Scholars@Duke
Julia Oh

Julia Oh

Professor in Dermatology
Dermatology
julia.oh@duke.edu
MSRB III, 3 Genome Court, Durham, NC 27708
3 Genome Ct, MSRBIII, Durham, NC 27710

Selected Publications

The human skin microbiome: from metagenomes to therapeutics.

Journal Article Nat Rev Microbiol · December 2025 The skin microbiome is composed of a diverse community of microorganisms, including bacteria, fungi, viruses and mites. These microorganisms have a crucial role in maintaining skin health, protecting against pathogens and modulating immune responses. In re ... Full text Link to item Cite

Host-specific bacterial modulation of airway gene expression and alternative splicing.

Journal Article mSphere · November 25, 2025 The human microbiome varies extensively between individuals. While there are numerous studies investigating the effects of inter-individual differences on microbiome composition, there are few studies investigating inter-individual effects on microbial mod ... Full text Link to item Cite

AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome.

Journal Article Nat Med · September 2025 Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic illness with a multifactorial etiology and heterogeneous symptomatology, posing major challenges for diagnosis and treatment. Here we present BioMapAI, a supervised deep neural networ ... Full text Link to item Cite

Host-specific bacterial modulation of airway gene expression and alternative splicing.

Journal Article bioRxiv · July 18, 2025 The human microbiome varies extensively between individuals. While there are numerous studies investigating the effects of inter-individual differences on microbiome composition, there are few studies investigating inter-individual effects on microbial mod ... Full text Link to item Cite

Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin.

Journal Article Nat Commun · July 1, 2025 The adult skin microbiome typically exhibits low microbial complexity, particularly on sebaceous sites, where lipophilic Cutibacterium and Malassezia spp. predominate. Current understanding of healthy skin microbiome is largely based on western, industrial ... Full text Link to item Cite

Genotype-Environment-Driven Dysbiosis in the Skin Microbiome of Ichthyosis.

Journal Article J Invest Dermatol · June 25, 2025 Many factors might be expected to influence the cutaneous microbiome, especially on diseased skin. Yet, few studies account for the complex interactions between host and environmental factors. To shed light on such interactions, we characterized the skin m ... Full text Link to item Cite

TEAL-Seq: targeted expression analysis sequencing.

Journal Article mSphere · May 27, 2025 Metagenome sequencing enables the genetic characterization of complex microbial communities. However, determining the activity of isolates within a community presents several challenges, including the wide range of organismal and gene expression abundances ... Full text Link to item Cite

Cutaneous dysbiosis characterizes the post-allogeneic hematopoietic stem cell transplantation period.

Journal Article Blood Adv · May 13, 2025 Gut dysbiosis is linked to mortality and the development of graft-versus-host disease after hematopoietic stem cell transplantation (HSCT), but the impact of cutaneous dysbiosis remains unexplored. We performed a pilot observational study, obtained retroau ... Full text Link to item Cite

Gut dysbiosis patterns in CVID patients with noninfectious complications observed in a germ-free mouse model through fecal microbiota transplantation.

Journal Article J Hum Immun · May 5, 2025 Patients with common variable immunodeficiency (CVID) who develop noninfectious complications (NIC) have worse clinical outcomes than those with infections only (INF). While gut microbiome aberrations have been linked to NIC, reductionist animal models tha ... Full text Link to item Cite

A blueprint for contemporary studies of microbiomes.

Journal Article Microbiome · April 8, 2025 This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submi ... Full text Link to item Cite

BioMapAI: Artificial Intelligence Multi-Omics Modeling of Myalgic Encephalomyelitis / Chronic Fatigue Syndrome.

Journal Article bioRxiv · February 13, 2025 Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a chronic illness with a multifactorial etiology and heterogeneous symptomatology, posing major challenges for diagnosis and treatment. Here, we present BioMapAI, a supervised deep neural netwo ... Full text Link to item Cite

Species- and strain-specific microbial modulation of interferon, innate immunity, and epithelial barrier in 2D air-liquid interface respiratory epithelial cultures.

Journal Article BMC Biol · January 29, 2025 BACKGROUND: The microbiome regulates the respiratory epithelium's immunomodulatory functions. To explore how the microbiome's biodiversity affects microbe-epithelial interactions, we screened 58 phylogenetically diverse microbes for their transcriptomic ef ... Full text Link to item Cite

Association of Neonatal and Maternal Nasal Microbiome Among Neonates in the Intensive Care Unit.

Journal Article Open Forum Infect Dis · November 2024 The neonatal nasal microbiota may help protect neonates in the neonatal intensive care unit from pathogen colonization and infection. This preliminary study characterized the biodiversity of nasal microbiota comparing neonates in the neonatal intensive car ... Full text Link to item Cite

A host-microbiota interactome reveals extensive transkingdom connectivity.

Journal Article Nature · April 2024 The myriad microorganisms that live in close association with humans have diverse effects on physiology, yet the molecular bases for these impacts remain mostly unknown1-3. Classical pathogens often invade host tissues and modulate immune responses through ... Full text Link to item Cite

Bioassay-Driven, Fractionation-Empowered, Focused Metabolomics for Discovering Bacterial Activators of Aryl Hydrocarbon Receptor.

Journal Article J Am Soc Mass Spectrom · March 6, 2024 Aryl hydrocarbon receptor (AhR) is a transcription factor that regulates gene expression upon ligand activation, enabling microbiota-dependent induction, training, and function of the host immune system. A spectrum of metabolites, encompassing indole and t ... Full text Link to item Cite

Human Microbiome and Frailty: From Observations of Clinically Relevant Associations to Insights into Biological Mechanisms

Chapter · January 1, 2024 Nearly all surfaces of the human body are colonized by communities of microbes such as bacteria, viruses, and fungi. Collectively called microbiota, microbiome colonizes both internal surfaces such as the gut, oral cavity, and bladder, as well as surfaces ... Full text Cite

Microbiome modulates immunotherapy response in cutaneous squamous cell carcinoma.

Journal Article Exp Dermatol · October 2023 The gut microbiome is increasingly recognized to alter cancer risk, progression and response to treatments such as immunotherapy, especially in cutaneous melanoma. However, whether the microbiome influences immune checkpoint inhibitor (ICI) immunotherapy r ... Full text Link to item Cite

Skin microbiome attributes associate with biophysical skin ageing.

Journal Article Exp Dermatol · September 2023 Two major arms of skin ageing are changes in the skin's biophysical conditions and alterations in the skin microbiome. This work partitioned both arms to study their interaction in detail. Leveraging the resolution provided by shotgun metagenomics, we expl ... Full text Link to item Cite

High-throughput bioprinting of the nasal epithelium using patient-derived nasal epithelial cells.

Journal Article Biofabrication · August 14, 2023 Progenitor human nasal epithelial cells (hNECs) are an essential cell source for the reconstruction of the respiratory pseudostratified columnar epithelium composed of multiple cell types in the context of infection studies and disease modeling. Hitherto, ... Full text Link to item Cite

High-Throughput Bioprinting of the Nasal Epithelium using Patient-derived Nasal Epithelial Cells.

Journal Article bioRxiv · March 30, 2023 Human nasal epithelial cells (hNECs) are an essential cell source for the reconstruction of the respiratory pseudostratified columnar epithelium composed of multiple cell types in the context of infection studies and disease modeling. Hitherto, manual seed ... Full text Link to item Cite

Multi-'omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients.

Journal Article Cell Host Microbe · February 8, 2023 Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex, debilitating disorder manifesting as severe fatigue and post-exertional malaise. The etiology of ME/CFS remains elusive. Here, we present a deep metagenomic analysis of stool combine ... Full text Link to item Cite

Microbiome modulates immunotherapy response in cutaneous squamous cell carcinoma.

Journal Article bioRxiv · January 25, 2023 The gut microbiome is increasingly recognized to alter cancer risk, progression, and response to treatments such as immunotherapy, especially in cutaneous melanoma. However, whether the microbiome influences immune checkpoint inhibitor (ICI) immunotherapy ... Full text Link to item Cite

Large-Scale CRISPRi and Transcriptomics of Staphylococcus epidermidis Identify Genetic Factors Implicated in Lifestyle Versatility.

Journal Article mBio · December 20, 2022 Staphylococcus epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, mainly due to the diffic ... Full text Link to item Cite

Strains to go: interactions of the skin microbiome beyond its species.

Journal Article Curr Opin Microbiol · December 2022 An extraordinary biodiversity of bacteria, fungi, viruses, and even small multicellular eukaryota inhabit the human skin. Genomic innovations have accelerated characterization of this biodiversity both at a species as well as the subspecies, or strain leve ... Full text Link to item Cite

Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults.

Journal Article Nat Aging · October 2022 Older adults represent a vulnerable population with elevated risk for numerous morbidities. To explore the association of the microbiome with aging and age-related susceptibilities including frailty and infectious disease risk, we conducted a longitudinal ... Full text Link to item Cite

Skin Microbiome Variation with Cancer Progression in Human Cutaneous Squamous Cell Carcinoma.

Journal Article J Invest Dermatol · October 2022 The skin microbiome plays a critical role in skin homeostasis and disorders. UVR is the major cause of nonmelanoma skin cancer, but other risk factors, including immune suppression, chronic inflammation, and antibiotic usage, suggest the microbiome as an a ... Full text Link to item Cite

State of Residency: Microbial Strain Diversity in the Skin.

Other J Invest Dermatol · May 2022 Human skin hosts a diversity of microbiota. Advances in sequencing and analytical methods have increasingly illuminated the importance of the finest resolution in understanding the genetic diversity of the skin microbiota, highlighting strain-level differe ... Full text Link to item Cite

Engineering a "detect and destroy" skin probiotic to combat methicillin-resistant Staphylococcus aureus.

Journal Article PLoS One · 2022 The prevalence and virulence of pathogens such as methicillin-resistant Staphylococcus (S.) aureus (MRSA), which can cause recurrent skin infections, are of significant clinical concern. Prolonged antibiotic exposure to treat or decolonize S. aureus contri ... Full text Link to item Cite

Using genome-wide expression compendia to study microorganisms.

Journal Article Comput Struct Biotechnol J · 2022 A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a tremendous opportunity ... Full text Link to item Cite

Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota.

Journal Article BMC Microbiol · October 14, 2021 BACKGROUND: Genomics-driven discoveries of microbial species have provided extraordinary insights into the biodiversity of human microbiota. In addition, a significant portion of genetic variation between microbiota exists at the subspecies, or strain, lev ... Full text Link to item Cite

3D Bioprinting for fabrication of tissue models of COVID-19 infection.

Journal Article Essays Biochem · August 10, 2021 Over the last few decades, the world has witnessed multiple viral pandemics, the current severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) pandemic being the worst and most devastating one, claiming millions of lives worldwide. Physician ... Full text Link to item Cite

Network Topology of Biological Aging and Geroscience-Guided Approaches to COVID-19.

Journal Article Front Aging · July 2021 Aging has emerged as the greatest and most prevalent risk factor for the development of severe COVID-19 infection and death following exposure to the SARS-CoV-2 virus. The presence of multiple co-existing chronic diseases and conditions of aging further en ... Full text Link to item Cite

Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery.

Journal Article Nat Commun · May 28, 2021 Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways e ... Full text Link to item Cite

Correction: Selective colonization ability of human fecal microbes in different mouse gut environments.

Journal Article ISME J · July 2020 An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Full text Link to item Cite

Controlling the Growth of the Skin Commensal Staphylococcus epidermidis Using d-Alanine Auxotrophy.

Journal Article mSphere · June 10, 2020 Using live microbes as therapeutic candidates is a strategy that has gained traction across multiple therapeutic areas. In the skin, commensal microorganisms play a crucial role in maintaining skin barrier function, homeostasis, and cutaneous immunity. Alt ... Full text Link to item Cite

Metagenomic growth rate inferences of strains in situ.

Journal Article Sci Adv · April 2020 We developed a method for strain-level metagenomic estimation of growth rate (SMEG) for inferring growth rates of bacterial subspecies, or strains, from complex metagenomic samples. We applied our method, which is based on both reference strains and de nov ... Full text Link to item Cite

A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes.

Journal Article mSphere · February 12, 2020 The CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive ... Full text Link to item Cite

Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin.

Journal Article Cell · February 6, 2020 Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a h ... Full text Link to item Cite

Skin Microbiome Alterations in Skin Diseases

Chapter · January 1, 2020 A common oversimplification of the skin microbiome is a binary classification of individual microbes as either “beneficial” or “harmful.” In reality, however, skin microbes are much more complex and can act as either beneficial or harmful in different scen ... Full text Cite

Immune cells for microbiota surveillance.

Journal Article Science · October 25, 2019 Full text Link to item Cite

Recoding the metagenome: microbiome engineering in situ.

Journal Article Curr Opin Microbiol · August 2019 Synthetic biology has enabled a new generation of tools for engineering the microbiome, including targeted antibiotics, protein delivery, living biosensors and diagnostics, and metabolic factories. Here, we discuss opportunities and limitations in microbio ... Full text Link to item Cite

A Mobile Prenatal Care App to Reduce In-Person Visits: Prospective Controlled Trial.

Journal Article JMIR Mhealth Uhealth · May 1, 2019 BACKGROUND: Risk-appropriate prenatal care has been asserted as a way for the cost-effective delivery of prenatal care. A virtual care model for prenatal care has the potential to provide patient-tailored, risk-appropriate prenatal educational content and ... Full text Link to item Cite

Selective colonization ability of human fecal microbes in different mouse gut environments.

Journal Article ISME J · March 2019 Mammalian hosts constantly interact with diverse exogenous microbes, but only a subset of the microbes manage to colonize due to selective colonization resistance exerted by host genetic factors as well as the native microbiota of the host. An important qu ... Full text Link to item Cite

Tuning of human MAIT cell activation by commensal bacteria species and MR1-dependent T-cell presentation.

Journal Article Mucosal Immunol · November 2018 Human mucosal-associated invariant T (MAIT) cell receptors (TCRs) recognize bacterial riboflavin pathway metabolites through the MHC class 1-related molecule MR1. However, it is unclear whether MAIT cells discriminate between many species of the human micr ... Full text Link to item Cite

Interaction between the microbiome and TP53 in human lung cancer.

Journal Article Genome Biol · August 24, 2018 BACKGROUND: Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infection ... Full text Link to item Cite

Resident risks.

Journal Article Nat Microbiol · August 2018 Full text Link to item Cite

A commensal strain of Staphylococcus epidermidis protects against skin neoplasia.

Journal Article Sci Adv · February 2018 We report the discovery that strains of Staphylococcus epidermidis produce 6-N-hydroxyaminopurine (6-HAP), a molecule that inhibits DNA polymerase activity. In culture, 6-HAP selectively inhibited proliferation of tumor lines but did not inhibit primary ke ... Full text Link to item Cite

ReprDB and panDB: minimalist databases with maximal microbial representation.

Journal Article Microbiome · January 18, 2018 BACKGROUND: Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compati ... Full text Link to item Cite

Draft Genome Sequence of Cloacibacterium normanense NRS-1 Isolated from Municipal Wastewater.

Journal Article Genome Announc · December 15, 2016 Cloacibacterium normanense is a Gram-negative bacterium recovered from untreated human wastewater. Given its high abundance in wastewater and its apparent absence in human stool, it may contribute to biological phosphate removal. Here, we perform a whole-g ... Full text Link to item Cite

Testing the Feasibility of Remote Patient Monitoring in Prenatal Care Using a Mobile App and Connected Devices: A Prospective Observational Trial.

Journal Article JMIR Res Protoc · November 18, 2016 BACKGROUND: Excessive weight gain and elevated blood pressure are significant risk factors for adverse pregnancy outcomes such as gestational diabetes, premature birth, and preeclampsia. More effective strategies to facilitate adherence to gestational weig ... Full text Link to item Cite

Temporal Stability of the Human Skin Microbiome.

Journal Article Cell · May 5, 2016 Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples coll ... Full text Link to item Cite

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing.

Journal Article mBio · February 9, 2016 UNLABELLED: Deep metagenomic shotgun sequencing has emerged as a powerful tool to interrogate composition and function of complex microbial communities. Computational approaches to assemble genome fragments have been demonstrated to be an effective tool fo ... Full text Link to item Cite

Biogeography and individuality shape function in the human skin metagenome.

Journal Article Nature · October 2, 2014 The varied topography of human skin offers a unique opportunity to study how the body's microenvironments influence the functional and taxonomic composition of microbial communities. Phylogenetic marker gene-based studies have identified many bacteria and ... Full text Link to item Cite

The altered landscape of the human skin microbiome in patients with primary immunodeficiencies.

Journal Article Genome Res · December 2013 While landmark studies have shown that microbiota activate and educate host immunity, how immune systems shape microbiomes and contribute to disease is incompletely characterized. Primary immunodeficiency (PID) patients suffer recurrent microbial infection ... Full text Link to item Cite

Topographic diversity of fungal and bacterial communities in human skin.

Journal Article Nature · June 20, 2013 Traditional culture-based methods have incompletely defined the microbial landscape of common recalcitrant human fungal skin diseases, including athlete's foot and toenail infections. Skin protects humans from invasion by pathogenic microorganisms and prov ... Full text Link to item Cite

Genomics: Resident risks.

Other Nature · October 4, 2012 An innovative method for probing the genomes of the vast community of microorganisms that inhabit the human gut provides an alternative approach to identifying risk factors for type 2 diabetes. ... Full text Link to item Cite

Competitive genomic screens of barcoded yeast libraries.

Journal Article J Vis Exp · August 11, 2011 By virtue of advances in next generation sequencing technologies, we have access to new genome sequences almost daily. The tempo of these advances is accelerating, promising greater depth and breadth. In light of these extraordinary advances, the need for ... Full text Link to item Cite

Signature-tagged mutagenesis to characterize genes through competitive selection of bar-coded genome libraries.

Chapter · 2011 The availability of collections of genome-wide deletion mutants greatly accelerates systematic analyses of gene function. However, each of the thousands of genes that comprise a genome must be phenotyped individually unless they can be assayed in parallel ... Full text Link to item Cite

Gene annotation and drug target discovery in Candida albicans with a tagged transposon mutant collection.

Journal Article PLoS Pathog · October 7, 2010 Candida albicans is the most common human fungal pathogen, causing infections that can be lethal in immunocompromised patients. Although Saccharomyces cerevisiae has been used as a model for C. albicans, it lacks C. albicans' diverse morphogenic forms and ... Full text Link to item Cite

A universal TagModule collection for parallel genetic analysis of microorganisms.

Journal Article Nucleic Acids Res · August 2010 Systems-level analyses of non-model microorganisms are limited by the existence of numerous uncharacterized genes and a corresponding over-reliance on automated computational annotations. One solution to this challenge is to disrupt gene function using DNA ... Full text Link to item Cite

Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions.

Journal Article Nat Genet · February 2007 Systematic genetic interaction studies have illuminated many cellular processes. Here we quantitatively examine genetic interactions among 26 Saccharomyces cerevisiae genes conferring resistance to the DNA-damaging agent methyl methanesulfonate (MMS), as d ... Full text Link to item Cite

Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes.

Journal Article Gene · February 1, 2006 One of the most important aspects of the evolution of development and physiology is the interplay between gene expression and the environment, by which traits become altered in response to environmental triggers. This feature is known as phenotypic plastic ... Full text Link to item Cite