What drives us

Research

Our work sits at the intersection of classical microbiology, ecology, and genomics. We care equally about the biology we uncover and the reproducibility of how we uncover it. Below are the questions we keep returning to, followed by our publications. Every paper links to a freely downloadable PDF.

What we study

Research themes

01

Microbiome Disruption

Determining how microbiomes are disrupted in disease, and how to restore them.

02

What defines the commensal to pathogen transition?

Identifying the molecular and ecological factors that drive the transition from commensal to pathogen

03

Open, reproducible research

Software and pipelines that anyone can run, audit, and build on — because results should be repeatable.

Selected work

Publications

2025

  • Host- and microbial-mediated mucin degradation differentially shape Pseudomonas aeruginosa physiology and gene expression.

    Arif SJ, Hoffman KM, Flynn JM, Wiggen TD, Lucas SK, Villarreal AR, Gilbertsen AJ, Dunitz JM, Hunter RC.

    PLoS Pathog. 21(10):e1013568, 2025

    Pseudomonas aeruginosamucin
    PDF DOI

  • Dual oxic-anoxic co-culture enables direct study of anaerobe-host interactions at the airway epithelial interface.

    Moore PJ, Hoffman K, Ahmed S, Fletcher JR, Wiggen TD, Lucas SK, Arif SJ, Gilbertsen AJ, Kent LA, Fiege JK, Langlois RA, O'Grady SM, Hunter RC.

    mBio. 16(5):e0133824, 2025

    airwayanaerobesco-culture
    PDF DOI

2024

  • Genomics and synthetic community experiments uncover the key metabolic roles of acetic acid bacteria in sourdough starter microbiomes.

    Rappaport HB, Senewiratne NPJ, Lucas SK, Wolfe BE, Oliverio AM.

    mSystems. 9(10):e0053724, 2024

    sourdoughmicrobiomegenomics
    PDF DOI

2023

  • Industrialized human gut microbiota increases CD8+ T cells and mucus thickness in humanized mouse gut.

    Vangay P, Ward T, Lucas S, Beura LK, Sabas D, Abramson M, Till L, Hoops SL, Kashyap P, Hunter RC, Masopust D, Knights D.

    Gut Microbes. 15(2):2266627, 2023

    gut microbiome
    PDF DOI

  • High-throughput quantification of microbial-derived organic acids in mucin-rich samples via reverse phase high performance liquid chromatography.

    Villarreal AR, Lucas SK, Fletcher JR, Hunter RC.

    J Med Microbiol. 72(6), 2023

    methodsHPLCmucin
    DOI

2022

  • Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research.

    Lapp Z, Sovacool KL, Lesniak N, King D, Barnier C, Flickinger M, Krüger J, Armour CR, Lapp MM, Tallant J, Diao R, Oneka M, Tomkovich S, Anderson JM, Lucas SK, Schloss PD.

    J Open Source Educ. 5(47), 2022

    educationreproducibility
    PDF DOI

2021

  • Anaerobic Microbiota Derived from the Upper Airways Impact Staphylococcus aureus Physiology.

    Lucas SK, Villarreal AR, Ahmad MM, Itabiyi A, Feddema E, Boyer HC, Hunter RC.

    Infect Immun. 89(9):e0015321, 2021

    Staphylococcus aureusairway microbiota
    PDF DOI

  • Diversity of cystic fibrosis chronic rhinosinusitis microbiota correlates with different pathogen dominance.

    Lucas SK, Feddema E, Boyer HC, Hunter RC.

    J Cyst Fibros. 20(4):678-681, 2021

    cystic fibrosisrhinosinusitis
    PDF DOI

2020

  • Bioorthogonal non-canonical amino acid tagging reveals translationally active subpopulations of the cystic fibrosis lung microbiota.

    Valentini TD, Lucas SK, Binder KA, Cameron LC, Motl JA, Dunitz JM, Hunter RC.

    Nat Commun. 11(1):2287, 2020

    cystic fibrosisBONCAT
    PDF DOI

2019

  • Co-occurrence of Anaerobes in Human Chronic Wounds.

    Choi Y, Banerjee A, McNish S, Couch KS, Torralba MG, Lucas S, Tovchigrechko A, Madupu R, Yooseph S, Nelson KE, Shanmugam VK, Chan AP.

    Microb Ecol. 77(3):808-820, 2019

    chronic woundsanaerobes
    DOI

2018

  • US Immigration Westernizes the Human Gut Microbiome.

    Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, Lucas SK, Beura LK, Thompson EA, Till LM, Batres R, Paw B, Pergament SL, Saenyakul P, Xiong M, Kim AD, Kim G, Masopust D, Martens EC, Angkurawaranon C, McGready R, Kashyap PC, Culhane-Pera KA, Knights D.

    Cell. 175(4):962-972.e10, 2018

    gut microbiome
    PDF DOI

  • 16S rRNA gene sequencing reveals site-specific signatures of the upper and lower airways of cystic fibrosis patients.

    Lucas SK, Yang R, Dunitz JM, Boyer HC, Hunter RC.

    J Cyst Fibros. 17(2):204-212, 2018

    cystic fibrosis16S rRNA
    PDF DOI

2016

  • Electrochemical detection of Pseudomonas in wound exudate samples from patients with chronic wounds.

    Sismaet HJ, Banerjee A, McNish S, Choi Y, Torralba M, Lucas S, Chan A, Shanmugam VK, Goluch ED.

    Wound Repair Regen. 24(2):366-72, 2016

    Pseudomonasbiosensor
    PDF DOI

  • Looking Beyond Respiratory Cultures: Microbiome-Cytokine Signatures of Bacterial Pneumonia and Tracheobronchitis in Lung Transplant Recipients.

    Shankar J, Nguyen MH, Crespo MM, Kwak EJ, Lucas SK, McHugh KJ, Mounaud S, Alcorn JF, Pilewski JM, Shigemura N, Kolls JK, Nierman WC, Clancy CJ.

    Am J Transplant. 16(6):1766-78, 2016

    lung transplantmicrobiome
    DOI

2013

  • A multi-omic systems-based approach reveals metabolic markers of bacterial vaginosis and insight into the disease.

    Yeoman CJ, Thomas SM, Miller ME, Ulanov AV, Torralba M, Lucas S, Gillis M, Cregger M, Gomez A, Ho M, Leigh SR, Stumpf R, Creedon DJ, Smith MA, Weisbaum JS, Nelson KE, Wilson BA, White BA.

    PLoS One. 8(2):e56111, 2013

    bacterial vaginosismulti-omics
    PDF DOI

2012

  • Integrated next-generation sequencing of 16S rDNA and metaproteomics differentiate the healthy urine microbiome from asymptomatic bacteriuria in neuropathic bladder associated with spinal cord injury.

    Fouts DE, Pieper R, Szpakowski S, Pohl H, Knoblach S, Suh MJ, Huang ST, Ljungberg I, Sprague BM, Lucas SK, Torralba M, Nelson KE, Groah SL.

    J Transl Med. 10:174, 2012

    urine microbiomemetaproteomics
    PDF DOI