, words matter. I agree that this is a fun system to explore, but I hope that the science can stand on its own without adding falsehoods and making incorrect conclusions. 

Please don’t hesitate to reach out to scientists (including me) if you have questions about our research and possibly don’t believe or understand what you read in the news. We are honored to share this journey with you and are particularly delighted to hear from the next generation of researchers. Viruses are incredibly fascinating and, in my opinion, phage WO tops the charts. We are just beginning to explore the landscape of viruses infecting intracellular bacteria and I can’t wait to see what comes next.

Monday, July 11, 2016

Important Announcement: International Conference on Holobionts

Over the last few years, the terms holobiont and hologenome have received heightened attention, leading to a high-water mark of the 1st dedicated conference on the topic next year at the Paris Natural History Museum (see below). The meeting will be an important event for the community in order to set goals and achieve unity, understanding, and needs for the future. I think it will also be an opportunity to resolve misuses of the terms and associated concepts (Getting the Hologenome Concept Right, mSystems). Many factors have played a part in raising the profile of these terms and concepts including our work and others. Due to an existing heavy travel schedule, work-life balance, and teaching, I declined the invitation to speak at this conference and recommended several young scientists. I heartily endorse this conference and encourage keeping a close eye on developments that come from it. While it is the 1st conference dedicated to the topic, many other conference symposiums and workshops on the topic are brewing or have already taken place. There will hopefully be a 2nd International Conference on Holobionts in the future. 

International Conference on Holobionts,
Paris (Natural History National Museum), April 19-21, 2017

It is becoming increasingly clear that the development, nutrition, physiology and health of most organisms are influenced by the complex microbial communities they host, hereby shaping their ecology and evolution. Biology is indeed undergoing a paradigm shift, where individual phenotypes are seen as a result of the combined expression of the host and associated microbe genomes, leading to the popularization of the holobiont concept (the host and its microbiota) and the hologenome (the collective genomes of a holobiont). Ecological and technical advances, especially in next generation sequencing technologies, have greatly contributed to this conceptual shift, thereby revealing the diversity and roles of the microbes hosted by diverse organisms, from people and plants, to sponges and insects. The scientific community has now recognized that the host organisms cannot be studied without taking resident microbiomes into account, making holobiont research imperative across numerous fields of the life and medical sciences.

The objective of the International Conference on Holobionts, Paris 2017 is to, for the first time, bring scientists together who are interested in holobiont systems and their study. This conference will highlight major advances in defining the key roles of host-borne microbiota in the ecology and evolution of higher organisms and the potential implications for human health, food production and ecosystem functioning. In addition, the conference will offer a platform for debate related to the definition, assembly and evolution of holobionts. By bringing a range of holobiont researchers together, the International Conference on Holobionts seeks to help consolidate the field, facilitate exchange of knowledge across systems and approaches and stimulate further developments in this emerging discipline.

Scientific program
This conference will address the following topics:
  1. Holobionts and evolution
  2. Emerging approaches to holobiont research
  3. Microbiota and host health
  4. Mechanisms for holobiont assembly
  5. Metabolic interactions between host and microbiota
For each topic, we encourage oral and poster communications on holobiont systems from different perspectives including theoretical, empirical, fundamental and applied researches.

Provisional list of invited speakers:
Joël Doré
(INRA Jouy, France)
Ute Hentschel (Helmholtz Centre for Ocean Research, Kiel, Germany)
Thierry Heulin (CEA Cadarache, France), confirmed
Nancy Moran
(University of Texas, Austin, Texas, USA), confirmed 
Jeroen Raes (Vrije Universiteit, Brussel, Belgium), confirmed
Eugene Rosenberg
(Tel Aviv University, Israel), confirmed
Paul Schulze-Lefert
(Max Planck Institute Koln, Germany), confirmed 
Kevin Theis (Wayne State University, Detroit, Michigan)

Practical aspects
This conference will last 2.5 days, from April 19th 2 p.m. to from April 21st 4 p.m. It will take place right in the center of Paris, in the heart of “Quartier Latin” in the prestigious Grand Amphithéâtre of the Natural History National Museum ( Note that for space constraints, we won’t be able to take more than 300 registrations. Registrations will open by November 15, 2016 and be closed by January 30, 2017. A dedicated website for registration and practical information is under construction at

Organizing institutions:
CNRS (Centre National de la Recherche Scientifique), INRA (Institut National de la Recherche Agronomique), MNHN (Museum National d’Histoire Naturelle). This conference is a joint initiative of the Groupe de Recherche en Génomique Environnementale (GDR GE) and the INRA Métaprogramme Méta-omiques et écosystèmes microbiens (MEM).

Members of the Scientific Committee:
Bourguet-Kondracki Marie-Lise (CNRS, MNHN Paris), Bourtzis Kostas (FAO/IAEA, Vienna, Austria), Buée Marc (INRA Nancy, France), Faure Denis (CNRS Orsay, France), Heulin Thierry (CNRS Marseille, France), Joly Dominique (CNRS Paris, France), Kowalchuk George (Utrecht University, The Netherlands), Marchesi Julian (Imperial College, UK), Médigue Claudine (CNRS Genoscope Evry, France), Mougel Christophe (INRA Rennes, France), Selosse Marc- André (MNHN Paris), Simon Jean-Christophe (INRA Rennes, France), Vandenkoornhuyse Philippe, (University Rennes 1, France) 

Sunday, June 26, 2016

Science & SciLifeLab Prize for Recent Ph.D.'s in Biology

Announcement for a young scientist award:

Science & SciLifeLab Prize for Young Scientists

This Prize was created to recognize that global economic health is dependent upon a vibrant research community and we need to encourage our best and brightest to continue in their chosen fields of research.
The Prize is awarded annually to one young scientist for outstanding life science research for which he/she was awarded a doctoral degree in the previous two years. The topic of the entrant's thesis research must be in one of the following categories: Cell and Molecular Biology, Genomics and Proteomics, Ecology and Environment, Translational Medicine. Eligible entrants must have been awarded their doctoral degree in 2014 or 2015, and the subject of their thesis should match one of the Subject Tracks below. The winners from each category will compete for the grand prize.
Prize money: US$30,000 for the grand prize winner, US$10,000 for each of the category winners.
Publication: The grand prize winning essay will be published in Science and essays from the each of the category winners will be published online.
Application deadline: August 1, 2016

Rules of Eligibility

  • Entrants for the 2016 prize must have been awarded their Ph.D. between January 1 2014 and December 31 2015. As a rule, we will only accept submissions once within this time period.
  • The research described in the entrant’s thesis must fall within one of the following categories (Subject Tracks):
    • Cell and Molecular Biology: research in this category will include cellular and molecular processes at levels ranging from single molecule to single cell to tissue and organ systems,
    • Genomics and Proteomics: research in this category focuses on analyses of gene- and protein-related events, at the scale of gene or protein networks to the complete set of genes or proteins in an organism,
    • Ecology and Environment: research in this category encompasses interactions between organisms and their environment, and how these processes are influenced by human activity,
    • Translational Medicine: research in this category builds on in vitro or animal model studies of biological processes to develop potential therapies or medical procedures.
  • The prize will only recognize work that was performed while the entrant was a graduate student.
  • The prize will be awarded without regard to sex, race, or nationality.
  • Employees of SciLifeLab, Science/AAAS, and collaborators in the management or sponsorship of this Prize and their relatives are not eligible to compete.

Procedures for Entry

The entrant must submit the following items:
  • A completed Entry Form.
  • An essay, written by the entrant, describing the thesis work and its implications for research in the selected Subject Track. The essay must not exceed 1,000 words in length and may include one figure or table.
  • A one-page reference letter from your advisor or a member of your thesis committee. The letter should include an assessment of the applicant and comment on the significance of the applicant’s research.
  • The abstract of the thesis (not to exceed four double-spaced typed pages).
  • A list of the following:
    • Full citations of all published or in press papers on the research described in the essay;
    • Academic and professional awards and honors that the entrant has received; and
    • Relevant professional experience.
The Entry Form and additional submission materials must be submitted electronically through our prize management system here.
Below is a timeline for the prize selection process. You will be contacted only if there are additional materials or information needed.
August/September: Compilation and Review of Submissions
October/November: Selection of Prize Winner
December: Announcement of Prize Winner & Awards Ceremony in Stockholm

Deadline for Entries

August 1, 2016

Judging Procedures

First, Science editors will screen the essays and select three finalists from each Subject Track. Next, a committee of scientists chaired by the Editor-in-Chief of Science will select a winner for each Subject Track. The four winners will then compete for the grand prize. The grand prize winner and three category winners will be decided by October. Science will control both the evaluation process and the announcement of the winners.


Wednesday, May 18, 2016

Job Ad: Program Fellow in Symbiosis at Gordon and Betty Moore Foundation

Program Fellow, Science
The Gordon and Betty Moore Foundation’s science program supports exceptional scientists, invests in new technologies, and brings together new scientific partnerships. We believe in the inherent value of science and the sense of awe that discovery inspires. We believe that unleashing the potential of inquiry and exploration not only leads to scientific progress, but can also deliver important societal benefits. We take risks and look for opportunities to transform or create entire fields.
To complement activities in the Marine Microbiology Initiative (MMI) and other current science program grantmaking, we seek a program fellow to explore opportunities for further foundation impact in the realm of symbiosis. Here, we refer to symbiosis as the interactions between microbes (bacteria, archaea, and protists) and animals, plants, fungi, and other microbes. We also consider the role of viruses in these relationships. We consider symbiosis broadly in terms of habitat (terrestrial and marine), degree of interdependence (transient, obligatory, endosymbiotic, and that which results in organelle evolution), and time (ancient to modern).
The Position
The fellow will synthesize information regarding the state of symbiosis research and related fields in the U.S. and abroad. The fellow may also work on related topics that link with MMI and other current symbiosis grantmaking at the foundation.
The fellow will report to the MMI program director, and will work with MMI team members, colleagues in the science program, and across the foundation as needed. This role requires a highly developed ability to collaborate. Experience with or an ability to rapidly learn academic, government, and private funder structures and cultures is paramount.
The Program Fellow role has a term of 12 months, with the possibility of renewal for up to 12 additional months. Those with a relevant advanced graduate degree—as well as researchers considering a sabbatical—are welcome to apply.
Key Responsibilities
The fellow will:
  • Collaboratively explore opportunities within the realm of symbiosis, working with the MMI program director, MMI staff, and others.
  • Synthesize and present written and spoken communications of findings to internal foundation audiences; discuss and debate findings using the foundation strategic lenses.
  • Establish connections with relevant external communities and efforts, as appropriate.
  • Depending on needs, may develop and conduct workshops and other in-person forums.
Experience and Education
The ideal candidate will possess:
  • A Ph.D. in a relevant field (required).
  • Postdoctoral experience in a relevant field and/or other science-related post-graduate experience (required).
  • Demonstrated interest, initiative, and track record in the broad area of symbiosis and evolution of organismal interactions that includes microbes.
  • A track record of collaborative multidisciplinary work.
  • Experience working constructively within a team of diverse expertise, experience, and perspective.
The ideal candidate will also have:
  • Exceptional communication skills (speaking, writing, and listening).
  • A flexible, creative and positive approach to problem solving in a highly collaborative team environment; comfort with ambiguity.
  • An ability to view the big picture and long-term goals while keeping in mind tactical short-term ramifications.
  • Experience with contributing to and/or coordinating large, multi-stakeholder projects and events.
The ideal candidate will demonstrate the following attributes that describe how we at the Foundation strive to do our work with each other and our partners.
  • Committed to Excellence
  • Passionate
  • Collegial
  • Open and Honest
  • Humble and Self-Aware
Compensation and Benefits
Compensation includes a competitive base salary and an excellent package of health, retirement savings and other benefits.
Application Process
Applicants must be legally authorized to work in the United States. Pursuant to the San Francisco Fair Chance Ordinance, we will consider for employment qualified applicants with criminal histories in a manner consistent with the requirements of the ordinance.
The Gordon and Betty Moore Foundation is an equal opportunity employer. All correspondence will remain confidential.

Thursday, March 24, 2016

Guest Blog Post on Citizen Science: What Academic Scientists Can Do More Of

The front lines of science education and expanding scientific literacy are not in the ivory towers of universities, but in pre-college science education at all levels. Discover the Microbes Within! The Wolbachia Project has put many of us in contact with some of the most inspirational people we know - educators that love science, work hard, and want to bring that love to countless middle and high school students, and sometimes younger levels. Since 2007, the Wolbachia Project has been working with Carolyn Wilczynski. I first met Carolyn at a Wolbachia Project workshop held at Cornell University during that summer, and a couple of days ago, I received this message from her. It struck a chord with me, and perhaps it will do the same for you. She has agreed to let me post the message as she wants it to go: "as far and as wide as possible!  There are kids out there who LOVE science.  I hear them say it and I see it in their actions.  They need scientists to inspire and encourage them.  A little goes a long way.  Truly."


This school year, I started up a science club, hoping to encourage students to pursue a study of something - anything related to science or science inquiry.  A small grant from our district alumni foundation helped to fund the endeavor and I was able to buy supplies, pay entrance fees, get kids to/fro the fairs, and buy t-shirs and food.  We all learned a lot.  I took 10 kids to the local science fair and 8 advanced to the regional fair.  2 will now advance to the state-level and who knows beyond that!  Not too bad for a novice!

Perhaps because of my own bias towards organismal biology, most of the projects were biology based and most included some manner of organismal biology.  From Madagascar hissing cockroaches detecting pesticides in produce to humans yawning to evolutionary relationships of fish species using protein gel electrophoresis.  The projects were varied.  The work to get there was insanely time consuming (which is why you haven’t heard much from me lately!).  One thing I’ve learned is that while science depends on peer review and feedback, not so with science fairs.  It took a personal request to the local fair coordinator to reach out to a judge to provide feedback to a student.  That feedback resulted in a “highest honor” placement and a top award at the regional fair.  Kids are quick learners!  I hope that my suggestion to provide feedback to all students at the local science fair next year is taken to heart. 

The other lesson learned is that the majority of judges at science fairs are engineers and the sponsors are engineering organizations.  I realize that it’s a sample size of 2, but I reach out to all of you to volunteer to be a judge at a local, regional or state science fair.  Volunteer to speak at a science fair - again, the bias is towards engineers, The mindset of an engineer vs scientist is a bit different, though admittedly there is a lot of overlap.  Some of my students who did projects on organismal biology left yesterday’s fair discouraged.  One boy kept asking me what he’d done wrong.  I had no good answer for him.  His project was good, scientifically sound and completely appropriate for a science fair.  Yet he came away with only a certificate of participation.  One girl was asked by an engineer judge, why she provided water in her cockroach enclosures, since they might cause the produce to get moldy faster.  Nice suggestion, except that even roaches need to drink water.  The cleverness of her study was lost on trying to solve the problem of mold: scientist vs engineer. 

Lastly, if you are members of professional societies and have any ability to do so, I would encourage sponsoring an award.  While monetary awards are always appreciated by the fair sponsors and the kids (even as little as $25 goes a long way to say “way to go”), certificates or books also make good awards.  The local geological society in our area provided a fossil specimen.  Who wouldn’t love a rock as a prize?  Students know in advance who the sponsors are and the projects coming to the fair reflect that.  So again, basic science is left in the dust.  These young people, whether or not they become scientists, will at the least become voters in the future.  Science fairs give them a good appreciation for what scientists do and may pay dividends in support of science in the future. 

The New York State Science Congress is June 4th in Buffalo (, if you can find a way to support basic science in some way at this fair, I encourage you to do so.  Or perhaps forward this to friends and colleagues who live nearer to Buffalo.  Or if you can reach out to ESA, ABS, BSA, or whatever professional organization that you belong to, it would support science in those fields. 

Thanks for reading my soapbox speech! 


Thursday, February 4, 2016

Overdue community effort on getting the hologenome concept right

More and more, it is becoming clear that the population biology processes affecting animal and plant phenotypes interface with ecosystems science and the ecology of host-associated microbiomes. Indeed, the so-called individual animal or plant is increasingly appreciated as a "holobiont" comprised of the host plus all of its associated microbes. Resultantly, all genomes of the holobiont have been termed the “hologenome”. These terms and associated concepts are relatively new and liable to misinterpretation. Our new preprint at bioRxiv / manuscript published at mSystems is a community effort to pull various biologists and philosophers together around a definitive set of arguments that accurately reflect the original literature. As the largest collection of authors to date in this area, spanning fifteen junior and senior investigators in the life sciences and philosophy, we think this article will encourage productive discussion to stimulate new ideas and understanding on holobionts and hologenomes that consider the link between phenotype and genotype. I hope you check out the short piece. Feedback is most welcome!

Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes