Julie Segre Lab

We integrate DNA sequence technology, algorithm development and clinical studies to explore the diversity of microbes in and on humans in health and disease.

Our Research

The Segre lab studies the human microbiome, investigating both the transmission of hospital pathogens and the diversity of beneficial skin organisms, including bacteria, fungi and viruses. Their research spans the human lifespan, from childhood eczema to the microbiome of aging Americans, with the goal of developing precision medicine treatments.

Flourescent microscopy showing fungi attached to a hair follicle
Research
Lab Members
Publications

Publication Highlights

Strain sharing and persistence of microbial pathogens colonizing the skin of residents in a regional nursing home network

Hounmanou YMG, Gussin GM, Conlan S, Singh RD, Deming C, Proctor DM, Teixeira M, Earl AM, Worby CJ, Kong HH, Huang SS, Segre JA, Nat Commun (2026)

Shotgun metagenomics reveals skin microbiome composition and function in infant atopic disease

Shen Z, Eckert JK, Saffery R, Allen KJ, Walsh A; VITALITY team; Deming C, Chen Q, Laky K, Li JM, Chatman L; NISC Comparative Sequencing Program; Kong HH, Perrett KP, Segre JA, Frischmeyer-Guerrerio PA, Allergy (2026)

Trichophyton concentricum fungal infections and the skin microbiomes of Indigenous Peninsular Malaysians

Er YX, Lee SC, Aneke C, Conlan S, Muslim A, Deming C, Che Y, Yap NJ, Tee MZ, Abdull-Majid N, Shahrizal S, Leong KF, Han J, Shen Z, Than LTL, Park M, Sayed IM, NISC Comparative Sequencing Program, Seyedmousavi A, Kong HH, Loke P, Segre JA*, Lim YA L*, Cell (2025)

Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes

Proctor DM, Sansom SE, Deming C, Conlan S, Blaustein RA, Atkins TK, NISC Comparative Sequencing Program, Dangana T, Fukuda C, Thotapalli L, Kong HH, Lin MY, Hayden MK, Segre JA, Nature (2025)

Skin microbiome and dermatologic disorders

Scharschmidt TC, Segre JA, Journal of Clinical Investigation (2025)

Fungal impacts on Earth’s ecosystems

Case NT, Gurr SJ, Fisher MC, Blehert DS, Boone C, Casadevall A, Chowdhary A, Cuomo CA, Currie CR, Denning DW, Ene IV, Fritz-Laylin LK, Gerstein AC, Gow NA R, Gusa A, Iliev ID, James TY, Jin H, Kahmann R, Klein BS, Kronstad JW, Ost KS, Peay KG, Shapiro RS, Sheppard DC, Shlezinger N, Stajich JE, Stukenbrock EH, Taylor JW, Wright GD, Cowen LE*, Heitman J*, Segre JA*, Nature (2025)

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 Biology (2023)

Integrated genomic and functional analyses of human skin-associated Staphylococcus reveals extensive inter- and intraspecies diversity

Joglekar P, Conlan S, Lee-Lin SQ, Deming C, Kashaf SS, NISC Comparative Sequencing Program, Kong HH, Segre JA, PNAS (2023)

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

Kashaf SS, Proctor DM, Deming C, Saary P, Hölzer M, NISC Comparative Sequencing Program, Taylor ME, Kong HH, Segre JA*, Almeida A*, Finn RD*, Nature Microbiology (2022)

Integrated genomic, epidemiologic investigation of Candida auris skin colonization in a skilled nursing facility

Proctor DM, Dangana T, Sexton DJ, Fukuda C, Yelin RD, Stanley M, Bell PB, Baskaran S, Deming C, Chen Q, Conlan S, Park M, NISC Comparative Sequencing Program, Welsh RM, Vallabhaneni S, Chiller T, Forsberg K, Black SR, Pacilli M, Kong HH, Lin MY, Schoeny ME, Litvintseva AP, Segre JA*, Hayden MK*, Nature Medicine (2021)

View all publications on PubMed

Contact Us

Administrative Support

Natalie Bartolacci
734-615-9787
Life Sciences Institute
Mary Sue Coleman Hall
210 Washtenaw Avenue
Ann Arbor, MI 48109-2216
[email protected]