Similarly to the way computer simulations are used to forecast the weather, COMETS simulates how microbial communities and their surrounding environment change of over time, as a consequence of metabolic activity. In COMETS, metabolic networks of individual species are used to predict growth and the flow of molecules across the membrane. This is complemented by equations that describe how biomass and metabolites propagate in space, enabling complex virtual experiments with multiple species. … [Read more...]

Species- and Site-Specific Genome Editing in Complex Bacterial Communities A novel toolset and approach to modify bacterial genomes within complex laboratory consortia. Rubin, BE; Diamond, S; Cress, BF; Crits-Christoph A, Shivram H, He C, Xu M, Zhou Z, Smith SJ, Smock DC, Tang K, Owens TK, Krishnappa N, Sachdeva R, Barrangou R, Deutschbauer AM, Banfield JF, Doudna JA. (2021) Targeted Genome Editing of Bacteria Within Microbial Communities. Nature Microbiology 2021 [DOI]: … [Read more...]

The Science In this manuscript we study a key, but poorly understood determinant of microbial ecosystem structure: the number of different molecules available as substrates in the environment. How does a microbiome respond to a more diverse set of available food sources? How does a marine microbiome respond to diverse pollutants? These are very difficult questions that will require years of biomedical and field research. What is stunning, however, is that we lack an even basic understanding … [Read more...]

Plant root systems typically contain diverse microorganisms. Researchers have observed a rare exception to this rule, in which the root microbiome is dominated by a single bacterial genus. Image of Sorghum field courtesy of Dr. Dawn Chiniquy Sorghum bicolor, also known as sorghum, is an important bioenergy crop in the United States and staple in other parts of the world. Sorghum is often planted on poor agricultural land and arid climates due to its ability to grow with minimal … [Read more...]