Principal Investigator

Heidi H. Kong, M.D., M.H.Sc.

Dr. Kong studies the human microbiome and its roles in health and disease. Her research has advanced the understanding of microbial communities of human skin and combines clinical/translational research expertise with advanced genomic technologies.

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.

Core Research Facilities

Labs at the NIAMS are supported by the following state-of-the-art facilities and services:


Kong Lab - 2021
Senior Investigator
Research Nurse
Clinical Trials Research Nurse Practitioner
Postdoctoral Fellow (Visiting)
Postdoctoral Fellow
Guest Researcher
Postbaccalaureate Fellow
Postbaccalaureate Fellow
Research Nurse

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

  • 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

  • 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

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;
pii: eaal4651. doi: 10.1126/scitranslmed.aal4651
PMID: 28679656

Diverse Human Skin Fungal Communities in Children Converge in Adulthood.

Jo JH, Deming C, Kennedy EA, Conlan S, Polley EC, Ng WI, NISC Comparative Sequencing Program., Segre JA, Kong HH
J Invest Dermatol.
2016 Dec;
doi: 10.1016/j.jid.2016.05.130
PMID: 27476723

Key Publications

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

NIAMS-Related Article | October 22, 2020

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.
Spotlight on Research | November 5, 2018

Researchers unearth community of viruses on skin of people with rare disease

NIH researchers studied microbial populations in skin samples from 27 adults and children with a rare immune disorder, DOCK8 deficiency.
Last Updated: May 2021 Back to Top