Cysteine dependence of Lactobacillus iners is a potential therapeutic target for vaginal microbiota modulation

Compressed directories containing code and data files sufficient to reproduce analysis from Bloom et al paper on Lactobacillus iners (Nature Microbiology). An earlier, non-peer-reviewed manuscript version containing largely the same analysis was posted as a pre-print in bioRxiv at (https://doi.org/10.1101/2021.06.12.448098). Three compressed directory for analyses of:

1. Vaginal Lactobacillus genome catalog characterization and gene content analysis.
2. Analysis of relationship between cervicovaginal microbiota composition and cysteine concentrations in vaginal fluid from a South African cohort
3. Analysis of results of in vitro mixed culture competition assays including:
   1. Pairwise competition between L. iners and Lactobacillus crispatus in Lactobacillus MRS broth containing L-cysteine +/- S-methyl-L-cysteine (SMC)
   2. Defined bacterial-vaginosis (BV)-like communities including L. iners, L. crispatus, and BV-associated species Gardnerella vaginalis, Prevotella bivia, and Atopobium (Fannyhessea) vaginae cultured in S-broth with or without SMC and/or metronidazole.