Microbial communities profoundly influence global biogeochemical cycles and human life. Understanding their wiring is crucial to manage, rationally manipulate, or de novo assemble communities for environmental, industrial or medical applications. However, studying the complex web of microbial interactions and how they are affected by the spatial structure of the community is experimentally challenging. A crucial yet poorly understood aspect of microbial interactions is the spatial dimension. For example, in a biofilm or the intestinal mucosae in the human gut, bacteria find themselves in a highly structured environment where each cell is exposed to a unique set of environmental factors depending on its position in the community and its immediate neighbours. To better understand microbial communities, we need to know how individual cells interact with each other and how molecular and cellular processes in individuals scale up to determine the structure and activity of the entire community. The goal of the proposed research was to study microbial interactions at multiple levels, from the molecular processes involved, to the effects of these interactions on survival and growth, to how they are affected by environmental conditions and the spatial arrangement of cells.
To achieve this, we worked with a synthetic community consisting of two members of the human gastrointestinal microbiota, the commensal gut microbe Escherichia coli and the lactic acid bacterium Lactobacillus plantarum. L. plantarum is widely used in food fermentation and has been reported to have a number of health benefits. As is typical for lactic acid bacteria, L. plantarum has multiple amino acid and vitamin auxotrophies; however, these may be compensated for by co-culturing it with E. coli which produces the required compounds. Recent mathematical models suggest that the two species engage in diverse metabolic interactions in the gut and that these interactions drastically differ as a function of oxygen availability.
The project established the synthetic community of the two gut microbial strains E. coli and L. plantarum as a model system for future studies by us and others. By profiling different growth conditions and performing follow-up experiments in a spatially structured setting, we found conditions in which the two strains interact in a mutualistic way, i.e. both are benefiting of the presence of the other strain. We also made an interesting discovery where we found that L. plantarum can assume a “zombie” state in which it is itself unable to grow but metabolically active enough to support E. coli’s growth over extended periods of time. Such a phenomenon has, to the best of our knowledge, not yet been described before for any bacterial species and our research group is continuing the research on this project.
