Research | Lynch Lab

Research in the Lynch Lab focuses primarily on the human microbiota in both respiratory and gastrointestinal tracts, environmental microbial exposures that shape its development and its role in chronic inflammatory diseases.

Early-life Microbial Contributions to Disease

Leverage the gut microbiome to predict disease risk
Identify early-life pathogenic community states and the underlying mechanisms of disease genesis

Compositionally distinct gut microbiota classes (GMCs) in feces of 1-month-old infants

Precocious infant fecal microbioma promotes enterocyte barrier dysfunction, altered neuroendocrine signaling and associates with increased childhood obecity risk

Yong GJM, Porsche CE, Sitarik AR, Fujimura KE, McCauley K, Nguyen DT, Levin AM, Woodcroft KJ, Ownby DR, Rundle AG, Johnson CC, Cassidy-Bushrow A, Lynch SV. Gut Microbes. 2024, Jan-Dec;16(1):2290661. doi: 10.1080/19490976.2023.2290661

maternal and early-life epigenetic, immunologic and microbial features that influence asthma development during childhood

Maternal prenatal immunity, neonatal trained immunity, and early airway microbiota shape childhood asthma development

DeVries A, McCauley K, Fadrosh D, Fujimura KE, Stern DA, Lynch SV, Vercelli D. Allergy. 2022, Dec;77(12):3617-3628. doi: 10.1111/all.15442

Factors affecting human gut and airway microbiome development through the lifespan

The gut-airway microbiome axis in health and respiratory disease

Özçam M, Lynch SV. Nat Rev Microbiol. 2024, Aug;22(8):492-506. doi: 10.1038/s41579-024-01048-8.

Microbial Mechanisms of Chronic Inflammatory Disease

Developing tools to understand microbial interactions with host responses
Understanding microbiome-mediated clinical and immunological outcomes.
Evaluating microbiome dynamics in response to treatment interventions.
Exploring microbiome perturbations in respiratory and gastrointestinal diseases.

Enhanced microbiome protein metabolism associated with peanut oral immunotherapy failure

Gut microbial bile and amino acid metabolism associate with peanut oral immunotherapy failure

Özçam M, Lin DL, Gupta CL, Li A, Gomez JC, Wheatley LM, Baloh CH, Sanda S, Jones SM, Lynch SV. Nature Communications, 2025 Jul 9;16 (1):6330. doi: 10.1038/s41467-025-61161-x

DREAM challenge participants predicted preterm birth from vaginal microbiome data

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S; Preterm Birth DREAM Community; Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Cell Rep Med. 2024, Jan 16;5(1):101350. doi: 10.1016/j.xcrm.2023.101350

12,13-diHOME treatment reduced global chromatin accessibility specifically targeting interferon-response elements

12,13-diHOME Promotes Inflammatory Macrophages and Epigenetically Modifies Their Capacity to Respond to Microbes and Allergens

Lin DL, Magnaye KM, Porsche CE, Levan SR, Rackaityte E, Özçam M, Lynch SV. J Immunol Res. 2024, Jun 29;2024:2506586. doi: 10.1155/2024/2506586

Illustrating mechanisms, metrics and modifiers through the example of IBD

Clinical translation of microbiome research

Gilbert JA, Azad MB, Bäckhed F, Blaser MJ, Byndloss M, Chiu CY, Chu H, Dugas LR, Elinav E, Gibbons SM, Gilbert KE, Henn MR, Ishaq SL, Ley RE, Lynch SV, Segal E, Spector TD, Strandwitz P, Suez J, Tropini C, Whiteson K, Knight R. Nature Medicine, 2025 Apr;31(4):1099-1113. doi: 10.1038/s41591-025-03615-9

PCoA showing weighted UniFrac beta diversity for all baseline and 12-month samples color-coded by dominant genus found in the sample

Moraxella-dominated pediatric nasopharyngeal microbiota associate with upper respiratory infection and sinusitis

McCauley KE, DeMuri G, Lynch K, Fadrosh DW, Santee C, Nagalingam NN, Wald ER, Lynch SV. PLoS One., 2021 Dec 28;16(12):e0261179. doi: 10.1371/journal.pone.0261179

Staphylococcus and Moraxella species–dominated nasal airway microbiotas exhibit temporal stability in children with asthma.

Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma

McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, Merana G, Lynch K, Cohen RT, Pongracic J, Khurana Hershey GK, Kercsmar CM, Gill M, Liu AH, Kim H, Kattan M, Teach SJ, Togias A, Boushey HA, Gern JE, Jackson DJ, Lynch SV; National Institute of Allergy and Infectious Diseases–sponsored Inner-City Asthma Consortium. J Allergy Clin Immunol., 2019. Nov;144(5):1187-1197. doi: 10.1016/j.jaci.2019.05.035

Community ecology as a framework for human microbiome research

Gilbert JA, Lynch SV. Nature Medicine, 2019. Nat Med. 2019 Jun;25(6):884-889. doi: 10.1038/s41591-019-0464-9

Microbiome-Based Strategies for Immune Health and Disease Prevention

Develop rationally designed probiotic and synbiotic cocktails for induction of immune tolerance.
Modulating microbiota during critical early-life windows to reduce disease risk.
Investigating microbiome-based interventions for inflammatory diseases and allergies.

Antibiotic-pretreated FMT-responsive patients are depleted of transcriptionally active bacteria on the colonic mucosa

Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients

Zhang B, Magnaye KM, Stryker E, Moltzau-Anderson J, Porsche CE, Hertz S, McCauley KE, Smith BJ, Zydek M, Pollard KS, Ma A, El-Nachef N, Lynch SV. Scientific Reports, 2024 Aug 9;14(1):18558. doi: 10.1038/s4158-024-62463-8

Gut Bifidobacteria enrichment following oral Lactobacillus-supplementation is associated with clinical improvements in children with cystic fibrosis

Ray KJ, Santee C, McCauley K, Panzer AR, Lynch SV. Gut Bifidobacteria enrichment following oral Lactobacillus-supplementation is associated with clinical improvements in children with cystic fibrosis. BMC Pulmonalr Medicine, 2022 Jul 28;22(1):287. doi: 10.1186/s12890-022-02078-9

Neonatal gut-microbiome-derived EH genes from B. bifidum and E. faecalis produce 12,13-diHOME and decrease the number of lung Treg cells in mice challenged with CRA

Elevated faecal 12,13-diHOME concentration in neonates at high risk for asthma is produced by gut bacteria and impedes immune tolerance

Levan SR, Stamnes KA, Lin DL, Panzer AR, Fukui E, McCauley K, Fujimura KE, McKean M, Ownby DR, Zoratti EM, Boushey HA, Cabana MD, Johnson CC, Lynch SV. Nature Microbiology, 2019, Nov;4(11):1851-1861. doi: 10.1038/s41564-019-0498-2.

In healthy adults, the gut microbiome exists in a state of mutual symbiosis with its host

The gut microbiome:Relationships with disease and opportunities for therapy

Durack J, Lynch SV. J Exp Med. 2019, Jan 7;216(1):20-40. doi: 10.1084/jem.20180448

Developing tools to understand microbial interactions with host responses

Developing CRISPR-Cas tools to target inflammatory bacterial genes and advance microbiome-based asthma therapies.
Investigating gut and upper airway microbiomes to identify microbial traits linked to asthma risk.

Oral Microbiome in Periodontal Disease

Exploring how oral microbiome composition and activity contribute to periodontal disease progression.
Aims to inform personalized treatment strategies for periodontal disease.

The Oral Microbiome: From First Encounters to Lifelong Encounters

The oral microbiome: Role of key organisms and comples networks in oral health and disease

Sedghi L, DiMassa V, Harrington A, Lynch SV, Kapila YL. Periodontol 2000-2021, Oct;87(1):107-131. doi: 10.1111/prd.12393