Strain Library Imaging Protocol (SLIP)

Shi, H., Colavin, A., Lee, T. et al. Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates. Nat Protoc 12, 429–438 (2017). https://doi.org/10.1038/nprot.2016.181

SLIP is a high-throughput, automated single-cell microscopy platform for large bacterial collections, including collections of anaerobic communities and ordered mutant collections. So far, we have imaged dozens of bacterial communities across hundreds of conditions and several genome-scale ordered mutant collections.

Ordered mutant collection assembly

Shiver, A.L., Culver, R., Deutschbauer, A.M. et al. Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria. Nat Protoc 16, 3049–3071 (2021). https://doi.org/10.1038/s41596-021-00531-3

This protocol for diverse human gut commensals enables rapid and low-cost sorting and characterization across transposon insertion libraries.  Transposon libraries where nearly all non-essential genes have been disrupted can be genetically characterized and ordered into arrayed monocultures within 2 weeks.