What I did on my summer vacation: Microbial Diversity 2016

I just left Woods Hole, MA, where I spent the last 6 and a half weeks taking the Microbial Diversity course as a student. It was fun, exhausting, stimulating, and life changing!

The course had three components: a lecture series, in which world-class microbiologists gave 2-3 hrs of talks each morning, every Monday-Saturday of each week; a lab practical component, in which we learned to do environmental enrichments and isolations, use microscopes and mass specs and everything else; and a miniproject, a self-directed project that took place the last 2-3 weeks of the course, and for which we could make use of all of the equipment. The days typically went from 9am to 10pm, with a break every Sunday.

I think it's fair to say I've been microbiologized pretty thoroughly :).

The course directors were Dianne Newman and Jared Leadbetter, two Caltech professors that I knew of old (from my own days at Caltech). The main topic of the course was environmental microbiology and biogeochemistry, although we did cover some biomedical topics along with bioinformatics and genomics. The lectures were excellent, and there's only two or three for which I didn't take copious notes (or live-tweet under my student account, @tituslearnz). The other 18 students were amazing - most were grad students, with one postdoc and two other faculty. The course TAs were grad students, postdocs, and staff from the directors' labs as well as other labs. My just-former employee Jessica Mizzi had signed on as course coordinator, too, and it was great to see her basically running the course on a daily basis. Everyone was fantastic, and all in all, it was an incredibly intense and in-depth experience.

Why Microbial Diversity?

I applied to take the course for several reasons. The main one is this: even before I got involved in metagenomics at Michigan State, I'd been moonlighting on microbial genomics for quite a while. I have a paper on E. coli genomics, another paper on syntrophic interactions between methane oxidizing and sulfur reducing bacteria, a third paper on Shewanella oneidensis (with Dianne), and a fourth paper on bone-eating worm symbionts. While I do have a molecular biology background from my grad work in molecular developmental biology, these papers made me painfully aware that I knew essentially no microbial physiology. Yet I now work with metagenomics data regularly, and I'm starting to get into oceanography and marine biogeochemical cycling... I needed to know more about microbes!

On top of wanting to know more, I was also in a good position to take 6 weeks "off" to learn some new skills. I received tenure with my move to UC Davis, and with the Moore Foundation DDD Investigator Award, I have some breathing room on funding. Moreover, I have four new postdocs coming on board (I'll be up to 6 by September!) but they're not here yet, and most of the people in my lab were gone for some or all of the summer. And, finally, my wife had been invited to Woods Hole to lecture in both Microbial Diversity and the STAMPS course, so she would be there for three weeks.

I also expected it to be fun! I took the Embryology course back in 2005, and it was one of the best scientific experience of my life, and it's one of the reasons I stuck with academia. The combination of intense intellectualism, the general Woods Hole gemisch of awesome scientists hanging out for the summer, and the beautiful Woods Hole weather and beaches, make it a summer mecca for science -- so why not go back?

What were the highlights?

The whole thing was awesome, frankly, although by week three I was pretty exhausted (and then it went on for another three weeks :).

One part of the experience that amazed me was how easy it was to find new microbes. We split into groups of 4-5 students for the first three weeks, and each group did about 15 enrichments and isolations from the environment, using different media and growth conditions. (Some of these also formed the basis for some miniprojects.) As soon as we got critters into pure culture, we would sequence their 16s regions and evaluate whether or not they were already known. From this, I personally isolated about 8 new species; some other students generated dozens of isolates.

My miniproject was super fun, too. (You can read my final report here and see my powerpoint presentation here.) I set out to enrich for sulfur oxidizing autotrophs but ended up finding some likely heterotrophs that grew anaerobically on acetate and nitrate. It was great fun to research media design, perform and "debug" enrichments, and throw machines and equipment at problems (I learned to use the anaerobic chamber, the gas chromatograph, HPLC, and ion chromatography, along with reacquainting myself with autoclaves and molecular biology). I ended up finding a microbe that probably does something relatively pedestrian (oxidizing acetate with nitrate as an electron acceptor), with the twist that I identified the microbe as a Shewanella species, and apparently Shewanella do not generally metabolize acetate anaerobically (although it has been seen before). I sent Jeff Gralnick some of my isolates and he'll look into it, and maybe we'll sequence and analyze the genomes as a follow-on.

I also got to play with Winogradsky columns! Kirsten G. and I put together some Winogradsky columns from environmental silt from Trunk River, a brackish marine ecosystem. We spent a lot of time poking them with microsensors and we're hoping to follow up on things with some metagenomics.

More importantly for my lab's research, I got even more thoroughly confused about the role and value of meta-omics than I had been before. There is an interesting gulf between how we know microbes work in the real world (in complex and rich ecosystems) and how we study them (frequently in isolates in the lab). I've been edging ever closer to working on ecosystem and molecular modeling along with data integration of many 'omic data types, and this course really helped me get a handle on what types of data people are generating and why. I also got a lot of insight into the different types of questions people want to answer, from questions of biogeochemical cycling to resilience and environmental adaptation to phylogeny. I am now better prepared to read papers across all of these areas and I'm hoping to delve deeper into these research areas in the next decade or so.

Also, Lisa Cohen from my lab visited the course with our MinION sequencer and we finally generated a bunch of real genomic data from two isolates! The genomes each resolved into two contigs, and we hope to publish them soon. You can read Lisa's extremely thorough blog post on the Nanopore sequencer here and also see the tutorial she put together for dealing with nanopore data, here

A personal highlight: at the end of the course, the TAs gave me the Tenure Deadbeat award, for "the most disturbing degeneration from faculty to student and hopefully back." It's gonna go on my office wall.

Surely something wasn't great? Anything?


  • six weeks of cafeteria food was rough.

  • six weeks of dorm life was somewhat rough (ameliorated by an awesome roommate, Mike B. from Thea Whitman's lab).

  • there was no air conditioning (really, no airflow at all) in my dorm room. And it gets very hot and humid in Woods Hole at times. Doooooom.

    Luckily I was exhausted most of the time because otherwise getting to sleep would have been impossible instead of merely very difficult.

  • my family was in town for three weeks, but I couldn't spend much time with them, and I missed them when they weren't in town!

  • my e-mail inbox is now a complete and utter disaster.

...but all of these were more or less expected.

Interestingly, I ignored Twitter and much of my usual "net monitoring" for the summer and kind of enjoyed being in my little bubble. I doubt I'll be able to keep it up, though.

In sum

  • Awesome experience.
  • Learned much microbiology.
  • Need to learn more chemistry!

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