Harvard MSI symposium

2014 Harvard MSI symposium

I went to the annual Harvard Microbial Sciences Initiative symposium today for the forth year in a row. There are always some great talks at this event.

Harvard MSI is very much centered around microbial communities and social microbiology.  There were many great speakers but I was particularly interested in a talk about about swarming in Proteus mirabilis.

Proteus mirabilis is able to self-recognize cells of the same species using surface-bound proteins and differentiates into hyper-motile large swarming cells able to glide over solid surfaces.

Richard Dawkins at UConn

I have seen Richard Dawkins speak before, but today he came all the way to the UConn campus. His discussion with one of the UConn deans covered many topics–a nice change from a rehearsed talk.  Afterwards I had him sign this flask, since all of my Dawkins books are already signed!

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The Jorgensen Auditorium at UConn was filled to capacity.


Purple biofilm gives Bacillus subtilis a run for its money

Scott Chimileski

Colonies formed by purple soil isolate on agar medium.

One of the students in the Small World Initiative lab I instruct isolated this very interesting species with an intense purple pigmentation and robust biofilm formation.

We aren’t sure what it is yet, but it shows antimicrobial activity against some other bacterial species and from what research we have done we suspect it may a member of the genus Janthinobacterium.  These organisms produce a purple pigment called violacein.

The media we use contains a chemical to select against fungi, but being astonished by the three dimensional structure of this biofilm we were eager to confirm that it is indeed a bacterium.

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Gram stain of purple soil isolate. Conduced by SWI student Rofina Johnkennedy.

We did a Gram stain, which was a bit challenging considering the wax-like texture of this biofilm. After first failing to break apart he biofilm by aggressive vortexting and pippeting in liquid medium, we found that low power sonication was the most effective method for isolating and staining single cells and groups of cells. And, it is a Gram negative rod.


These colonies had a waxy texture with a clear sheen that reflected light.

How millions of individual seemingly identical and simple cells come together to form such complex structure is truly amazing.  This guy would give Bacillus subtilis a run for it’s money.


That’s a Winogradsky column


I found this Winogradsky column setup for a microbiology class at UConn.  Windogradsky columns are setup with sediment from a pond, and are left to sit for several months allowing gradients and different layers of microorganisms to form similar to those in the natural environment.  This is certainly the most living Winogradsky column I have ever seen.  I am surprised there aren’t fish swimming around at the top.

Collecting soil for the Small World Initiative

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Today I went on a hike on the Nipmuck trail near the Yale Forest in Connecticut to collect soil for an exciting new microbial ecology lab I am teaching.

Scott Chimileski 2014

The course is called Microbe Hunting: Crowd-sourcing the discovery antibiotics and is part of the Small World  Initiative. The Small World Initiative or SWI was designed by a group at Yale University and is an effort to crowdsource the discovery of novel antibiotics to address escalating problem of antibiotic resistance through undergraduate research.

What is different about this course as compared with any other undergraduate lab course is that the students will drive their own research. They will keep lab notebooks, present their data in poster format at the end of the semester, and the data produced across many universities across the country will be compiled and lead to “real” publications.  This same crowdsourcing model has been implemented successfully in other initiatives, such as the SEA-PHAGES project started by the Howard Hughes Medical Institute where students isolate and sequence undiscovered bacteriophages.

Scott Chimileski 2014

So I went on my own winter field trip in order to make a presentation demonstrating how to collect samples, what sorts of things to think about when selecting a sample site, and what information to collect. Hopefully we can isolate some species that produce antibiotics and produce robust biofilms!

The Extracellular Polymeric Substance (EPS) building

CBE Chimileski

Lightning storm over the Center for Biofilm Engineering, Montana State University

I had the opportunity to kick-start a biofilm project in the summer of 2012 at the Center for Biofilm Engineering (CBE) at Montana State University.

This building here is exceptional for a few reasons. First of all it has a very giant noodle sculpture in front of it.  This noodle swings around on the center pole in the wind, and as beautiful spontaneous storms shoot down over the Rocky Mountains through Bozeman on warm summer nights, it gets going pretty good (a great time-lapse subject).

Also, the building is known as “EPS.” Now according to Montana State University this stands for Engineering and Physical Sciences. But, come on, it houses a world class biofilm center …  no one is going to convince me it doesn’t really stand for extracellular polymeric substance!

Anyhow, all I can say is Montana is a wilderness wonderland and the CBE is top-notch in every way. Needless to say I sat with my tripod during this storm for quite some time to get some good lightning shots, but looking back, it was a truly magical moment.