Wednesday, July 24, 2013
I am at the Congress of European Microbiologists (FEMS 2013) in Leipzig http://www2.kenes.com/fems2013/pages/home.aspx. I helped organize a session on modeling, and presented a poster on intraspecific internal nutrient heterogeneity and a talk on bet hedging in yeast. This is a very interesting meeting and I am learning a lot about microbiology. Let me tell you about one thing that stands out to me. You know, there is now a lot of realization on the role of the gut bacteria (microbiome) on human health. A couple of people presented research linking (pretty conclusively in my mind) the biodiversity in the gut to obesity and infection risk. Those are important and interesting problems, but I am not a medical person so my interests are more in the tools they are using. In one experiment they took germ-free mice and inoculated them with various bacteria. Wow! I wish we could do this with our environmental systems. I mean, can I have a few sterile Charles Rivers that I can inoculate with different bacteria? Please? Of course, we can make lab experiments, but those don’t include any of the complexities of the real system. Whole lake experiments can be and are done (e.g. at the Experimental Lake Area in Canada), but there we are limited to simple perturbations – we don’t have direct control of the microbe population. I think because of these types of experimental capabilities (and also availability of funding in the medical area), some of the most exciting advances in microbial ecology in the near future will come from the medical arena. Next stop: Shanghai and Lake Taihu.
Tuesday, July 16, 2013
This Saturday, the Charles River opened for swimming! For the first time in over 50 years we had public swimming. This event was organized by the Charles River Conservancy, who also led the effort to bring swimming back to the river over the past years. My research group has helped out by doing some water quality monitoring at potential (ahem actual!) swimming sites. Of course I had to participate. And you know what? It was wonderfully refreshing! And surprisingly so! I didn’t even realize and I wonder if all those people on the Esplanade realize that there is a cool and refreshing (and swimmable) river just a few feet from where we sweat in the sun. The plan is to do more of this, and I think this would significantly improve the quality of life in Boston!
See the article on the NU news blog here:http://www.northeastern.edu/news/2013/07/love-that-clean-water/
Read the article in the Boston Globe here:http://www.boston.com/metrodesk/2013/07/13/charles-river-opens-for-public-swim-for-first-time-since/4tgCdQ1cONXeN6SPvhe6rI/story.html
Visit the swimming page at the Charles River Conservancy here:http://www.thecharles.org/projects-and-programs/swimmable-charles/
Tuesday, July 9, 2013
I am at DTW on my way back from MEWE in Ann Arbor, which was a very interesting meeting. http://www.mewe2013.org/ There are many areas where people study microbial ecology, including the ocean and the human gut, but also wastewater treatment plants (the “gut of the city”, Tong Zhang). It is interesting to see so many of the same problems (e.g. diversity) and tools (e.g. metagenomics) applied to these different environments. I participated in a session on antibiotic resistance and presented some of my modeling work on the Poudre River (see my post of June 16, 2013) and adaptation to the cost of resistance (see post of November 15, 2012). In this session, there were many very interesting data sets presented from treatment plants and ambient (“receiving”) water systems. Unfortunately they were all from different locations, which limits their utility for modeling. When I was developing my model I was able to take advantage of the large and comprehensive database developed for the Poudre River, and I think we need more of these concerted efforts - testbeds. It brings to mind a recent effort of the environmental engineering community to establish a network of testbed systems across the US (known initially as CLEANER, then WATERS). This effort did not succeed, maybe because it was too big, but it would have been really useful for developing models. Maybe a smaller-scale effort, focused on pharmaceuticals and personal care products (PPCPs) and antibiotic resistance, in one watershed could happen, and it should be pursued! Next stop: FEMS in Leipzig.
Friday, July 5, 2013
Earlier this week I was in Edinburgh for a workshop on microbe modeling. The meeting focused on biofilms and included many presentations of experimental and modeling research. My work is not directly focused on biofilms per se, but there are a lot of the same tools/methods/questions/problems, so I found it very useful. I felt like I got a good overview of where the state-of-the-science is in this area. There is an interesting story about the use of modeling in biofilm science, which I want to briefly outline. It has to do with social conflict in biofilms. Specifically, bacteria in biofilms produce a sort of glue (extracellular polymer substance, EPS), which helps to hold the biofilm together. This is believed to be a public good (i.e. it benefits all cells in the biofilm), but the production is carried out by individual cells. This raises the question why individual cells produce this substance. In other words, why do they not evolve to not produce EPS and grow faster, while taking advantage of the EPS produced by other cells (i.e. why do “cheaters” not evolve). A few years ago, Xavier and Foster (PNAS, 2007) explored this question using a model. They found that, EPS is not a public good, but that it helps the cells that produce it to push up into the high oxygen regions. Subsequently, there have been a number of experimental investigations that have explored this hypothesis, and indeed, confirmed it. For more information see the workshop outline below. I think its an interesting story which illustrates the role of models in moving science forward, at a time scale greater than an individual paper or project. http://www2.ph.ed.ac.uk/~rallen2/epsrcworkshop.html