BEACON Researchers at Work: The Age of Phage

This week’s BEACON Researchers at Work blog post is by MSU faculty member Kristin Parent, with John Dover. 

Kristin Parent (center), Natalia Porcek and Jason Schrad at the PVA meeting in Switzerland.

Jason Schrad, Kristin Parent, and Natalia Porcek at the PVA meeting in Switzerland.

This year marks the 100th anniversary of the discovery of viruses that infect bacteria—the bacteriophages. One may think (as many do) that there is little else to gain by continuing to study bacteriophages (often shortened to just phages), but like their bacterial hosts, there is actually still a lot to learn. In fact, I recently attended a Phage and Virus Assembly (PVA) meeting, and the same theme kept coming up: despite 100 years of research, there is still so much that we don’t know.

It might be surprising to learn that the number of phages (~1031) is ten times greater than the number of bacteria (~1030). In fact, one handful of water from lake Michigan contains more phages than there are people on Earth. Think about that the next time you go swimming!

Frederick Twort, in 1915, discovered that bacteria were susceptible to phages, along with Felix d’Herelle’s independent discovery two years later. The next few decades proved to be a robust period for phage research, with an avalanche of studies culminating in >62,700 published papers (as of June 23rd 2015).

  • The 1920s saw the birth of “phage therapy”, in which phages are used to combat bacterial disease.
  • In the 1930s, the phage life cycle was established and is now an introductory biology textbook staple.
  • The 1940s and 1950s saw the use of phages in the famous Hershey/Chase experiment that conclusively showed that DNA is the genetic material, and phages were used in the explosion of molecular genetics studies that followed. In actuality, phages were used as tools that directly contributed to the vast majority of genetic manipulations that are now routine in the laboratory.
  • Phage work continued strong into the 1960s and 1970s where phages again led the way in the creation of methods that are commonplace in the modern laboratory: negative staining in electron microscopy, the use of transposable elements, and DNA sequencing, wherein the first complete genome sequenced by the eponymous Sanger was a phage genome.
  • Research in the 1980s and 1990s revealed that phages were everywhere—in all terrestrial and aquatic biomes.
  • The metagenomics boom starting in the early 2000s gave clues to phages in the human microbiome, and they are now actively being investigated as part of the virome of the microbiome. There are more bacterial cells and phages in your body than there are human cells, and phage/host interactions contribute an enormous amount to our bacterial diversity, and yet, we know so little about them and how they evolve.
  • In the last ten years, advances in cryo-electron microscopy have given us images of the beautiful structures of entire phage particles, which are complexes of thousands and thousands of proteins. We are only now starting to understand how these elegantly assembled structures work as molecular machines.

Despite the huge mass of information gained during the past “phage century”, there are still numerous aspects of phage biology that remain a mystery. One part of this mystery is how a phage, or any virus, recognizes and successfully infects its “favorite” host. Such a process is critical to virus survival. In all environments there is great diversity in both viruses and hosts resulting in an enormous challenge for viruses to encounter and infect suitable targets. My laboratory is focused on how phages efficiently recognize their hosts and transfer their genomes into those hosts. We use a combination of microbiology, biochemistry, structural biology, and experimental evolution to investigate these processes.

One of the phages that we use as a model system is Sf6, which infects Shigella flexneri. Natalia Porcek, a graduate student in my lab, has shown that Sf6 uses a host cell outer membrane protein, or “Omp”, for infection. Her work has shed light on protein-protein interactions critical to Sf6 entry into its host, and her work has contributed to an understanding of host range—specifically, how Sf6 can recognize Shigella and Salmonella species but not E. coli. Another graduate student in my lab, Jason Schrad, is also working toward understanding this process by using cryo-electron microscopy to look at Sf6 during the process of infection.

John Dover counting plaques in the lab.

John Dover counting plaques in the lab.

John Dover, a technician in my lab, and Alita Burmeister, a collaborating student from the Lenski lab, are using Sf6 for experimental evolution studies aimed at understanding how phages can adapt to infect different hosts. These studies have revealed a potentially novel evolutionary mechanism distinct from other phages such as lambda. Sf6 is a member of a class of phages that packages “headfuls of DNA” in its capsid, a protein shell that encloses the DNA. This means that the phage packages DNA until no more can fit in the capsid container, which is more DNA than needed to encode a single genome. We have seen parallel evolution across ten phage lineages that show whole gene deletions as a path to fitness. In some cases, as much as 15% of the ancestral genome was deleted. Since the phage packages headful, that would mean that a new genomic composition (replacing 15% of the DNA), is contributing in some way to a faster life cycle. Their work has also found parallel evolution of cell lysis timing, which is the temporarily controlled stage of the phage life cycle that breaks open the bacteria and releases new phage “babies”. Faster lysis allows the phages to infect the next group of cells in its controlled environment earlier, making the phage more fit.

We still have much more to do to fully understand bacteriophages. We are in an exciting time as experimental advances have evolved to provide many robust tools for dissecting phage biology, and we are looking forward to the next 100 years of phage discovery.

For more information about work in the Parent lab, you can contact Kristin at kparent at msu dot edu.

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BEACON Researchers at Work: An Adventure in Thailand

This week’s BEACON Researchers at Work blog post is by MSU postdoc Eben Gering.

I. The Land of the Leech

Figure 1. Golden Naga in Emerald Buddha temple Wat Pra Kaeo, Bangkok, Thailand

Figure 1. Golden Naga in Emerald Buddha temple Wat Pra Kaeo, Bangkok, Thailand

This spring I received a last-minute invitation to join a French film crew in Thailand, which left me a) totally stoked! b) with virtually no prep time. And so I found myself arriving in Khao Yai National Park with a mess of hastily borrowed equipment, abundant enthusiasm, and very little basic information about the region.

For example: did you know that Southeast Asian forests are home to a 150 million-year-old, ten-eyed beast whose name means blood thirsting guts? If you don’t perhaps you are picturing something along the lines of the fantastical Naga (Figure 1) – a ferocious serpent believed to protect the Buddha. Naga guard temple entrances throughout Thailand, but are nowhere near as ubiquitous as Haemodipsidae (Figure 2) which, FYI, are hermaphroditic land leeches.

Figure 2.  Haemodipsidae zylandica. One of ~90 species of terrestrial (“land”) leeches.

Figure 2. One of ~90 species of terrestrial (“land”) leeches.

When our guide first offered us prophylactic “leech sox” I didn’t want them. In my undergraduate days I had read a terrific book1 about tropical biology which eventually helped land me in this Thai jungle many years later. One of the book’s most memorable chapters (recapped in a recent radiolab episode) concerns an evolutionary biologist who lets a parasitic botfly pupate in his head for heuristic (learning) purposes. Botfly husbandry has since become a fashionable act among a small and hardcore subset of tropical biologists.

The idea of joining Club Botfly makes me a little queasy, and involves an apparently painful initiation too. But leeches – painless, virtually incapable of transmitting disease, a boon to human health and medicine for at least three millennia – provided an attractive alternative source of field “cred.” In fact, I’ve been quite curious about these animals since meeting Mark Siddall, a passionate and persuasive expert on leech biology who “fishes” for his study subjects by dangling his legs in murky water. In parallel manner, Dr. Siddall advocates for these greatly maligned creatures. He lures his listeners past the ‘ick’ reflex into a reluctant appreciation for their elegance and mystery. It is, after all, an animal which once fed on dinosaurs, and outlived them, and will probably outlast us.

An enlightened view of the leech is also apparent in Khao Yai’s local, Buddhist residents, who point out their relative harmlessness with the saying:

The hero of Khao Yai National Park…


They eat blood but not the trees! 2

Will I be able to get a leech if I don’t wear the sox? I asked Tony, our guide. But I needn’t have worried. In the coming days I would have many chances to observe sanguivory (bloodfeeding) first hand. Leeches would be so abundant at times that we would see and hear them moving towards us on the forest floor.

II. Why won’t the chickens cross the road?

Figure 3.  Red Junglefowl (Gallus gallus) eating ectoparasites from a sambar deer (Rusa unicolor). Photo courtesy of Tontantravel.

Figure 3. Red Junglefowl (Gallus gallus) eating ectoparasites from a sambar deer (Rusa unicolor). Photo courtesy of Tontantravel.

The chief purpose of our expedition was to visit the Red Junglefowl (Gallus gallus) within its native range. These extremely wild and elusive birds (figure 3) are the domestic chickens’ closest relatives. The French guys (Figure 4) were out to gather the world’s first 4k footage of wild Red Junglefowl. I, in turn, hoped to gather audio recordings and compare vocalizations to those from a non-native (Hawaiian) G. gallus population. Our recent research3 indicated that Pacific island G. gallus share both Red Junglefowl and “chicken” (i.e. domestic) ancestry. We are now investigating which wild, domestic, and/or hybrid traits have been favored in these feralized populations.

Figure 4. Wildlife filmmakers Benoit Demarle and Nicolas Cailleret

Figure 4. Wildlife filmmakers Benoit Demarle and Nicolas Cailleret

During our first days out, we occasionally heard Red Junglefowls calling from deep within the forest. That’s a somewhat surreal experience for western eyes and ears, because they look and sound just like backyard roosters, yet glide through primary tropical forests without effort, thriving among leopard cats and pythons.

From day one, I was able to collect audio recordings, but our efforts to film (with a menagerie of cumbersome gear) typically sent our targets fleeing dozens, or even hundreds of meters into impenetrable growth. A day’s work yielded only a few precious minutes of 4k video.

On day two, the production director (Benoit) put his cameraman (Nicolas Cailleret, a professional falconer back in France) in a camouflaged bird blind. We left him there before sunrise in an area where we’d seen junglefowl eating figs. Later a hornbill polished off the figs, so we decided to bait the area with another of the Red Junglefowl’s preferred food sources: elephant dung (figure 5).


Figure 5a,b. Elephant dung collected in an attempt to lure Red Junglefowl into the open

Figure 5a,b. Elephant dung collected in an attempt to lure Red Junglefowl into the open

As I grabbed my first handfuls of the dung, which was surprising lofty, fibrous, and not the least bit stinky, I thought how much I love my job. I was 11 time zones from home, and almost intoxicated by the nearly deafening whirs of the cicadas, the sweet and mournful ‘bwoooooops’ of gibbons, the bright flapping of birdwing butterflies gliding on hot, humid air.

While we picked the freshest dung we could find, the waste of our planet’s largest herbivore was already becoming a complex ecosystem. By coincidence, the book I mentioned earlier 1 (and highly recommend) also contained a whole chapter on poop – specifically, how scatophagic4 organisms colonize and compete for this rich resource within minutes of its “birth.”

III. In praise of Bill Nye

Figure 6. Stealth camerawork by Nicolas Cailleret

Figure 6. Stealth camerawork by Nicolas Cailleret

While our brief experiment with elephant dung brought on an existential rapture, it did not bring any Junglefowl in front of the camera. Soon, however, Benoit and Nicolas found other ways to catch clips of the birds in stealth (figure 6). They crouched underneath a camouflage tarp in the bed of Tony’s rolling truck, ready to start shooting when Junglefowl were spotted. They learned and patrolled a few territories’ boundaries. And then, when they had acquired sufficient footage of their non-human prey, they turned the camera on me.

I am curious to see myself on French television, but not worried a bit. I cannot possibly look worse than I felt. For two days I had been crowing for the camera, a one-eyed monster that emitted so much heat it required its own water breaks. Usually this work was done standing in direct sunlight, sometimes while peeling off leeches… whose novelty was waning (sorry, Mark!). The heat seemed to fog up my brain, making it a struggle to follow simple instructions or speak intelligibly. And I could see that this was beginning to try the (extraordinary) patience of the crew – two men who had just spent uncomplaining days in a sauna-like blind surrounded by elephant poop.

On our last afternoon, we all spent an hour crouched in that small, poorly vented vinyl blind collecting footage of me photographing imaginary junglefowl. Nicolas held the camera a few inches from my face while Benoit held the microphone over my head. We were as close together as the heads of the Naga (Figure 1), and it was so hot in there – so very hot and humid (and the whole shot seemed so unimportant) that I wondered if perhaps they were trying to kill me in order to increase their film’s marketability.

But apart from such moments of heat and performance-induced panic, it was a joy to watch Benoit and Nicolas work. There was boldness and creativity in every step of their process, from handling equipment failure, to avoiding extortion by corrupt officials, to framing a narrative arc across this wild landscape, its diverse wildlife, and their bumbling biologist that would eventually reach into the homes of French families.

I was eager to participate in Benoit and Nicolas’ film because nature documentaries helped cultivate my interest in biology. And as a scientist on the more right-brained end of the spectrum, I enjoy seeing artists at work. While I would jump at another such chance, our filming of just one segment (25%) of a 45 minute show was both physically and mentally exhausting. I couldn’t do this work everyday, and have redoubled my respect for the stamina of David Attenboroughs and Bill Nyes.

When I first read Tropical Nature1, my game plan was to become a writer for a documentary production company. But I have since become increasingly fascinated with basic research questions, which take sustained (and sometimes boring) effort to answer. Benoit, on the other hand, began his career as an acarologist (mite expert) before transitioning out of research and into film. The mite work, he said, was much too specialized to match his interests. I could understand this, I said, but also asked him to tell me more about the mites. I think we have chosen wisely.

1 Forsyth, A., & Miyata, K. (2011). Tropical Nature: Life and Death in the Rain Forests of Central and South America. Simon and Schuster.

2 Translation by Elizabeth Borda

3 Gering, E., Johnsson, M., Willis, P., Getty, T., & Wright, D. (2015). Mixed ancestry and admixture in Kauai’s feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs. Molecular ecology.

4scat feeding

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BEACON Researchers at Work: The Social Lives of Bacteria

This week’s BEACON Researchers at Work blog post is by MSU faculty member Chris Waters.

Nature red in tooth and claw”-Lord Alfred Tennyson

Tennyson’s famous phrase eloquently describes the adversarial nature (pun intended) that arises from Darwin’s concepts of natural selection and survival of the fittest. From a human perspective, these concepts are easy to understand. One only needs to attend my son’s little league games to see how competition is ingrained in humans. Competition for limited resources leads to genetic winners and losers. This idea permeates throughout the tree of life; indeed, visit the Lenski lab at Michigan State to see the ongoing results of a 25 year Escherichia coli “cage match”.

But we all know that natural interactions are not always adversarial. Humans are also highly cooperative individuals, often helping one another at their own expense. Bees, wasps, and ants, live in highly cooperative communities in which individual members forgo their own reproduction for the net good of the group.

Bioluminescent Vibrio harveyi actively quorum sensing.

Bioluminescent Vibrio harveyi actively quorum sensing.

It has become abundantly clear that even unicellular lifeforms participate in highly complex social interactions. The first appreciation for social interactions in bacteria came with the discovery of chemical communication in bioluminescent Vibrios. It was found that these ocean growing bacteria prematurely induced bioluminescence when exposed to cell-free supernatant harvested from a dense culture. It was subsequently determined that bacteria produce and secrete small chemical signals, termed autoinducers, to coordinate behaviors in response to cell density. We now appreciate that this process, known as quorum sensing, is widespread in bacteria and it is generally hypothesized that all bacteria engage in some form of chemical communication. Autoinducers, and their sensing apparatuses, come in many flavors, suggesting that this is a highly beneficial trait that has coevolved multiple times.

Quorum sensing is often considered to be a mechanism for coordinating cooperative behavior in bacteria. While I think this aspect of quorum sensing is often overstated, it is quite true that many cooperative tasks are controlled by quorum sensing. For example, secreted “public goods” (i.e. shared benefits that all of the members of the community can utilize, not just the producers) are often clearly induced by quorum sensing. This cooperative situation leads to a strong selection for freeloading cheats which can gain the benefit of the public good without paying the production cost. Imagine five students working on a group project-at least one is typically a freeloader who gets the benefit of the grade without putting in the effort. This is an evolutionary smart strategy for the freeloading individual, but this strategy destabilizes cooperation within the group.

Eric Bruger pondering the evolutionary underpinnings of quorum sensing in bacteria.

Eric Bruger pondering the evolutionary underpinnings of quorum sensing in bacteria.

Eric Bruger, a graduate student in my laboratory, is studying this fundamental social evolution question-the evolution of cooperation-in the bioluminescent bacterium Vibrio harveyi. Studying social evolution using bacteria has a multitude of benefits including fast generation times, huge population sizes, easily measurable phenotypes, exquisite control of the environment, and, perhaps most importantly, the ability to genetically manipulate the cooperative state of test subjects (the ethics of genetic manipulation are much less stringent with microbes!).

Eric has found that quorum sensing in V. harveyi does indeed induce public good production, and he has identified environments where public good production is required for growth. When Eric genetically manipulated V. harveyi to unlink public good production from quorum sensing control, leading to constitutive public good secretion, he found that this mutant strain was rapidly invaded by cheating cells. This led to a population crash, typically referred to as a “tragedy of the commons”. However, having the public good linked to quorum sensing stabilized cooperation and the cheats could not invade. Thus, Eric experimentally demonstrated that the ability of cooperating cells to communicate stabilizes cooperation!

Eric then extended these experiments to study the natural emergence of cheats following experimental evolution of V. harveyi for over 2,000 generations. He observed that quorum sensing control of cooperation delayed cheater invasion, but eventually cheaters did emerge. However, communication prevented cheaters from sweeping the population, leading to a complex mixture of cooperators and cheats that is reminiscent of V. harveyi strains observed in the natural world.

Will Soto and Chris Waters glean wisdom from all sources including Bob Marley and Star Wars to study quorum sensing.

Will Soto and Chris Waters glean wisdom from all sources including Bob Marley and Star Wars to study quorum sensing.

Public good production is but one of hundreds of traits regulated by quorum sensing in V. harveyi. How do the other regulated behaviors impact the stability of quorum sensing? Enter Dr. Will Soto, a BEACON funded postdoctoral fellow in my laboratory. Will is exploring the impact of quorum sensing on central metabolism in V. harveyi. Will examined the growth of three strains-the wild type strain with functional quorum sensing, a strain that cannot communicate, and the constitutive quorum sensing strain-in a hundred different laboratory growth media. He found dramatically different growth patterns of these strains, but, surprisingly, the wild type quorum sensing strain did as well or better than both quorum sensing mutants in virtually all environments examined! This result shows that communication in bacteria not only stabilizes cooperation, but it is also a mechanism to enhance colonization of many different ecological niches, suggesting that quorum sensing provides bacteria a large fitness benefit in the real world when faced with ever changing environments.

Quorum sensing is but one of many social traits in bacteria. Most bacteria can also form multicellular communities encased in a protective matrix called biofilms. Some photosynthetic cyanobacteria actually grow as multicellular filaments and exhibit striking differentiation and division of labor. Yet others, like Myxococcus, undergo complex cooperative development and form multicellular fruiting bodies upon starvation. All of these systems are excellent unicellular models to test concepts of social evolution.

Clearly, cooperation is not limited to us multicellular organisms; unicellular organisms have a robust social life. It is important therefore to consider not just nature’s “tooth and claw” but perhaps also “Nature gentle with helping hand”.

To learn more about research in the Waters lab follow us on twitter (@WatersLabMSU) or visit our website:

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3rd Annual Big Data in Biology Symposium at UT Austin

Summary by UT Austin graduate student and symposium organizer Rayna Harris.


The 3rd Annual Big Data in Biology Symposium on May 15, 2015 was hosted by the Center for Computational Biology at UT Austin and organized by some BEACON members. This annual symposium provided an ideal opportunity to interact with attendees from UT Austin and nearby institutions with an interest in computational biology, bioinformatics, and systems biology. Here, I summarize scientific content of the talks, breakout sessions, poster session, and industry dinner.

The Talks

The symposium talks covered research into epigenetics, genomics, transcriptomics, and immune repertoires in a wide range of organisms. We heard from graduate students, postdocs, and faculty members, providing a diversity of experience and perspective of the impact of big data on biology.

This year’s keynote lecture was delivered by Dr. Shelley Berger from The University of Pennsylvania. She discussed her research into the epigenetic mechanisms regulating of caste-specific phenotypes in eusocial ants. Amelia Hall, a graduate student in the Iyer lab, also focused on epigenetics, describing her analyses of histone pattering in glioblastoma tumors and the effects on gene expression.

BEACONite Dr. Jeffrey Barrick talked about technological advances for mapping beneficial mutations in the E. coli Long-term Experimental Evolution Experiment and the exciting implications for evolution and adaptation. Dr. Kasie Raymann, a postdoc in the Moran lab, talked about her thesis research using large scale genomic data to understand the evolutionary origins of eukaryotes.

Justine Murray, graduate student in the Whiteley lab, discussed her use of RNA-seq and Transposon (Tn) Seq to understand the dynamics of poly-bacterial infections. Dr. Mikhail Matz talked about recent computational tools his lab has developed for analyzing RNA-seq data. BEACONite Dr. Becca Young (Hofmann lab) also described new computational tools that can be used for identifying homologous genes groups, an important step for comparative transcriptomics. Jeff Hussmann, a graduate student in the Press and Sawyer labs, discussed how systematic biases in ribosome profiling experiments can lead to an incorrect understanding of translation speed.

Dr. Jenny Jiang talked about using high-throughput sequencing and single cell analysis to characterize immune repertoires, and Dr. Oana Lungu, a postdoc in the Georgiou and Ellington labs, shared her in silico approach for characterizing changes in protein structure of immune after antigen experience.

The Lunch Breakout Sessions

The lunch breakout sessions provided attendees the opportunity to have small-group discussions with various big data professionals over a catered lunch. These sessions were aimed at helping attendees network with other like-minded researchers and discover resources for different aspects of and opportunities in data science. The three breakout session topics included 1) Big Data in Medicine & Health, which highlighted the tremendous opportunities and technical challenges for evidence-based medicine arising from electronic health records; 2) Careers in Biotech/Industry, which provided insights into non-academic careers; and 3) Open Science, which discussed the importance of data sharing, public access to research, and the increasing role of social media in scientific communication.

The Poster Session

A poster session followed the symposium and allowed trainees to explain their work and facilitate fruitful exchanges. There were twenty posters on various topics, including genomics, transcriptomics, epigenetics, and proteomics. BEACONite Dr. Daniel Deatherage (Barrick lab) and Claire McWhite (Marcotte lab), respectively, won the best postdoc and student poster awards.

Figure 2. The Poster Session. Left: The poster session took place in a lovely ballroom. Right: The symposium ended with a postdoc and graduate student poster award presentation. L-R: Dr. Scott Hunicke-Smith, BEACONite Dr. Daniel Deatherage (postdoc winner), BEACONite Dr. Hans Hofmann, Claire McWhite (grad student winner), and BEACONite Rayna Harris.

The Poster Session. Left: The poster session took place in a lovely ballroom. Right: The symposium ended with a postdoc and graduate student poster award presentation. L-R: Dr. Scott Hunicke-Smith, BEACONite Dr. Daniel Deatherage (postdoc winner), BEACONite Dr. Hans Hofmann, Claire McWhite (grad student winner), and BEACONite Rayna Harris.

The Industry Partners Dinner

This year, we hosted an Industry Partners Dinner for representatives of the local biotech and high-tech industry corporations to meet a diverse set of graduate students in the College of Natural Sciences who are interested in careers in industry. Graduate students from multiple graduate programs and a handful of faculty members networked with associates from Asuragen, Bioo Scientific, Dell (who generously sponsored this event), IBM, Lab7, Macromoltek, and Sonic Healthcare USA.

We invited 12 industry partners, 12 faculty/staff members, and 24 students. We have found that 8-person tables work well for promoting discussion, so seats were assigned such that every industry partner and faculty member was flanked by two students. Everyone agreed that this seating arrangement works very well for facilitating conversation between people at different career stages and with diverse backgrounds, many of whom had never met.

Based on the many positive and encouraging comments we received most of the attendees, our first formal event with our Industry Partners was a huge success, as it opened many doors for new graduate students interested in different career options and for industry-academia partnerships.

The Industry Partners Dinner. This cocktail hour and dinner provide more than 20 graduate students the oportunity to chat with people from the thriving biotech and bioinformatic industry in Austin Texas. Seating was arranged so that Industry partners were flanked by students, providing ample oportunity to learn about graduate research at UT Austin.

The Industry Partners Dinner. This cocktail hour and dinner provide more than 20 graduate students the oportunity to chat with people from the thriving biotech and bioinformatic industry in Austin Texas. Seating was arranged so that Industry partners were flanked by students, providing ample oportunity to learn about graduate research at UT Austin.


The Organizers

The symposium and the dinner would not have happened without the efforts of Hans Hofmann (Director of the CCBB) and Scott Hunicke-Smith (Director of the GSAF). BEACONite Laurie Alvarez (CCBB) is a crucial team member who handles all the finances and so much more. Nicole Elmer (CCBB) is an excellent graphic designer and helped design and distribute all communication materials. Thanks to Becca Tarvin and Sean Leonard for helping organize the Industry Partner Dinner. 

The Sponsors

We are grateful to BEACON for providing travel support to BEACON Managing Director Dr. Danielle Whitaker and to The Graduate School Academic Enrichment Fund for providing travel support for Dr. Shelley Berger. Graduate Student Assembly Appropriations were used for printed materials and speaker gifts. We want to extend a special thanks to Dell for generously sponsoring the Big Data in Biology Industry Partners Dinner.

For more information about the Big Data in Biology Symposium, visit the website at

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BEACON Researchers at Work: What ice cream and biofuels have in common: vanillin and the microbes that eat it

This week’s BEACON Researchers at Work blog post is by University of Idaho postdoc Jessica Audrey Lee.

Greetings, BEACON fans. I’m writing from beautiful Moscow, ID, where I work as a postdoctoral researcher in the Marx Lab at the University of Idaho, and where our incubator smells like a cookie factory. It smells that way because the model compound we’re working with at the moment is vanillin, which is not only an important substance in the global food and fragrance industries, but is also a key intermediate in the microbial degradation of lignin.

Oenophiles (of which I am one) may already know this: vanilla-like flavors in wine are almost always a sign that the wine has aged in oak barrels, because oak wood, with its high lignin content, flavors the wine by releasing aromatic bits and pieces of that lignin into it. Foodies (of which I also am one) may also already know this: more than 99% of the vanilla flavoring used today doesn’t actually come from Vanilla planifolium (the vanilla orchid, the source of “real vanilla extract”), but instead is produced industrially either from fossil fuels or from chemical processing of lignin (Walton et al., 2003). And biofuels researchers also know that vanillin (and its derivative, vanillic acid) can be used as a decent stand-in for the monomers that make up the very complex polymer that is lignin.

vanillin_vanillate_MethylobacteriumMy current research is part of a larger project, with collaborators at BU and LBNL, to create a microbial consortium for degrading lignocellulosic biomass (that is, assorted plant parts, some of them woody) into fatty acids that can be used as biofuels. Our consortium will include some of the usual suspects—bacteria from the well-known soil-dwelling genus Streptomyces, and the fatty-acid-accumulating yeast Yarrowia lipolytica—as well as a more unusual player, Methylobacterium extorquens. This Methylobacterium species is typically found on plant leaves—not in the soil, degrading dead plant matter—but we’re introducing it to our consortium because it has a special talent: handling formaldehyde.

Lignin is a difficult compound to degrade, and one of the reasons it’s difficult is that it contains a great number of methoxy (-OCH3) groups. The typical microbial approach for dealing with these methoxy groups is to remove them and turn them into formaldehyde, but the subsequent process of detoxifying the accumulating (very toxic!) formaldehyde can severely slow down lignin degradation (Mitsui et al., 2003). Happily, Methylobacterium, because it typically eats methanol for a living, is very efficient at processing formaldehyde as a metabolic intermediate, so if we could just get it to pull the methoxy groups off of the lignin monomers we could potentially make significant gains in biofuel production from lignocellulose.

M. extorquens (and most Methylobacterium species) carries pink sunscreen-like pigments. M. nodulans, adapted to living in the dark, is white.

M. extorquens (and most Methylobacterium species) carries pink sunscreen-like pigments. M. nodulans, adapted to living in the dark, is white.

This is where the evolution and ecology get interesting. Methylobacterium is in the order Rhizobiales, and therefore not too distantly related to some other plant-associated bacteria that have been shown to degrade lignin, for instance Bradyrhizobium japonicum (Sudtachat et al., 2009) (which can often be found in plant root nodules). In fact, if you compare the two genomes at the locus of the B. japonicum vanillate-demethylating genes (vanAB), you’ll find that all Methylobacterium species also have a gene that looks similar enough to be part of the same pathway (I call it vanA-like). Sadly, M. extorquens can’t demethylate vanillin (hey, it was worth a try—it’s possible we’re the first lab that ever bothered to ask). However, we’ve found that it has a close relative, M. nodulans, that can! We’ve located the M. nodulans gene cluster that we think is responsible, and it seems to have nothing to do with the vanA-like gene that I mentioned earlier; it’s located far away in the genome and doesn’t resemble anything that any of the other Methylobacterium species has (as far as I can tell). What’s even cooler is that M. nodulans is the one species of Methylobacterium that lives not on leaves but in nodules on plant roots. So I suspect that lignin degradation might be a talent it retains specifically because it’s useful in the soil environment.

So, in M. nodulans, we’ve found a great source of lignin-degradation genes for engineering into M. extorquens—a close family member willing to donate an organ, if you will. What I find even more interesting, though, is that at the same time we’re working toward a tangible, potentially industrially important, goal, we also get to peek into the ecology and evolution of some really cool plant-associated bacteria. When several species of a genus diversify to fill radically different niches (leaf versus root), how and when do they pick up the genes they need, or lose the genes they no longer need? I like to think that when we clone a new set of lignin-degrading genes into M. extorquens, we’ll be either restoring a function it once lost, or repeating an acquisition that an ancestor of M. nodulans once experienced. (Which one? I don’t know, but I’m definitely inspired to delve deeper into the phylogeny of these genes across the diverse species that have them.)

We’re likely to follow up cloning with evolution in the lab to help M. extorquens get used to its new genes… and when we do, what kind of changes can we expect to see? I’m new both to experimental evolution and to the metabolism of aromatic compounds, so I have a great deal still to learn. I’m looking forward to finding out more about the evolution has happened in the environment to separate M. nodulans and M. extorquens on the plant, and the evolution that will happen soon in our lab, on the way to creating a microbial consortium for biofuel production.


Mitsui R, Kusano Y, Yurimoto H, Sakai Y, Kato N, Tanaka M. (2003). Formaldehyde Fixation Contributes to Detoxification for Growth of a Nonmethylotroph, Burkholderia cepacia TM1, on Vanillic Acid. Appl Environ Microbiol 69:6128–6132.

Sudtachat N, Ito N, Itakura M, Masuda S, Eda S, Mitsui H, et al. (2009). Aerobic Vanillate Degradation and C1 Compound Metabolism in Bradyrhizobium japonicum. Appl Environ Microbiol 75:5012–5017.

Walton NJ, Mayer MJ, Narbad A. (2003). Vanillin. Phytochemistry 63:505–515.

For more information about Jessica’s research, you can contact her at jessicalee at uidaho dot edu.

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