Biogeographical Landscape of the Human Face Skin Microbiome Viewed in High Definition


  • Michael Brandwein
  • Garold Fuks
  • Avigail Israel
  • Emmilia Hodak
  • Fareed Sabbah
  • Doron Steinberg
  • Zvi Bentwich
  • Noam Shental Department of Mathematics and Computer Science, The Open University of Israel, POB 808, Raanana 4353701, Israel
  • Shiri Meshner Cutaneous Microbiology Laboratory, The Skin Research Institute, The Dead Sea and Arava Science Center, Masada 8693500, Israel



skin microbiome, facial microbiome, 3D carto­graphy, Cutibacterium acnes, Staphylococcus epidermidis, Staphylococcus aureus


The bacterial community that colonizes the human face imparts physiochemical and physiological effects on the facial skin. These skin-microbe interactions impact dermatological, cosmetic and skincare applications due to the centrality of the human face in daily interactions. However, fine-scale characterization of the human face skin microbiome is lacking. Using 16S rRNA sequencing and 3D cartography, this study plotted and characterized the facial skin microbiome in high- definition, based on 1,649 samples from 12 individuals. Analysis yielded a number of novel insights, including that of the relative uniformity of skin microbiome composition within skin sites, site localization of certain microbes, and the interpersonal variability of the skin microbiome. The results show that high-resolution topographical mapping of the skin microbiome is a powerful tool for studying the human skin microbiome. Despite a decade of skin microbiome research, there is still much to be discovered.


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Brandwein M, Fuks G, Israel A, Nejman D, Straussman R, Hodak E, et al. Identification of a unique Staphylococcus aureus ribosomal signature in severe atopic dermatitis. Br J Dermatol 2018; 179: 1222-1224. DOI:

Gimblet C, Meisel JS, Loesche MA, Cole SD, Horwinski J, Novais FO, et al. Cutaneous leishmaniasis induces a transmissible dysbiotic skin microbiota that promotes skin inflammation. Cell Host Microbe 2017; 22: 13-24.e14. DOI:

Nakamura Y, Oscherwitz J, Cease KB, Chan SM, Muñoz-Planillo R, Hasegawa M, et al. Staphylococcus δ-toxin induces allergic skin disease by activating mast cells. Nature 2013; 503: 397-401. DOI:

Brandwein M, Katz I, Katz A, Kohen R. Beyond the gut: skin microbiome compositional changes are associated with BMI. Hum Microb J 2019; 13: 100063. DOI:

Two AM, Nakatsuji T, Kotol PF, Arvanitidou E, Du-Thumm L, Hata TR, et al. The cutaneous microbiome and aspects of skin antimicrobial defense system resist acute treatment with topical skin cleansers. J Invest Dermatol 2016; 136: 1950-1954. DOI:

SanMiguel AJ, Meisel JS, Horwinski J, Zheng Q, Bradley CW, Grice EA. Antiseptic agents elicit short-term, personalized, and body site-specific shifts in resident skin bacterial communities. J Invest Dermatol 2018; 138: 2234-2243. DOI:

Totte JE, van Doorn MB, Pasmans SG. Successful treatment of chronic Staphylococcus aureus-related dermatoses with the topical endolysin Staphefekt SA. 100: a report of 3 cases. Case Rep Dermatol 2017; 9: 19-25. DOI:

Byrd AL, Belkaid Y, Segre JA. The human skin microbiome. Nat Rev Microbiol 2018; 16: 143. DOI:

Grice EA, Segre JA. The skin microbiome. Nat Rev Microbiol 2011; 9: 244-253. DOI:

Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, et al. Topographical and temporal diversity of the human skin microbiome. Science 2009; 324: 1190-1192. DOI:

Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, et al. Topographic diversity of fungal and bacterial communities in human skin. Nature 2013; 498: 367-370. DOI:

Oh J, Byrd AL, Deming C, Conlan S, Kong HH, Segre JA, et al. Biogeography and individuality shape function in the human skin metagenome. Nature 2014; 514: 59-64. DOI:

Bouslimani A, Porto C, Rath CM, Wang M, Guo Y, Gonzalez A, et al. Molecular cartography of the human skin surface in 3D. Proc Natl Acad Sci U S A 2015; 112: E2120-E2129. DOI:

Brandwein M, Fuks G, Israel A, Al-Ashhab A, Nejman D, Straussman R, et al. Temporal stability of the healthy human skin microbiome following dead sea climatotherapy. Acta Derm Venereol 2018; 98: 256-261. DOI:

Fuks G, Elgart M, Amir A, Zeisel A, Turnbaugh PJ, Soen Y, et al. Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling. Microbiome 2018; 6: 17. DOI:

Nejman D, Livyatan I, Fuks G, Gavert N, Zwang Y, Geller LT, et al. The human tumor microbiome is composed of tumor type-specific intracellular bacteria. Science 2020; 368: 973-980. DOI: DOI:

Brandwein M, Fuks G, Israel A, Sabbah F, Hodak E, Szitenberg A, et al. Skin microbiome compositional changes in atopic dermatitis patients accompany dead sea climatotherapy. Photochem Photobiol 2019; 95: 1446-1453. DOI:

DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72: 5069-5072. DOI:

Cole JR, Chai B, Farris RJ, Wang Q, Kulam S, McGarrell DM, et al. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 2005; 33: D294-D296. DOI:

TEAM RC. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. [Accessed December 18, 2019] Available from: http://www.R-project org, 2010.

Oksanen J, Kindt R, Legendre P, O'Hara B, Stevens MHH, Oksanen MJ, et al. The vegan package. Community Ecology Package 2007; 10: 631-637.

McMurdie PJ, Holmes S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS One 2013; 8: e61217. DOI:

Protsyuk I, Melnik AV, Nothias L-F, Rappez L, Phapale P, Aksenov AA, et al. 3D molecular cartography using LC-MS facilitated by Optimus and'ili software. Nat Protoc 2018; 13: 134. DOI:

Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, Gonzalez A, Stombaugh J, et al. Moving pictures of the human microbiome. Genome Biol 2011; 12: 1-8. DOI:

Oh J, Byrd AL, Park M, Kong HH, Segre JA, Program NCS. Temporal stability of the human skin microbiome. Cell 2016; 165: 854-866. DOI:

Gallo RL. Human skin is the largest epithelial surface for interaction with microbes. J Invest Dermatol 2017; 137: 1213-1214. DOI:

Welch JLM, Ramírez-Puebla ST, Borisy GG. Oral microbiome geography: micron-scale habitat and niche. Cell Host Microbe 2020; 28: 160-168. DOI:

Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, et al. Three-dimensional microbiome and metabolome cartography of a diseased human lung. Cell Host Microbe 2017; 22: 705-716.e4. DOI:

Grice EA, Kong HH, Renaud G, Young AC, Bouffard GG, Blakesley RW, et al. A diversity profile of the human skin microbiota. Genome Res 2008; 18: 1043-1050. DOI:

Nakatsuji T, Chiang H-I, Jiang SB, Nagarajan H, Zengler K, Gallo RL. The microbiome extends to subepidermal compartments of normal skin. Nat Commun 2013; 4: 1431. DOI:

Flores GE, Caporaso JG, Henley JB, Rideout JR, Domogala D, Chase J, et al. Temporal variability is a personalized feature of the human microbiome. Genome Biol 2014; 15: 531. DOI:

Brandwein M, Horev A, Bogen B, Fuks G, Israel A, Shalom G, et al. The role of sweat in the composition of skin microbiome: lessons learned from patients with congenital insensitivity to pain with anhidrosis. J Eur Acad Dermatol Venereol 2020; 34: e183-e186. DOI:

Engen SA, Rørvik GH, Schreurs O, Blix IJ, Schenck K. The oral commensal Streptococcus mitis activates the aryl hydrocarbon receptor in human oral epithelial cells. Int J Oral Sci 2017; 9: 145-150. DOI:

Mergenhagen KA, Starr KE, Wattengel BA, Lesse AJ, Sumon Z, Sellick JA. Determining the utility of methicillin-resistant Staphylococcus aureus nares screening in antimicrobial stewardship. Clin Infect Dis 2020; 71: 1142-1148. DOI:

Oh J, Conlan S, Polley EC, Segre JA, Kong HH. Shifts in human skin and nares microbiota of healthy children and adults. Genome Med 2012; 4: 77. DOI:




How to Cite

Brandwein, M., Fuks, G., Israel, A., Hodak, E., Sabbah, F., Steinberg, D., Bentwich, Z., Shental, N., & Meshner, S. (2021). Biogeographical Landscape of the Human Face Skin Microbiome Viewed in High Definition. Acta Dermato-Venereologica, 101(11), adv00603.