An official website of the United States government
          Here’s how you know
        Here’s how you know**Official websites use .gov**A
              **.gov** website belongs to an official government
              organization in the United States.
        **Secure .gov websites use HTTPS**A
              **lock** (
              Locked padlock icon) or **https://** means you’ve safely connected to the .gov website. Share sensitive information only on official, secure websites.
 Top Utility Nav
        
        
        Asian-Language Resources
        
        Portal en español


Site search Mega Menu
  

        

        Home
                  Health Topics
                                      
    
  Health Topics

    Arthritis and Rheumatic Diseases
          
    Muscle and Bone Diseases
          
    Skin Diseases
          
    All Diseases and Conditions
          
    Publication Catalog
                  Grants & Funding
                                      
    
  Grants & Funding

    Current Funding Opportunities
          
    Supported Scientific Programs
          
    NIAMS-Supported Programs
          
    Applying for a Grant
          
    NIH Policies and Guidance
          
    Peer Review and Grants Administration Resources
          
    Types of Funding Mechanisms (Activity Codes)
                  Labs @ NIAMS
                                      
    
  Labs @ NIAMS

    NIAMS Labs and Core Facilities
          
    Research Faculty
          
    Research Areas
          
    NIAMS Scientific Advances
          
    Training and Career Development
                  Clinical Trials
                                      
    
  Clinical Trials
      
            For Principal Investigators

    Clinical Trial Policies, Guidelines, and Templates
          
    Conducting Clinical Trials
          
    Register with ClinicalTrials.gov

For Patients

What is a Clinical Trial?
	Clinical Trials at NIAMS
	Clinical Trials in the Spotlight
                  News & Events
                                      
    
  Newsroom

    All NIAMS News
          
    NIAMS Newsletters
          
    Meetings & Events
                  About NIAMS
                                      
    
  About NIAMS

    Director's Page
          
    NIAMS Organization
          
    Strategic Plan Fiscal Years 2020-2024
          
    Staff Directory
          
    NIAMS Budget
          
    Partnerships
          
    Contact NIAMS
                  Community Outreach
                                      
    
  Community Outreach

    Bone Health
          
    Joint Health
          
    Muscle, Tendon, and Ligament Health
          
    Skin Health
          
    Health Information For Kids And Young Adults
          
    Health Information For Older Adults/Seniors
          
    Printable Materials for Community Events
          
    Resources in Other Languages
          
    Annual Health Observances
          
    Social Media Resources Breadcrumb
    Home
          Labs @ NIAMS
          Cutaneous Microbiome and Inflammation Section








Cutaneous Microbiome and Inflammation Section


Heidi H. Kong, M.D., M.H.Sc. FacebookEmailPrintFacebookEmail
        Excerpts of scientific figures arranged on an abstract background.

      Overview

                                  Senior Investigator
      
  


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


            konghe@mail.nih.gov
      
                                                                        

  
   Research Areas (IRP Lab Groups)
          Clinical Research,
          Computational Biology,
          Genetics and Genomics,
          Microbiology and Infectious Diseases,
          Skin Biology
                                
            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 FocusOur 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 skinHuman skin hosts a diverse community of microbesInvestigating 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.
      

                                            Related NIAMS LabsCutaneous Development and Carcinogenesis SectionCutaneous Leukocyte Biology SectionDermatology Consultation ServicePartner Labs at NIHTranslational Functional Genomics Branch (NHGRI)
  Scientific Advances
      
  

      September 26, 2023The Microbiomes of People with Recombination-Activating Gene (RAG) Deficiency Have Distinct Features, Including Antimicrobial Resistance Signatures
    September 6, 2023Early Treatment Helps Reduce Long-Term Complications in Children with Job’s Syndrome
    September 4, 2023Early-Onset Rash in Children with APECED Syndrome Accelerates Diagnosis
    December 22, 2021Alterations of Human Skin Microbiome and Expansion of Antimicrobial Resistance After Systemic Antibiotics

                                                      Core Research Facilities

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

Biodata Mining and Discovery
	Flow Cytometry
	Genomic Technology
	Laboratory Animal Care and Use
	Light Imaging
	Translational Immunology

                                    Staff
                            Image
              Staff of the Kong Lab, photographed outside in front of some trees.
                            
            **Heidi H. Kong, M.D., M.H.Sc.**Senior Investigatorkonghe@mail.nih.gov
    **Adel Amirkhani, M.S.**Biologistadel.amirkhani@nih.gov
    **Leslie Castelo-Soccio, M.D., Ph.D.**Staff Clinicianleslie.castelo-soccio@nih.gov
    **You Che, Ph.D.**Postdoctoral Fellowyou.che@nih.gov
    **Jiwoong Choi, M.D., Ph.D.**Special Volunteerjiwoong.choi@nih.gov
    **Alexandra Firek, B.S.**Medical Student Research Fellowfirekak@nih.gov
    **Ryleigh Griffin, B.S.**Postbaccalaureate FellowRyleigh.griffin@nih.gov
    **Jungmin Han, Ph.D.**Research Fellowjungmin.han@nih.gov
    **Cassie Holmes, M.S., CRNP, FNP-C**Clinical Trials Research Nurse Practitionercassie.holmes@nih.gov
    **Peng Hou, Ph.D.**Postdoctoral Fellowpeng.hou@nih.gov
    **Milan Stolpman, B.S.**Postbaccalaureate Fellowstolpmanmd@nih.gov
    **Grace Suh, B.S.**Postbaccalaureate Fellowsuhgs@nih.gov
    **Monica Taylor, R.N., B.S.N.**Research Nursemonica.taylor@nih.gov
      

                            *‌*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 ScholarsJin Park, M.D., Ph.D., 2019-2021Hai Liang, Ph.D., 2018-2021Jay-Hyun Jo, Ph.D., 2015-2021Catriona P. Harkins, M.B.Ch.B., M.R.C.P., Ph.D., Katz Scholar in Dermatology Research, 2019-2020Martin Glatz, M.D., Visiting Fellow, 2012-2014Medical StudentsMargaret MacGibeny, Clinical Electives Program Student, 2020Therese Woodring, Medical Research Scholars Program Fellow, 2016-2017Radhika Nakrani, Medical Research Scholars Program Fellow, 2013-2014Postbaccalaureate FellowsCoralys Citron, 2023-2023Layne Oram, 2021-2022Jessica Portillo, 2019-2021Meridith Pensler, 2020-2021Nicole Schwardt, 2017-2019Elizabeth A. Kennedy, 2015-2017Amanda Johnson, 2013-2015Elizabeth Bassett, 2007-2008
            
                                                Image & Media Gallery
              
            The Kong and Segre Labs Annual Cherry Blossom Picnic (2020)
The Kong and Segre Labs Annual Cherry Blossom Picnic (2020)
        ×
      Staff of Heidi Kong's Lab unde cherry blossom trees (2020)
    Dr. Heidi Kong with swab.
Dr. Heidi Kong with swab.
        ×
      Dr. Kong in the lab.
        Dr. Heidi Kong places a skin swab in storage tubes for future skin microbiome studies.
    Dr. Heidi Kong collecting samples.
Dr. Heidi Kong collecting samples.
        ×
      Dr. Kong in the lab.
        Dr. Heidi Kong collects non-invasive skin samples to study the human skin microbiome.
    Dr. Heidi Kong and research nurse Mrs. Sheila Phang.
Dr. Heidi Kong and research nurse Mrs. Sheila Phang.
        ×
      Dr. Kong in the lab.
        Dr. Heidi Kong, assisted by research nurse Mrs. Sheila Phang, collects non-invasive skin samples for microbiome studies.
    Drs. Heidi Kong and Martin Glatz.
Drs. Heidi Kong and Martin Glatz.
        ×
      Dr. Kong in the lab.
        Drs. Heidi Kong and Martin Glatz review skin microbiome experimental data.
            
                        
                                    Clinical Trials
              
              
            RecruitingEffects of Treatments on the Microbiome in Healthy Volunteers and Patients With Atopic DermatitisClinicalTrials.gov Identifier: NCT01631617Atopic dermatitis, or eczema, is a chronic skin disorder. 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.
    RecruitingNatural History and Pathogenesis of Alopecia in Children and AdultsClinicalTrials.gov Identifier: NCT05502796Dr. Leslie Castelo-Soccio is the Principal Investigator of this study. Alopecia is the loss of hair or lack of hair growth. It is often related to an immune disorder that disrupts the growth of hair. Hair loss can affect a person s physical and mental health. The causes of alopecia are not well understood. This natural history study will examine causes of alopecia so better treatments can be developed.
    RecruitingStudies of Dermatologic Diseases-Biospecimen Acquisition ProtocolClinicalTrials.gov Identifier: NCT02471352Skin 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.
            
                                    Scientific Publications
              Selected Recent Publications
                  
      Calciphylaxis in POEMS syndrome: Case report.

    Novacic D, Uldrick T, Dulau-Florea A, Howe CE, Lee CR, Kong HH, Gahl WA
        

                    Rare.
        
                    2024;
        
                    2().
        
                    pii: 100019. doi: 10.1016/j.rare.2024.100019
                            PMID: 38435320
              The skin microbiome in pediatric atopic dermatitis and food allergy.

    Tham EH, Chia M, Riggioni C, Nagarajan N, Common JEA, Kong HH
        

                    Allergy.
        
                    2024 Feb 3;
        
        
                    doi: 10.1111/all.16044
                            PMID: 38308490
              Integrated genomic and functional analyses of human skin-associated Staphylococcus reveal extensive inter- and intra-species diversity.

    Joglekar P, Conlan S, Lee-Lin SQ, Deming C, Kashaf SS, NISC Comparative Sequencing Program, Kong HH, Segre JA
        

                    Proc Natl Acad Sci U S A.
        
                    2023 Nov 21;
        
                    120(47).
        
                    doi: 10.1073/pnas.2310585120
                            PMID: 37956283
              A genome catalog of the early-life human skin microbiome.

    Shen Z, Robert L, Stolpman M, Che Y, Allen KJ, Saffery R, Walsh A, Young A, Eckert J, Deming C, Chen Q, Conlan S, Laky K, Li JM, Chatman L, Kashaf SS, NISC Comparative Sequencing Program, VITALITY team, Kong HH, Frischmeyer-Guerrerio PA, Perrett KP, Segre JA
        

                    Genome Biol.
        
                    2023 Nov 10;
        
                    24(1).
        
                    doi: 10.1186/s13059-023-03090-w
                            PMID: 37946302
              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;
        
                    4(10).
        
                    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;
        
                    31(4).
        
                    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;
        
                    150(4).
        
                    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;
        
                    158(9).
        
                    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
        

                    Oncotarget.
        
                    2022;
        
                    13().
        
                    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;
        
                    142(5).
        
                    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;
        
                    7(1).
        
                    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;
        
                    142(1).
        
                    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
        

                    Immunity.
        
                    2021 Oct 12;
        
                    54(10).
        
                    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;
        
                    385(10).
        
                    doi: 10.1056/NEJMoa2102715
                            PMID: 34469647
              Cultivating fungal research.

    Kong HH, Segre JA
        

                    Science.
        
                    2020 Apr 24;
        
                    368(6489).
        
                    doi: 10.1126/science.aaz8086
                            PMID: 32327584
              Manipulating the Human Microbiome to Manage Disease.

    Harkins CP, Kong HH, Segre JA
        

                    JAMA.
        
                    2020 Jan 28;
        
                    323(4).
        
                    doi: 10.1001/jama.2019.19602
                            PMID: 31876898
                
                                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 HHSci Transl Med.2021 Dec 22;13(625).doi: 10.1126/scitranslmed.abd8077PMID: 34936382Temporal Stability of the Human Skin Microbiome.Oh J, Byrd AL, Park M, NISC Comparative Sequencing Program., Kong HH, Segre JACell.2016 May 5;165(4).doi: 10.1016/j.cell.2016.04.008PMID: 27153496Biogeography and individuality shape function in the human skin metagenome.Oh J, Byrd AL, Deming C, Conlan S, NISC Comparative Sequencing Program., Kong HH, Segre JANature.2014 Oct 2;514(7520).doi: 10.1038/nature13786PMID: 25279917Topographic 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 JANature.2013 Jun 20;498(7454).doi: 10.1038/nature12171PMID: 23698366Temporal 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 JAGenome Res.2012 May;22(5).doi: 10.1101/gr.131029.111PMID: 22310478Topographical 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 JAScience.2009 May 29;324(5931).doi: 10.1126/science.1171700PMID: 19478181 
                            See more publications at PubMed
            
                                    News & Highlights
              
            Spotlight on Research | May 25, 2023
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.
Read More
    NIH Director's Blog | March 24, 2022
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.
Read More
    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.
Read More
    | April 5, 2019
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!
Read More



    FacebookEmailPrintFacebookEmail
        Last Updated: April 2024
 About NIAMS
                    Clinical Trials
                    Grants & Funding
                    Health Topics
                    Labs @ NIAMS
              News Room
                    NIAMS Multimedia Library
                    Disclaimer
                    FOIA
                    Contact us
              Privacy Statement
                    Accessibility
                    HHS Vulnerability Disclosure
                    Social Media Moderation Policy
                    NIAMS Archives
        Subscribe to Our E-Newsletters
            Click the button to see different options to sign up for newsletters.
            Click Here to Subscribe
          Follow us on
  
  About NIH
                  Accessibility Support
            FOIA requests
                  No FEAR Act data
            Office of the Inspector General
                  Performance reports
            Privacy Policy Back to Top