University of Oregon


Microbial Communities Workshop

PANO_20170707_175612_Trieste Italy_3

Last month, META Center scientist Raghuveer Parthasarathy attended and spoke at a conference on Microbial Communities — the “Joint ICGEB-ICTP-APCTP Workshop on Systems Biology and Molecular Economy of Microbial Communities”. The workshop brought ecologists, microbiologists, physicists, plant biologists, and others to the the ICTP (The Abdus Salam International Center for Theoretical Physics), a well-known research institute in Trieste, Italy, whose areas of interest have expanded in recent years to include Quantitative Life Sciences.
The meeting was fascinating, and several recurring themes intersected META research interests.
Several talks and conversations noted the importance of spatial structure on multi-species coexistence and interactions, as well as our ignorance of spatial structure from both empirical and theoretical perspectives. Parthasarathy’s talk described imaging-based experiments on gut microbial communities, and especially the insights that direct observation can give into mechanisms of inter-species interactions and responses to perturbations like antibiotics, a major conclusion of which is that the spatial organization of gut microbial species is a key determinant of their population dynamics. Both Parthasarathy, looking at the zebrafish intestine, and Jonas Cremer (UCSD), who constructs fluidic devices to mimic intestinal flow structure, emphasized that the gut is a vigorously churned, high-flow environment, and its physical processes are major influences on resident microbes.
In contrast, several talks, for example from Workshop co-organizer Daniel Segrè (Boston University), focused on metabolic networks connecting microbial species. To what extent can we understand a microbial community as a “bag of enzymes?” This question spurred lots of discussion; the answer remains unknown. In terms of technique, computational tools for modeling metabolic networks are becoming increasingly powerful, incorporating for example diffusion of metabolites. Given the well-cataloged collection of zebrafish gut microbiota that META has assembled, it seems like integrating this information with computational metabolic analysis could lead to insights.
Several speakers described elegant experiments and theories on minimal systems, asking for example how multi-species coexistence can emerge from chemically simple environments. Jeff Gore (MIT) and Alvaro Sanchez (Yale), for example, each reported on combinatorial studies of soil microbes in different sorts of controlled combinations or nutrient environments. This touches the general question of “assembly rules” for microbial communities, which is relevant for META’s gut communities as well.
The impact of antibiotics on microbial communities was discussed in several talks, in contexts ranging from clinical studies tracing lineages of antibiotic-resistant bacteria (Roy Kishony, Technion, Israel) to lab studies examining the coexistence of differently resistant strains (Kalin Vetsigian, U. Wisconsin). As mentioned, antibiotics are already being examined by META researchers, and the topic is fascinating, important, and also intersects issues of spatial structure.
The week was densely packed, and talks and discussions also explored things like biofilms, plants, marine microbes, and more. The diversity of topics was mirrored in the diversity of participants, who came from a remarkable variety of countries. One of the ICTP’s aims is fostering science in developing countries, which includes bringing faculty and students to workshops like this (as well as longer-term visits).
Parthasarathy also notes that Trieste, perched on the Adriatic coast, is a gorgeous town. (The photo above shows the view from the ICTP guest housing.) Of course, it can’t beat the location of, META’s microbial ecology symposia, but it’s a close second.


August 3, 2017





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