1.4. Microbial interactions can also be investigated from a purely metabolic perspective
A “reverse ecology” approach can be used to infer pairwise ecological interactions between specific microbes based on their cellular metabolisms inferred in silico from whole genome data. For example, complementarity in metabolite requirement and production in different microbes pointed to host-parasite interactions11. A similar strategy has been used to predict competition and mutualisms in bacteria12. Alternatively, metagenomic approaches can be applied to investigate the functioning of the whole community as an integrated metabolism, analysing functions that are distributed among interacting species and identifying those taxa that carry out specific functions for the whole community. Such cooperative interactions could be more important than previously thought, determining community assembly and promoting the co-occurrence of taxa that exchange metabolites, particularly in nutritionally challenging habitats13. Cooperative interactions do not necessarily need physical contact, and therefore metagenomics of samples including important co-occurring taxa, together with relevant Single Amplified Genomes (SAGs) (Figure 2), can provide evidence that cells are interacting.
Figure 2. Single Cell Genomics workflow designed for this project.
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