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JGM, SS1, Humans, Staphylococcal Infections, Staphylococcus epidermidis, Clustered Regularly Interspaced Short Palindromic Repeats, Transcriptome, Skin





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This work was funded by the National Institutes of Health (DP2 GM126893-01 and K22 AI119231-01). M.S. is funded by the National Institutes of Health (1F30DE027870-01 and T90-DE022526). J.O. is additionally supported by the NIH (1U54NS105539, 1 U19 AI142733, 1 R21 AR075174, and 1 R43 AR073562), the Department of Defense (W81XWH1810229), the NSF (1853071), the American Cancer Society, and Leo Foundation.


Staphylococcus epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, mainly due to the difficulties of genetic manipulation, precluding high-throughput functional profiling of this species. To probe the versatility of S. epidermidis to survive across a diversity of environmental conditions, we developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA sequencing) across 24 diverse conditions and piloted a droplet-based CRISPRi approach to enhance throughput and sensitivity. We identified putative essential genes, importantly revealing amino acid metabolism as crucial to survival across diverse environments, and demonstrated the importance of trace metal uptake for survival under multiple stress conditions. We identified pathways significantly enriched and repressed across our range of stress and nutrient-limited conditions, demonstrating the considerable plasticity of S. epidermidis in responding to environmental stressors. Additionally, we postulate a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, such as those encountered on human skin. Finally, we examined the survival of S. epidermidis under acid stress and hypothesize a role for cell wall modification as a vital component of the survival response under acidic conditions. Taken together, this study integrates large-scale CRISPRi and transcriptomics data across multiple environments to provide insights into a keystone member of the human skin microbiome. Our results additionally provide a valuable benchmarking analysis for CRISPRi screens and are a rich resource for other staphylococcal researchers.


This is an open- access article distributed under the terms of the Creative Commons Attribution 4.0 International license.