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

Senior Investigator

Cutaneous Microbiome and Inflammation Section


Building 10, Room 12N240D
10 Center Drive
Bethesda, MD 20814



Research Topics

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, individualized, and relatively stable in healthy individuals. Other major findings include the strain-specificity of Staphylococcus aureus in severe flares of atopic dermatitis (or commonly known as eczema) and the distinct viromes in patient cohorts with primary immunodeficiencies.

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.

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

  • 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 microbiota in disease. Our mission is to understand how microbes interact with the human host to elicit or ameliorate disease.


Dr. Heidi H. Kong received her undergraduate degree from Stanford University and MD from Baylor College of Medicine. After training in Dermatology at Duke University, she completed a clinical research fellowship in the Dermatology Branch, Center for Cancer Research, National Cancer Institute and the Duke-NIH Masters Program in Clinical Research. Dr. Kong is an attending physician on the NIH Dermatology Consultation Service and an Adjunct Investigator at the National Cancer Institute. She is a Senior Investigator and Head of the Cutaneous Microbiome and Inflammation Section at the National Institute of Arthritis and Musculoskeletal and Skin Diseases.

Selected Publications

  1. 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. Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics. Sci Transl Med. 2021;13(625):eabd8077.
  2. 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. Staphylococcal diversity in atopic dermatitis from an individual to a global scale. Cell Host Microbe. 2023;31(4):578-592.e6.
  3. Oh J, Byrd AL, Park M, NISC Comparative Sequencing Program, Kong HH, Segre JA. Temporal Stability of the Human Skin Microbiome. Cell. 2016;165(4):854-66.
  4. Oh J, Byrd AL, Deming C, Conlan S, NISC Comparative Sequencing Program, Kong HH, Segre JA. Biogeography and individuality shape function in the human skin metagenome. Nature. 2014;514(7520):59-64.
  5. 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. Topographic diversity of fungal and bacterial communities in human skin. Nature. 2013;498(7454):367-70.

Related Scientific Focus Areas

This page was last updated on Tuesday, September 19, 2023