Friday, December 21, 2018

Two Postdoc Positions Available

Two postdoctoral positions are offered to join the Bordenstein Lab in the Departments of Biological Sciences and Pathology, Microbiology and Immunology at Vanderbilt University in Nashville, TN. The candidates will join one of two projects.
  • (Closed) The first project seeks applicants with interests and/or skill sets in personalized medicine and multi-omic analyses (genome, metabolome, metagenome, and metallome) to investigate the consequences of diet, ethnicity, and genetic variation on the human microbiome (recent paper). The candidate will join and have the opportunity to take a leading role in the fast growing, trans-institutional Vanderbilt Microbiome Initiative.  Strong computational expertise (data analysis, coding, and bioinformatics) will be important in this position.
  • (Closed) The second project seeks applicants with interests and skill sets in animal-microbe interactions, evolution, endosymbiosis, phylosymbiosis, quantitative genetics, transcriptomes, fluorescent microscopy, or gene knockdowns/knockouts. The candidate will in part join a National Science Foundation project to study the genetic basis of symbioses between insects (Nasonia parasitoid wasps) and endosymbiotic bacteria (Wolbachia). The candidate will also participate in launching a second project (related paper) on the genetic basis of phylosymbiosis (host phylogenetic signal in the gut microbiome) and speciation. 
More information about the lab, topics, and systems can be found at the lab website:

Additional information and resources for postdocs at Vanderbilt can be found at the Office of Postdoctoral Affairs and Postdoctoral Resources pages.

If interested, please contact Seth Bordenstein immediately with a single pdf including (i) earliest start date (ii) a full curriculum vitae noting at least three references (iii) a statement of intent, career goal, research experience, and areas of growth and (iv) two example publications or other writings.

Vanderbilt University campus is a National Arboretum located in the heart of Nashville, the capital of Tennessee, and known internationally as “Music City USA”. Nashville is also the home to Nashville Hot Chicken, professional sports teams, the Nashville Symphony, the Frist Center for the Visual Arts, and numerous activities for outdoor enthusiasts. Nashville, Tennessee is a wonderful place to live, work, and raise a family.

Thursday, December 13, 2018

New publication on the ethnicity hypothesis for gut microbiome variation

Our latest research published at PLOS Biology last week answers the question of whether self-declared ethnicity significantly associates with the diversity of microbes in human gut microbiomes, particularly from individuals residing in the same country. Importantly, results are replicated across two datasets within the United States of America, and we identify 12 microbial taxa that consistently vary in abundance between ethnicities. Machine learning approaches were able to predict ethnicity from the gut microbiome data alone. Many of the 12 taxa also associate with human genotype variation, and some have been linked to gut health disparities. While the work remains to be replicated in larger datasets, this one is a small step towards potentially adding the microbiome into more personalized health and medicine approaches. The work was led by senior graduate student Andy Brooks and was conducted in collaboration with the Blekhman lab at the University of Minnesota.


Tuesday, May 8, 2018

The Vanderbilt Microbiome Initiative website

The Vanderbilt Microbiome Initiative (VMI), sponsored by the Vanderbilt University Trans-Institutional Programs, is very pleased to announce the launch of its new website. VMI aims to unify the community within and beyond the region, support innovative research, and engage in outreach and science education.

As the science of the microbiome matures, Vanderbilt will lead basic, translational, and clinical research, build new devices and technologies, help communicate the research, evaluate new developments, fund new projects, and train the next generation of scientists, philosophers, lawyers, and educators in this discipline.

Check in for recent research and education developments, resources, awards, etc. Join us there!

Wednesday, April 25, 2018

New paper on the phage genes that hijack animal reproduction

Wolbachia are maternally transmitted bacteria that are estimated to infect millions of arthropod species worldwide. One of Wolbachia's greatest weapons is the ability to poison sperm and nullify that poison in eggs, all of which enable the bacteria to spread like wildfire in arthropods and to control mosquitoes. Indeed, the World Health Organization recently recommended pilot deployment of Wolbachia-infected mosquitoes to curb viral transmission to humans. Turns out that under the hood of this cunning phenomena called cytoplasmic incompatibility is a simple genetic basis: two phage genes poison the sperm and one of those same genes ensures the infected eggs live. Ergo, the 'Two-by-One' model of cytoplasmic incompatibility by talented graduate student Dylan Shropshire, former undergraduate and technician Danny On, and two current undergraduates Helen Zhou and Emily Layton. See below for a link to the paper, VU news story, and graphical summary.


Vanderbilt Research:

Graphical Summary:

Friday, January 12, 2018

Postdoctoral position in functional genetics of animal-microbe symbioses

(Note: Position is no longer available; applicants with independent funding are welcome)

A postdoctoral position is available in the Bordenstein laboratory ( to functionally characterize endosymbiont-host interactions in Drosophila. This project will dissect the number and types of Drosophila genes and functional pathways that are manipulated by bacteria in the genus Wolbachia. The candidate will develop methods and apply multiple technologies to dissect how the bacteria modify fly embryonic development and induce lethality at the molecular, genetic, and/or biochemical levels. As Wolbachia are increasingly relevant to vector control efforts to curb arbovirus transmission, translational aspects of this work include development of transgenic strategies for vector and pest control.

Applicants soon to acquire their Ph.D. or with previous postgraduate experience are welcome. Applicants should have a demonstrated ability to work both independently and collaboratively, possess excellent oral and written communication skills, and have a record of productivity as evidenced by publication history. Successful candidates will have some of the following skills: proteomics, transcriptomics, functional genetics, computational biology, Drosophila and Wolbachia rearing, fluorescent microscopy, molecular evolution, and molecular biology of phages. 

Vanderbilt University campus is a National Arboretum located in the heart of Nashville, the capital of Tennessee. Known internationally as Music City USA, Nashville is also the home to professional sports teams, the Nashville Symphony, the Frist Center for the Visual Arts, and numerous activities for outdoor enthusiasts. Nashville, Tennessee is a wonderful place to live, work, and raise a family and has been named one of the 15 best U.S. cities for work and family and one of the 25 cities most likely to have the country's highest job growth over the coming five years. Major industries include tourism, printing and publishing, technology manufacturing, music production, higher education, finance, insurance, automobile production and health care management.

To apply, please send a single pdf including a cover letter stating career interests, research strengths, areas to develop, earliest start date, curriculum vitae, an example publication, and contact information for three or more references to 

The position is available now and renewable up to two years contingent upon satisfactory performance. Salary is commensurate with experience and includes a comprehensive benefits package. Review of applications will begin immediately and continue until the position is filled.

Wednesday, August 23, 2017

Tenure-track job, Assistant Professor in Microbiome, Vanderbilt University, Nashville, TN, USA

We are hiring a microbiome professor this year as part of Vanderbilt’s growing investment in the microbial sciences. If you know anyone on the market who cuts across basic and translational endeavors in the microbiome, please share this ad with them and beyond. It’s an awesome opportunity.     

Vanderbilt University is a private, internationally renowned research university located in vibrant Nashville, Tennessee. Its 10 distinct schools share a single cohesive campus that nurtures interdisciplinary activities. With a metro population of approximately 1.5 million people, Nashville has been named one of the 15 best U.S. cities for work and family and one of the 25 cities most likely to have the country's highest job growth over the coming five years. Major industries include tourism, printing and publishing, technology manufacturing, music production, higher education, finance, insurance, automobile production and health care management..

Vanderbilt Institute for Infection, Immunology and Inflammation

Vanderbilt University’s Department of Biological Sciences and the Vanderbilt Institute for Infection, Immunology and Inflammation invite applications for a tenure-track, faculty position in host-microbiome interactions at the Assistant Professor rank. The individual will be expected to develop her or his own independent laboratory research program and contribute to departmental strengths in evolution, chemical biology, neuroscience, and cell and molecular biology ( The faculty member will play an integral role within the new trans-institutional Vanderbilt Microbiome Initiative and may benefit from collaborations with internationally recognized programs including the Vanderbilt Genetics Institute, the Vanderbilt Institute of Chemical Biology, or the Vanderbilt Institute for Global Health. The selection criteria are excellence in research and the ability to teach undergraduate and graduate students with a high level of effectiveness. Applicants should submit a letter of interest, full curriculum vitae, statement of current and future research interests, and statement of teaching philosophy and competency directly to  Applicants will arrange for four letters of recommendation to be sent to the same address. Completed applications must be received no later than October 27, 2017. Vanderbilt University has a strong institutional commitment to recruiting and retaining an academically and culturally diverse community of faculty. Minorities, women, individuals with disabilities, and members of other underrepresented groups, in particular, are encouraged to apply. Vanderbilt is an Equal Opportunity/ Affirmative Action employer. Vanderbilt University is a National Arboretum located in the heart of Nashville, TN and consistently ranks in the top 15 US Best Colleges.

Thursday, March 23, 2017

Two recent papers from the lab focus on functions of host-associated microbiomes and endosymbionts:

Just sharing the lab's two recent papers that examine how microbial communities and specific bacterial endosmbionts (Wolbachia) function in their hosts. 

1. Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility. Nature.  Lepage, D.*, J.A. Metcalf*, S.R. Bordenstein, J. On, J. Perlmutter, J.D. Shropshire, E. Layton, J. Beckmann, and S.R. Bordenstein (*Co-first authors) Select coverage:
Major point: Two genes, cifA and cifB, in the eukaryotic association module of prophage WO (related paper from the lab) enable Wolbachia to cause cytoplasmic incompatibility

Description: The genus Wolbachia is an archetype of maternally inherited intracellular bacteria that infect the germline of numerous invertebrate species worldwide. They can selfishly alter arthropod sex ratios and reproductive strategies to increase the proportion of the infected matriline in the population. The most common reproductive manipulation is cytoplasmic incompatibility, which results in embryonic lethality in crosses between infected males and uninfected females. Females infected with the same Wolbachia strain rescue this lethality. Despite more than 40 years of research and relevance to symbiont-induced speciation, as well as control of arbovirus vectors and agricultural pests, the bacterial genes underlying cytoplasmic incompatibility remain unknown. Here we use comparative and transgenic approaches to demonstrate that two differentially transcribed, co-diverging genes in the eukaryotic association module of prophage WO from Wolbachia strain wMel recapitulate and enhance cytoplasmic incompatibility. Dual expression in transgenic, uninfected males of Drosophila melanogaster crossed to uninfected females causes embryonic lethality. Each gene additively augments embryonic lethality in crosses between infected males and uninfected females. Lethality associates with embryonic defects that parallel those of wild-type cytoplasmic incompatibility and is notably rescued by wMel-infected embryos in all cases. The discovery of cytoplasmic incompatibility factor genes cifA and cifB pioneers genetic studies of prophage WO-induced reproductive manipulations and informs the continuing use of Wolbachia to control dengue and Zika virus transmission to humans.

2. Phylosymbiosis: Relationships and functional effects of microbial communities across host evolutionary history PLOS Biology (open access) By Brooks AW*, Kohl KD*, Brucker RM*, van Opstal EJ, Bordenstein SR (Co-first authors) Select coverage:
Major point: Host-associated microbial communities can be specific and beneficial to their hosts, even among closely-related host species.

Description: Studies on the assembly and function of host-microbiota symbioses are inherently complicated by the diverse effects of diet, age, sex, host genetics, and endosymbionts. Central to unraveling one effect from the other is an experimental framework that reduces confounders. Using common rearing conditions across four animal groups (deer mice, flies, mosquitoes, and wasps) that span recent host speciation events to more distantly related host genera, this study tests whether microbial community assembly is generally random with respect to host relatedness or "phylosymbiotic," in which the phylogeny of the host group is congruent with ecological relationships of their microbial communities. Across all four animal groups and one external dataset of great apes, we demonstrate phylosymbiosis to varying degrees in each group. Moreover, consistent with selection on host–microbiota or holobiont interactions driving phylosymbiosis, transplanting interspecific microbial communities in mice significantly decreased their ability to digest food. Similarly, wasps that received transplants of microbial communities from different wasp species had lower survival than those given their own microbiota. Overall, this experimental and statistical framework shows how microbial community assembly and functionality across related species can be linked to animal evolution, health, and survival.

Tuesday, January 24, 2017

The Most Important Blog Post - Scientist March on Washington

Everybody has a reason to march. This is the most important post of this blog. Tune in.


What is the Scientists' March on Washington

UPDATE: 4:00 1-24-16 : Since 10am today, over 50 people have volunteered to help make this event a reality! We're going to get back to everyone and try to make sure that everyone's time is put to the best use possible. A single google hangout looks unfeasible if volunteers keep coming in at this rate until Saturday, so we're working ways to break into working groups. Stay tuned!

Twitter: @ScienceMarchDC
Reddit: /r/scientistsmarch
Get Email Updates
To help:

We accept the following as provisionally true:

  • The Earth is becoming warmer due to human action.
  • The diversity of life arose by evolution.
  • An American government that ignores science to pursue ideological agendas threatens not only the environment of which humans are a part, but America itself.
  • Scientific research in the United States is underfunded.
  • Politicians who devalue expertise risk making decisions that do not reflect reality.

Who can participate:

Science is a methodology and a way of thinking. Anyone who uses and values these tools for understanding the world, not just professional scientists, may participate.

How can I help?
We are still in the very early stages of organizing this event. We need all the help we can get, especially from people with expertise in the following areas:

  • Web Design
  • Logo/Graphic design
  • Law, incorporation of a not-for-profit
  • Fundraising
  • Public relations and media relations
  • Social media management
  • Organizing large events
  • Acquiring permits in DC
  • Contacts with possible speakers

You don’t need to be a professional scientist to participate. Just fill out this google form: and please let us know how you can help.

How can I donate?
You can’t yet. We’re working on figuring out a legal framework that will allow you to donate.

When will it be?

We’re still in the very earliest stages. The date will be announced as soon as it is available.

Isn’t science apolitical?

Yes. Scientists, however are not. The march is non-partisan, however it is intended to have 
an impact on policy makers

Monday, October 31, 2016

Guest Blog Post on Holobiont Theory by Jonathan Klassen and Sarah Kopac

Recently, Sarah Kopac and Jonathan Klassen described a new model to understand the evolution of host-microbe symbioses in their paper “Can They Make It on Their Own? Hosts, Microbes, and the Holobiont Niche”. In this model, hosts and microbes can change the shape of their respective niches, and thereby the context in which selection can act. This permits a test of holobiont theory by identifying instances where an organism’s phenotype depends on its symbiotic partners. Jonathan answered the following questions, incorporating feedback from Sarah. Be sure to read all the way through.

              SMK       Jonathan Klassen

1.     What motivated the theory reported in the paper?

It feels a bit murky now, but looking back I think there were three main motivations. First, we were quite struck by how host-microbe relationships can be thought of as a community ecology problem, i.e., where and how do interspecific relationships form and what is their outcome? So because much of the holobiont/hologenome literature has started from a population-genetics perspective (e.g.,, we thought that drawing from a different intellectual tradition might be a way to get beyond current sticking points in the field's discussion. Another interesting aspect of the community ecology perspective is that it defines the context in which selection might act, leaving whether or not selection does act as a separate question. I think that it is too common to assume selection without rigorously testing against alternative hypotheses, e.g., drift or dispersal limitation, to our detriment. Second, we wanted to strongly highlight how any selection that did occur likely impacted hosts and microbes differently, e.g., because microbes have shorter lifespans and higher population sizes and dispersal rates than their hosts ( Third, one major take-away from my years of reading the lovely Dynamic Ecology blog ( is that mathematical models have a rigor and testability that verbal models cannot match, and thereby overcome the potential for verbal models to become misconstrued. Expressing our ideas mathematically so that they would be unambiguously testable therefore became an important goal.

2.     How did you come up with the title?

Truthfully, this was a revision suggested by one of the reviewers. (And they were right - thanks!) Sarah came up with this version, and I think it’s great because it really captures the key question of our model: do host-microbe interactions matter for the evolution of either partner? I think the answer is that it depends on the context, i.e., does the interaction change the shape of either partner’s niche in a way that changes how selection might act? I also love how (in my mind at least) there’s a U2 reference - I’ve long been a fan.

3.     When and how did you two come together and agree on this paper? Were there varied opinions about how to approach the problem?

We agreed on the central idea of explaining holobionts in terms of niche theory early on, and so were unified on that front. There was a bit of divide and conquer after that, with Sarah focusing more on the examples of different niche shifts and I focusing more on the models themselves. Then we came back together and made sure that the examples we saw in the literature could be explained using our models. I found it very helpful to get someone else’s view of the literature – accurately synthesizing everything that’s out there alone would have been a massive challenge.

4.     What are the most salient findings?

I think that it is striking how our models are agnostic towards any particular mechanism of host-microbe interaction. For example, a similar shift in a host’s niche could be result from that host selecting microbes with a particular trait from the environment each generation, or it could be due to tight host-microbe co-evolution and vertical transmission. The important thing is that in either case the interaction changes the shape of a host’s niche in a way that selection might act upon. Both partners are therefore needed to completely describe host evolution. I am also struck by how our models accommodate the full diversity of symbiotic relationships, including the various forms of conflict that change the shape of a host’s niche but in a different way than mutualism. Finally, it seems that the symbiosis community has already been at least implicitly thinking in terms of our model because it was easy to find studies that had already tested it by changing one parameter at a time, e.g., by swapping microbiomes between constant host genotypes and vice versa. Hopefully our work can guide future experiments that continue to explicitly test these ideas.

5.     What are the most crucial questions moving forward in your mind? What do you want to do next? 

Perhaps one problem with our model is that precisely defining the shape of an organism’s niche is fiendishly difficult, mostly because there are a potentially infinite number of niche axes to consider. I think it will be interesting to understand how many of these are actually needed to come up with an accurate niche description. For example, to what extent to do microbe-microbe interactions need to be considered to describe how microbes alter a host’s niche? I also think it will be critical to learn more about microbes in non-host environments so that we can determine if hosts modify the niches of their microbial symbionts outside of obvious cases like intracellular mutualists and pathogens. Lastly and as described above, I think it will be crucial to explicitly test whether any host-microbe interaction phenotype actually arises due to selection, e.g., vs drift or dispersal limitation.

6.     Anything else you want to add?

Thanks to our colleagues in the symbiosis field for being so collegial, even in disagreement! I look forward to increasing the rigor of our studies, and to a deeper understanding of how ecology and evolution both shape host-microbe relationships.

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!