Grice, E. A. & Segre, J. A. The pores and skin microbiome. Nat. Rev. Microbiol. 9, 244–253 (2011).
Kloos, W. E. & Schleiferi, Ok. H. Isolation and characterization of Staphylococci from human pores and skin. Int. J. Syst. Bacteriol. 25, 62–79 (1975).
Kloos, W. E. & Musselwhite, M. S. Distribution and persistence of Staphylococcus and Micrococcus species and different cardio micro organism on human pores and skin. Appl. Microbiol. 30, 381–385 (1975).
Oh, J. et al. Biogeography and individuality form perform within the human pores and skin metagenome. Nature 514, 59–64 (2014).
Oh, J. et al. Temporal stability of the human pores and skin microbiome. Cell 165, 854–866 (2016).
Zhou, W. et al. Host-specific evolutionary and transmission dynamics form the useful diversification of Staphylococcus epidermidis in human pores and skin. Cell 180, 454–470 e418 (2020).
Bruggemann, H., Salar-Vidal, L., Gollnick, H. P. M. & Lood, R. A Janus-faced bacterium: host-beneficial and -detrimental roles of Cutibacterium acnes. Entrance. Microbiol. 12, 673845 (2021).
Paetzold, B. et al. Pores and skin microbiome modulation induced by probiotic options. Microbiome 7, 95 (2019).
Stacy, A. & Belkaid, Y. Microbial guardians of pores and skin well being. Science 363, 227–228 (2019).
Brown, M. M. & Horswill, A. R. Staphylococcus epidermidis—pores and skin good friend or foe? PLoS Pathog. 16, e1009026 (2020).
Luqman, A. et al. Hint amines produced by pores and skin micro organism speed up wound therapeutic in mice. Commun. Biol. 3, 277 (2020).
Luqman, A. et al. The neuromodulator-encoding sadA gene is extensively distributed within the human pores and skin microbiome. Entrance. Microbiol. 11, 573679 (2020).
Conlan, S. et al. Staphylococcus epidermidis pan-genome sequence evaluation reveals variety of pores and skin commensal and hospital infection-associated isolates. Genome Biol. 13, R64 (2012).
Espadinha, D. et al. Distinct phenotypic and genomic signatures underlie contrasting pathogenic potential of Staphylococcus epidermidis clonal lineages. Entrance. Microbiol. 10, 1971 (2019).
Meric, G. et al. Ecological overlap and horizontal gene switch in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol. Evol. 7, 1313–1328 (2015).
Lee, J. Y. H. et al. International unfold of three multidrug-resistant lineages of Staphylococcus epidermidis. Nat. Microbiol. 3, 1175–1185 (2018).
Mansson, E., Hellmark, B., Sundqvist, M. & Soderquist, B. Sequence kinds of Staphylococcus epidermidis related to prosthetic joint infections are usually not current within the laminar airflow throughout prosthetic joint surgical procedure. APMIS 123, 589–595 (2015).
Lomholt, H. B. & Kilian, M. Inhabitants genetic evaluation of Propionibacterium acnes identifies a subpopulation and epidemic clones related to pimples. PLoS ONE 5, e12277 (2010).
McDowell, A., Nagy, I., Magyari, M., Barnard, E. & Patrick, S. The opportunistic pathogen Propionibacterium acnes: insights into typing, human illness, clonal diversification and CAMP issue evolution. PLoS ONE 8, e70897 (2013).
Scholz, C. F., Jensen, A., Lomholt, H. B., Bruggemann, H. & Kilian, M. A novel high-resolution single locus sequence typing scheme for combined populations of Propionibacterium acnes in vivo. PLoS ONE 9, e104199 (2014).
Dagnelie, M. A. et al. Lower in variety of Propionibacterium acnes phylotypes in sufferers with extreme pimples on the again. Acta Derm. Venereol. 98, 262–267 (2018).
Lomholt, H. B., Scholz, C. F. P., Bruggemann, H., Tettelin, H. & Kilian, M. A comparative research of Cutibacterium (Propionibacterium) acnes clones from pimples sufferers and wholesome controls. Anaerobe 47, 57–63 (2017).
McDowell, A. et al. An expanded multilocus sequence typing scheme for Propionibacterium acnes: investigation of ‘pathogenic’, ‘commensal’ and antibiotic resistant strains. PLoS ONE 7, e41480 (2012).
McDowell, A. et al. A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterization of kind I cell surface-associated antigens. Microbiology 157, 1990–2003 (2011).
Nakase, Ok., Hayashi, N., Akiyama, Y., Aoki, S. & Noguchi, N. Antimicrobial susceptibility and phylogenetic evaluation of Propionibacterium acnes remoted from pimples sufferers in Japan between 2013 and 2015. J. Dermatol. 44, 1248–1254 (2017).
Nakase, Ok. et al. Characterization of pimples sufferers carrying clindamycin-resistant Cutibacterium acnes: a Japanese multicenter research. J. Dermatol. 47, 863–869 (2020).
O’Neill, A. M. et al. Identification of a human pores and skin commensal bacterium that selectively kills Cutibacterium acnes. J. Make investments. Dermatol. 140, 1619–1628 (2020).
Christensen, G. J. et al. Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic foundation. BMC Genomics 17, 152 (2016).
Wang, Y. et al. Staphylococcus epidermidis within the human pores and skin microbiome mediates fermentation to inhibit the expansion of Propionibacterium acnes: implications of probiotics in pimples vulgaris. Appl. Microbiol. Biotechnol. 98, 411–424 (2014).
Ahle, C. M. et al. Staphylococcus saccharolyticus: an missed human pores and skin colonizer. Microorganisms 8, 1105 (2020).
Ahle, C. M. et al. Comparability of three amplicon sequencing approaches to find out staphylococcal populations on human pores and skin. BMC Microbiol. 21, 221 (2021).
Hanssen, A. M. et al. Localization of Staphylococcus aureus in tissue from the nasal vestibule in wholesome carriers. BMC Microbiol. 17, 89 (2017).
Rohde, H. et al. Detection of virulence-associated genes not helpful for discriminating between invasive and commensal Staphylococcus epidermidis strains from a bone marrow transplant unit. J. Clin. Microbiol. 42, 5614–5619 (2004).
Gotz, F., Perconti, S., Popella, P., Werner, R. & Schlag, M. Epidermin and gallidermin: Staphylococcal lantibiotics. Int. J. Med. Microbiol. 304, 63–71 (2014).
Byrd, A. L., Belkaid, Y. & Segre, J. A. The human pores and skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018).
Otto, M. Staphylococcus epidermidis—the ‘unintended’ pathogen. Nat. Rev. Microbiol. 7, 555–567 (2009).
McLaughlin, J. et al. Propionibacterium acnes and pimples vulgaris: new insights from the mixing of inhabitants genetic, multi-omic, biochemical and host-microbe research. Microorganisms 7, 128 (2019).
Mayslich, C., Grange, P. A. & Dupin, N. Cutibacterium acnes as an opportunistic pathogen: an replace of its virulence-associated elements. Microorganisms 9, 303 (2021).
Cobian, N., Garlet, A., Hidalgo-Cantabrana, C. & Barrangou, R. Comparative genomic analyses and CRISPR-Cas characterization of Cutibacterium acnes present insights into genetic variety and typing purposes. Entrance. Microbiol. 12, 758749 (2021).
Barnard, E. et al. Porphyrin manufacturing and regulation in cutaneous propionibacteria. mSphere 5, e00793-19 (2020).
Spittaels, Ok. J. et al. Porphyrins produced by acneic Cutibacterium acnes strains activate the inflammasome by inducing Ok(+) leakage. iScience 24, 102575 (2021).
Dagnelie, M. A. et al. Cutibacterium acnes phylotypes variety loss: a set off for pores and skin inflammatory course of. J. Eur. Acad. Dermatol Venereol. 33, 2340–2348 (2019).
Nakatsuji, T. et al. Antimicrobials from human pores and skin commensal micro organism shield in opposition to Staphylococcus aureus and are poor in atopic dermatitis. Sci. Transl. Med. 9, eaah4680 (2017).
Leyden, J. J., Marples, R. R. & Kligman, A. M. Staphylococcus aureus within the lesions of atopic dermatitis. Br. J. Dermatol. 90, 525–530 (1974).
Tauber, M. et al. Staphylococcus aureus density on lesional and nonlesional pores and skin is strongly related to illness severity in atopic dermatitis. J. Allergy Clin. Immunol. 137, 1272–1274 e1273 (2016).
Kellner, R. et al. Gallidermin: a brand new lanthionine-containing polypeptide antibiotic. Eur. J. Biochem. 177, 53–59 (1988).
Vuong, C. et al. Regulated expression of pathogen-associated molecular sample molecules in Staphylococcus epidermidis: quorum-sensing determines pro-inflammatory capability and manufacturing of phenol-soluble modulins. Cell Microbiol. 6, 753–759 (2004).
Queck, S. Y. et al. RNAIII-independent goal gene management by the agr quorum-sensing system: perception into the evolution of virulence regulation in Staphylococcus aureus. Mol. Cell 32, 150–158 (2008).
Olson, M. E. et al. Staphylococcus epidermidis agr quorum-sensing system: sign identification, cross discuss, and significance in colonization. J. Bacteriol. 196, 3482–3493 (2014).
Peng, P. et al. Impact of co-inhabiting coagulase damaging Staphylococci on S. aureus agr quorum sensing, host issue binding, and biofilm formation. Entrance. Microbiol. 10, 2212 (2019).
Williams, M. R. et al. Quorum sensing between bacterial species on the pores and skin protects in opposition to epidermal harm in atopic dermatitis. Sci. Transl. Med. 11, eaat8329 (2019).
Todd, O. A. et al. Candida albicans augments Staphylococcus aureus virulence by partaking the staphylococcal agr quorum sensing system. mBio 10, e00910-19 (2019).
Ebner, P. et al. Lantibiotic manufacturing is a burden for the manufacturing staphylococci. Sci. Rep. 8, 7471 (2018).
Rendboe, A. Ok. et al. The Epidome—a species-specific strategy to evaluate the inhabitants construction and heterogeneity of Staphylococcus epidermidis colonization and an infection. BMC Microbiol. 20, 362 (2020).
Bolyen, E. et al. Reproducible, interactive, scalable and extensible microbiome information science utilizing QIIME 2. Nat. Biotechnol. 37, 852–857 (2019).
Callahan, B. J. et al. DADA2: Excessive-resolution pattern inference from Illumina amplicon information. Nat. Strategies 13, 581–583 (2016).
McMurdie, P. J. & Holmes, S. phyloseq: an R bundle for reproducible interactive evaluation and graphics of microbiome census information. PLoS ONE 8, e61217 (2013).
Wickham H. ggplot2: Elegant Graphics for Information Evaluation (Springer-Verlag New York, 2009).
Warnes GRB, B. et al. gplots: Numerous R Programming Instruments for Plotting Information (2020).
Treangen, T. J., Ondov, B. D., Koren, S. & Phillippy, A. M. The Harvest suite for speedy core-genome alignment and visualization of 1000’s of intraspecific microbial genomes. Genome Biol. 15, 524 (2014).
Thomsen, M. C. et al. A bacterial evaluation platform: an built-in system for analysing bacterial entire genome sequencing information for scientific diagnostics and surveillance. PLoS ONE 11, e0157718 (2016).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an internet instrument for phylogenetic tree show and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
Eren, A. M. et al. Neighborhood-led, built-in, reproducible multi-omics with anvi’o. Nat. Microbiol. 6, 3–6 (2021).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a versatile trimmer for Illumina sequence information. Bioinformatics 30, 2114–2120 (2014).
Patro, R., Duggal, G., Love, M. I., Irizarry, R. A. & Kingsford, C. Salmon offers quick and bias-aware quantification of transcript expression. Nat. Strategies 14, 417–419 (2017).
Soneson, C., Love, M. I. & Robinson, M. D. Differential analyses for RNA-seq: transcript-level estimates enhance gene-level inferences. F1000Res 4, 1521 (2015).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq information with DESeq2. Genome Biol. 15, 550 (2014).
Zhu, A., Ibrahim, J. G. & Love, M. I. Heavy-tailed prior distributions for sequence rely information: eradicating the noise and preserving massive variations. Bioinformatics 35, 2084–2092 (2019).
Wei, T. & Simko, V. R bundle ‘corrplot’: Visualization of a Correlation Matrix. model 0.90 (2021).
Lin, H. & Peddada, S. D. Evaluation of compositions of microbiomes with bias correction. Nat. Commun. 11, 3514 (2020).
Kolde, R. pheatmap: Fairly Heatmaps. model 1.0.12. (2019).
Blighe, Ok., Rana, S. & Lewis, M. EnhancedVolcano: publication-ready volcano plots with enhanced colouring and labeling. model 1.8.0 (2020).