Lab leader: Kalin Vetsigian, Assistant Professor of Bacteriology
Nothing in biology makes sense except in light of evolution. At the same time, little in evolution makes sense outside the community context. Due to phenotypic interactions and genetic exchange, both selection and mutation pressures on organisms depend on what other organisms are around. To improve our understanding of the collective aspects of evolution, our lab studies the dynamics of microbial interactions in natural and synthetic microbial communities. We are primarily focused on bacteria from the genus Streptomyces because they are prolific producers of secondary metabolites, which mediate interactions, and because the genetic determinants of these interactions are hierarchically modular and subject to horizontal gene transfer. We develop protocols for quantifying the community dynamics at the phenotypic and genetic levels, and seek simplified theoretical models that reproduce aspects of the experimentally measured dynamics.
- Ye Xu and Kalin Vetsigian, Phenotypic variability and community interactions of germinating Streptomyces spores. Scientific Reports 7, Article number: 699 (2017).
- Kalin Vetsigian, Diverse modes of eco-evolutionary dynamics in communities of antibiotic-producing microorganisms. Nature Ecology & Evolution 1, 0189 (2017).
- Erik S. Wright and Kalin Vetsigian, DesignSignatures: a tool for designing primers that yield amplicons with distinct signatures, Bioinformatics (2016).
- David Baum and Kalin Vetsigian, An experimental framework for generating evolvable chemical systems in the laboratory. Origins of Life and Evolution of Biospheres doi:10.1007/s11084-016-9526-x (2016).
- Erik S. Wright and Kalin Vetsigian, Quality filtering of Illumina index reads mitigates sample cross-talk. BMC Genomics, pp. 1–7, Nov (2016).
- Wright, E. & Vetsigian, K., Inhibitory interactions promote frequent bistability among competing bacteria. Nature Communications 7, Article number: 11274 (2016).
- Kelsic, E., Zhao, J., Vetsigian, K.# & Kishony, R.#. Counteraction of antibiotic production and degradation stabilizes microbial communities. Nature 521, 516-519 (2015). #corresponding authors
- Chait, R., Vetsigian, K. H. & Kishony, R. What counters antibiotic resistance in nature? Nat. Chem. Biol. 8, 2–5 (2012).
- Vetsigian, K. H., Jajoo, R. & Kishony, R. Structure and evolution of Streptomyces interaction networks in soil and in silico. PLoS Biol. 9, e1001184 (2011).
- Vetsigian, K. H. & Goldenfeld, N. Genome rhetoric and the emergence of compositional bias. Proc. Natl. Acad. Sci. U.S.A. 106, 215–220 (2009).
- DeLuna, A. et al. Exposing the fitness contribution of duplicated genes. Nat. Genet. 40, 676–681 (2008).
- Bollenbach, T., Vetsigian, K. H. & Kishony, R. Evolution and multilevel optimization of the genetic code. Genome Res. 17, 401–404 (2007).
- Vetsigian, K. H., Woese, C. & Goldenfeld, N., Collective evolution and the genetic code, PNAS 2006 103 (28) 10696-10701 (2006)
- Vetsigian, K. and Goldenfeld, N., Global divergence of microbial genome sequences mediated by propagating fronts. PNAS 102 (20) 7332-7337 (2005 ).
- Vetsigian, K. H. & Goldenfeld, N. Computationally efficient phase-field models with interface kinetics. Phys Rev E 68, 060601 (2003).