The Cutaneous Microbiome and Inflammation Section uses genomics to study the skin microbes in healthy individuals and patients with skin diseases and to expand our understanding of host-microbe interactions.

Our group studies the diversity and complexity of bacterial, fungal, and viral communities in healthy skin and in eczema from patients with atopic dermatitis and with primary immunodeficiencies. We integrate advanced genomic sequencing methods to investigate clinical samples and cultured isolates to more deeply understand these human microbial communities. Our work has demonstrated how the skin microbiome is patterned based on the location on the body surface (Grice et al., Science. 2009;  Findley et al., Nature. 2013; Oh et al., Nature. 2014; Oh, Byrd et al., Cell. 2016), and can be distinguished in certain skin diseases and with specific immunodeficiencies (Kong et al., Genome Research. 2012; Byrd et al., Science Translational Medicine. 2017; Oh et al., Genome Research. 2013; Tirosh et al., Nature Medicine . 2018)

These studies have highlighted how the host shapes, and in turn may be shaped by, the skin microbiome. Our current efforts continue to explore these host-microbial interactions.

Research Focus

Our highly collaborative group studies the complexity of the microbial communities residing in and on the human body. We are focused on: 

Close up illustration of the surface of skin
Human skin hosts a diverse community of microbes
  • Investigating the alterations in the human skin microbiome related to skin diseases, primary immunodeficiencies, and therapeutic interventions.
  • Utilizing advances in microbiome and transcriptome sequencing to explore host-skin microbe interactions.

The translational team approach has been successful in integrating clinical medicine, genomics, microbiology, and immunology to study the role of staphylococci in atopic dermatitis as well as microbes in patients with immunodeficiencies. Our mission is to understand how microbes interact with the human host to elicit or ameliorate disease.

Ongoing Studies

The following studies are currently active. Further details are available following the links to the respective pages on the clinicaltrials.gov web site.


Studies of Dermatologic Diseases-Biospecimen Acquisition Protocol

ClinicalTrials.gov Identifier: NCT02471352 [12-AR-0144]

Skin diseases represent one of the most common medical problems in the United States, affecting 1 in 3 people at any given time. This study aims to procure biologic samples for exploratory cellular, molecular, genetic and genomic biological studies from subjects with dermatologic conditions, subjects at risk for developing dermatologic conditions and healthy volunteers in the support of NIH biomedical studies.


Effects of Antimicrobial Treatments on the Microbiome in Healthy Volunteers and Patients with Atopic Dermatitis

ClinicalTrials.gov Identifier: NCT01631617 [12-AR-0159]

The use of antibiotics has revolutionized medicine, yet the impact of antimicrobials on the human microbiome is incompletely understood. This study aims to characterize microbiome alterations in healthy adult volunteers and patients with atopic dermatitis after antimicrobial treatments.


The Acquisition of Blood and Skin Samples From Normal Volunteers to Support Research Activities on Dermatologic Diseases

ClinicalTrials.gov Identifier: NCT00001505 [96-AR-0097]

This study aims to collect blood, skin, or mucosal samples from healthy volunteers or patients with selected skin or systemic diseases as needed to support the research activities of our branch and other laboratories and branches.


Staff of the Kong Lab, photographed outside in front of some trees.

Our lab is always seeking to recruit the best talent in the scientific community. If you are interested in joining our team, please contact us.

Former Lab Members

Postdoctoral Fellows/Katz Scholars

  • Jin Park, M.D., Ph.D., 2019-2021
  • Hai Liang, Ph.D., 2018-2021
  • Jay-Hyun Jo, Ph.D., 2015-2021
  • Catriona P. Harkins, M.B.Ch.B., M.R.C.P., Ph.D., Katz Scholar in Dermatology Research, 2019-2020
  • Martin Glatz, M.D., Visiting Fellow, 2012-2014

Medical Students

  • Margaret MacGibeny, Clinical Electives Program Student, 2020
  • Therese Woodring, Medical Research Scholars Program Fellow, 2016-2017
  • Radhika Nakrani, Medical Research Scholars Program Fellow, 2013-2014

Postbaccalaureate Fellows

  • Layne Oram, 2021-2022
  • Jessica Portillo, 2019-2021
  • Meridith Pensler, 2020-2021
  • Nicole Schwardt, 2017-2019
  • Elizabeth A. Kennedy, 2015-2017
  • Amanda Johnson, 2013-2015
  • Elizabeth Bassett, 2007-2008

Image & Media Gallery

Scientific Publications

Selected Recent Publications

Expanded microbiome niches of RAG-deficient patients.

Blaustein RA, Shen Z, Kashaf SS, Lee-Lin S, Conlan S, NISC Comparative Sequencing Program, Bosticardo M, Delmonte OM, Holmes CJ, Taylor ME, Banania G, Nagao K, Dimitrova D, Kanakry JA, Su H, Holland SM, Bergerson JRE, Freeman AF, Notarangelo LD, Kong HH, Segre JA
Cell Rep Med.
2023 Oct 17;
doi: 10.1016/j.xcrm.2023.101205
PMID: 37757827

Staphylococcal diversity in atopic dermatitis from an individual to a global scale.

Saheb Kashaf S, Harkins CP, Deming C, Joglekar P, Conlan S, Holmes CJ, NISC Comparative Sequencing Program, Almeida A, Finn RD, Segre JA, Kong HH
Cell Host Microbe.
2023 Apr 12;
doi: 10.1016/j.chom.2023.03.010
PMID: 37054678

Sharing is caring? Skin microbiome insights into staphylococci in patients with atopic dermatitis and caregivers.

Kong HH
J Allergy Clin Immunol.
2022 Oct;
doi: 10.1016/j.jaci.2022.07.010
PMID: 35931225

Antibiotic Stewardship in Dermatology-Reducing the Risk of Prolonged Antimicrobial Resistance in Skin.

MacGibeny MA, Jo JH, Kong HH
JAMA Dermatol.
2022 Sep 1;
doi: 10.1001/jamadermatol.2022.3168
PMID: 35947396

Predicting cancer immunotherapy response from gut microbiomes using machine learning models.

Liang H, Jo JH, Zhang Z, MacGibeny MA, Han J, Proctor DM, Taylor ME, Che Y, Juneau P, Apolo AB, McCulloch JA, Davar D, Zarour HM, Dzutsev AK, Brownell I, Trinchieri G, Gulley JL, Kong HH
doi: 10.18632/oncotarget.28252
PMID: 35875611

State of Residency: Microbial Strain Diversity in the Skin.

Kong HH, Oh J
J Invest Dermatol.
2022 May;
doi: 10.1016/j.jid.2021.10.005
PMID: 34688614

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions.

Saheb Kashaf S, Proctor DM, Deming C, Saary P, Hölzer M, NISC Comparative Sequencing Program, Taylor ME, Kong HH, Segre JA, Almeida A, Finn RD
Nat Microbiol.
2022 Jan;
doi: 10.1038/s41564-021-01011-w
PMID: 34952941

Shifts in the Skin Bacterial and Fungal Communities of Healthy Children Transitioning through Puberty.

Park J, Schwardt NH, Jo JH, Zhang Z, Pillai V, Phang S, Brady SM, Portillo JA, MacGibeny MA, Liang H, Pensler M, Soldin SJ, Yanovski JA, Segre JA, Kong HH
J Invest Dermatol.
2022 Jan;
doi: 10.1016/j.jid.2021.04.034
PMID: 34252398

Disruption of the endopeptidase ADAM10-Notch signaling axis leads to skin dysbiosis and innate lymphoid cell-mediated hair follicle destruction.

Sakamoto K, Jin SP, Goel S, Jo JH, Voisin B, Kim D, Nadella V, Liang H, Kobayashi T, Huang X, Deming C, Horiuchi K, Segre JA, Kong HH, Nagao K
2021 Oct 12;
doi: 10.1016/j.immuni.2021.09.001
PMID: 34582748

Treatment of Relapsing HPV Diseases by Restored Function of Natural Killer Cells.

Lisco A, Hsu AP, Dimitrova D, Proctor DM, Mace EM, Ye P, Anderson MV, Hicks SN, Grivas C, Hammoud DA, Manion M, Starrett GJ, Farrel A, Dobbs K, Brownell I, Buck C, Notarangelo LD, Orange JS, Leonard WJ, Orestes MI, Peters AT, Kanakry JA, Segre JA, Kong HH, Sereti I
N Engl J Med.
2021 Sep 2;
doi: 10.1056/NEJMoa2102715
PMID: 34469647

Cultivating fungal research.

Kong HH, Segre JA
2020 Apr 24;
doi: 10.1126/science.aaz8086
PMID: 32327584

Manipulating the Human Microbiome to Manage Disease.

Harkins CP, Kong HH, Segre JA
2020 Jan 28;
doi: 10.1001/jama.2019.19602
PMID: 31876898

Expanded skin virome in DOCK8-deficient patients.

Tirosh O, Conlan S, Deming C, Lee-Lin SQ, Huang X, NISC Comparative Sequencing Program, Su HC, Freeman AF, Segre JA, Kong HH
Nat Med.
2018 Dec;
doi: 10.1038/s41591-018-0211-7
PMID: 30397357

Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis.

Byrd AL, Deming C, Cassidy SKB, Harrison OJ, Ng WI, Conlan S, NISC Comparative Sequencing Program, Belkaid Y, Segre JA, Kong HH
Sci Transl Med.
2017 Jul 5;
doi: 10.1126/scitranslmed.aal4651
PMID: 28679656

Key Publications

Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics.

Jo JH, Harkins CP, Schwardt NH, Portillo JA, NISC Comparative Sequencing Program., Zimmerman MD, Carter CL, Hossen MA, Peer CJ, Polley EC, Dartois V, Figg WD, Moutsopoulos NM, Segre JA, Kong HH
Sci Transl Med.
2021 Dec 22;
doi: 10.1126/scitranslmed.abd8077
PMID: 34936382

Temporal Stability of the Human Skin Microbiome.

Oh J, Byrd AL, Park M, NISC Comparative Sequencing Program., Kong HH, Segre JA
2016 May 5;
doi: 10.1016/j.cell.2016.04.008
PMID: 27153496

Biogeography and individuality shape function in the human skin metagenome.

Oh J, Byrd AL, Deming C, Conlan S, NISC Comparative Sequencing Program., Kong HH, Segre JA
2014 Oct 2;
doi: 10.1038/nature13786
PMID: 25279917

Topographic diversity of fungal and bacterial communities in human skin.

Findley K, Oh J, Yang J, Conlan S, Deming C, Meyer JA, Schoenfeld D, Nomicos E, Park M, NIH Intramural Sequencing Center Comparative Sequencing Program., Kong HH, Segre JA
2013 Jun 20;
doi: 10.1038/nature12171
PMID: 23698366

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis.

Kong HH, Oh J, Deming C, Conlan S, Grice EA, Beatson MA, Nomicos E, Polley EC, Komarow HD, NISC Comparative Sequence Program., Murray PR, Turner ML, Segre JA
Genome Res.
2012 May;
doi: 10.1101/gr.131029.111
PMID: 22310478

Topographical and temporal diversity of the human skin microbiome.

Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young AC, NISC Comparative Sequencing Program., Bouffard GG, Blakesley RW, Murray PR, Green ED, Turner ML, Segre JA
2009 May 29;
doi: 10.1126/science.1171700
PMID: 19478181

News & Highlights

Spotlight on Research |

NIH Researchers Survey the Genetic Diversity of Skin Microbes in Eczema Patients

Using a combination of sequencing techniques, researchers from NIAMS and the National Human Genome Research Institute (NHGRI) surveyed the skin microbiome of patients with atopic dermatitis (AD, also called eczema) to understand the genetic diversity of the bacteria present on the skin and how genetic variants may contribute to disease severity.
NIH Director's Blog |

NIH Director's Blog

Human skin is home to diverse ecosystems including bacteria, viruses, and fungi. These microbial communities comprise hundreds of species and are collectively known as the skin microbiome.
NIAMS-Related Article |

Drs. Heidi Kong and Ian Myles — Derm Germs: The Human Skin Microbiome

Dr. Heidi Kong uses genomics to uncover the microbe-host interactions taking place all over our skin.

NIAMS Investigators Elected to the American Society for Clinical Investigation

Congratulations to Drs. Isaac Brownell, Heidi Kong, and Chris Nagao who were elected to the American Society for Clinical Investigation!