Single-cell omics applied to micro-organisms could become a gold standard in microbial ecology. A knowledge upshot is
expected in microbial interactions and eco-evolutionary boundaries through the enabling of mechanistic characterization
of populations and community assembly processes. Currently, the use of meta-omics and single-cell omics on the same
sample appears to be the best option, combining the strengths of the two approaches: (i) high throughput and alpha/beta
diversity and (ii) fine-scale analysis by scWGS and/or scRNAseq.
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