Skin MicrobiomeElizabeth Grice, PhD

Assistant Professor, Dermatology & MicrobiologyUniversity of Pennsylvania

The ecosystem of the skin• Terminally differentiated keratinocytes (corneocytes)• Average skin temp = 32-33 C• Varied topography: thickness, hair, glands, occlusion

Mary Marples, The Ecology of the Human Skin, 1965 

Grice et al. (2011) Nature Reviews Microbiology

Topography of the skin microbiome

Oh et al. (2014) Nature.

Kingdom‐level diversity of the skin microbiome

K Findley et al. Nature (2013)

Fungal diversity of the skin

The skin virome: lots of “dark matter”

Hannigan et al. mBio 2015 and Hannigan et al. under review

Umbilicus

Toeweb

Scalp

Behind ear

Palm

Forehead

Axilla

Inner elbow

The skin microbiome is surprisingly stable over time

Oh et al. (2016) Cell.

• Generally, same dominant bacteria are present between individuals• The remainder is highly variable

Grice and Segre (2011) Nature Reviews MicrobiologyData from Grice et al (2009) Science

Skin microbiome interpersonal variability

Signatures of individuality are low abundance, shared across sites

Oh et al. (2014) Nature.

Meisel et al J of Investigative Dermatology, 2016 Jackie Meisel

Benchmarking best practices for skin microbiome characterization

Mock community analysis to compare taxonomic result of sequencing approach

Meisel et al J of Investigative Dermatology, 2016

V4 primers exclude Propionibacterium

Meisel et al. J. of Invest. Derm. 2016

V1V3 region allows for increased phylogenetic placement of Staphylococcus species

Meisel et al. J. of Invest. Derm. 2016

Skin Microbiome Summary• Skin is a multi-niche habitat that supports the colonization and

growth of microbes;• Skin site is an important determinant of the dominant colonizing

bacteria and diversity;• Signatures of individuality are apparent in the lower abundance

members;• Temporal diversity is surprisingly stable despite constant

environmental exposures and perturbations;• Non-bacterial members of the skin microbiota are still being

resolved, but are important components to consider;• Optimal approaches for skin microbiome characterization may

be different than other body sites and/or the environment.

Lab members:Jacquelyn MeiselAdam SanMiguelCharles Bradley, VMDMichael LoescheJoseph HorwinskiQi Zheng, PhDCasey Bartow-McKenneyJulia BugayevGeorgia Sfyroera PhDLindsay Kalan PhDGeoffrey Hannigan PhD (former)

Funding:NIAMS R01AR066663NINR R01NR015639Janssen Pharmaceutical CompaniesPennsylvania Department of Health

Collaborators:Sue Gardner RN PhD (U of Iowa Nursing)David Margolis MD PhD (Penn Derm & Epidemiology)Rick Bushman PhD (Penn Microbiology)Samir Mehta MD (Penn Orthopaedic Surgery)Junko Takeshita MD (Penn Derm)John Lambris PhD (Penn Pathology and Lab Medicine)Kara Spiller PhD (Drexel Biomedical Engineering)Phil Scott PhD (Penn Vet Medicine)Meghan Davis DVM MPH (Johns Hopkins SPH)Dan Morris DVM MPH (Penn Vet Medicine)Elizabeth Mauldin DVM (Penn Vet Medicine)