library_construction_protocol: One GEM well of a Chromium single cell chip was used targeting a collection of 5000 cells contained NA19160 control, NA18856 control, and NA18855 strain-treatment cells combined in equal proportions. Single cell cDNA libraries were established following the 10x Genomics Chromium Single Cell protocol. In brief, the RNA of the captured cells was released by lysis, barcoded via a reverse transcription process, and amplified to produce a gene expression library. The library was sequenced to 100 base pairs, paired-end on one lane using the Illumina HiSeq4000 at the University of Chicago Genomics Core Facility according to manufacturer instructions.