Overview

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.

RECRUITING

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.

RECRUITING

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.

RECRUITING

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

Image
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

Career Opportunities

Postdoctoral Position - Microbiome and Immunity


A funded postdoctoral fellow position is available immediately in the Kong lab in the Cutaneous Microbiome and Inflammation Section, Dermatology Branch, NIAMS. Our group studies human-associated microbes in healthy volunteers and patients with atopic dermatitis and primary immunodeficiency syndromes. We currently are investigating antimicrobial resistance, altered microbiomes in skin disorders, and integrated microbiome-host transcriptomics in immunodeficiency. This work will provide insights into microbial-host interactions and microbial contributions to human diseases. We work closely with our collaborators to utilize multidisciplinary approaches including microbiome analyses, microbial genomics, molecular biology, microbiology, and host transcriptomics and immunology.

We are seeking outstanding, highly motivated individuals to join our dynamic research team. In addition to a rich mentoring environment, fellows will have access to cutting-edge technologies and core facilities.

For more information, please visit our website . Our long-time collaborators include the Segre lab and the Nagao lab.

Qualifications

Applicants must have:

  • a Ph.D. or M.D. with less than 5 years of postdoctoral experience.
  • a strong background in molecular biology, microbiology, bioinformatics and/or immunology.
  • peer-reviewed publications.
  • strong oral and written communications skills.
  • the ability to work well both independently and collaboratively on an interdisciplinary team.

Compensation

NIH offers excellent salary and health care packages to its trainees and is consistently ranked among the best places to work for postdoctoral fellows.

To Apply

Applicants should email a brief statement of research interests, a CV, and three references to Dr. Heidi Kong at kongresearchgroup@gmail.com.


Employer Name:
National Institutes of Arthritis and Musculoskeletal and Skin Diseases

Position Location:
Bethesda, MD

This position is subject to a background investigation.

The NIH and HHS are dedicated to building a diverse community in their training and employment programs.

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.

Scientific Publications

Selected Recent Publications

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

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;
24(12).
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;
9(397).
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;
13(625).
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
Cell.
2016 May 5;
165(4).
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
Nature.
2014 Oct 2;
514(7520).
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
Nature.
2013 Jun 20;
498(7454).
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;
22(5).
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
Science.
2009 May 29;
324(5931).
doi: 10.1126/science.1171700
PMID: 19478181

News & Highlights

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.
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.
| 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!