The Kelly lab: through the microbiome looking glass.

The microbiome is a personal and flexible ecosystem of bacteria, viruses, fungi, and small eukaryotes living in and on our bodies. Our lab is interested in the microbiome as a sentinel of human physiology, constantly sensing, processing, and responding to signals from internal and external perturbations. My lab seeks to understand the processes and interactions that drive microbiome connections to, and influence over, human physiology by studying microbiomes as complex, interconnected systems using multi-disease, multi-ecosystem approaches. The broader goal of our work is to understand how to harness microbial ecology, from our bodies to the global oceans, to improve ecosystem health. Our publications have generated new insights into microbiome drug metabolism, discovered novel phage populations, pioneered computational approaches to improve analysis of microbiome data, and characterized novel connections between microbiome dynamics and disease.

Flamholz ZN, Biller SJ, Kelly L. Large language models improve annotation of prokaryotic viral proteins. Nat Microbiol. 2024 Feb;9(2):537-549. doi: 10.1038/s41564-023-01584-8. Epub 2024 Jan 29. PMID: 38287147

Li H, Kazmi JS, Lee S, Zhang D, Gao X, Maryanovich M, Torres L, Verma D, Kelly L, Ginzburg YZ, Frenette PS, Manwani D. Dietary iron restriction protects against vaso-occlusion and organ damage in murine sickle cell disease. Blood. 2023 Jan 12;141(2):194-199. doi: 10.1182/blood.2022016218. PMID: 36315910; PMCID: PMC10023724.

Wolfson SJ, Hitchings R, Peregrina K, Cohen Z, Khan S, Yilmaz T, Malena M, Goluch ED, Augenlicht L, Kelly L. Bacterial hydrogen sulfide drives cryptic redox chemistry in gut microbial communities. Nat Metab. 2022 Oct;4(10):1260-1270. doi: 10.1038/s42255-022-00656-z. Epub 2022 Oct 20. PMID: 36266544.

Kauffman KM†, Chang WK†, Brown JM, Hussain FA, Yang J, Polz MF*, Kelly L*. Resolving the structure of phage-bacteria interactions in the context of natural diversity. Nat Commun. 2022 Jan 18;13(1):372. PMID: 35042853; PMCID: PMC8766483.

Lasso G†, Khan S†, Allen SA†, Mariano M, Florez C, Orner EP, Quiroz JA, Quevedo G, Massimi A, Hegde A, Wirchnianski AS, Bortz RH 3rd, Malonis RJ, Georgiev GI, Tong K, Herrera NG, Morano NC, Garforth SJ, Malaviya A, Khokhar A, Laudermilch E, Dieterle ME, Fels JM, Haslwanter D, Jangra RK, Barnhill J, Almo SC, Chandran K*, Lai JR*, Kelly L*, Daily JP*, Vergnolle O*. Longitudinally monitored immune biomarkers predict the timing of COVID-19 outcomes. PLoS Comput Biol. 2022 Jan 18;18(1):e1009778. doi: 10.1371/journal.pcbi.1009778. PMID: 35041647; PMCID: PMC8812869.  

Yang JY, Fang W, Miranda-Sanchez F, Brown JM, Kauffman KM, Acevero CM, Bartel DP*, Polz MF*, Kelly L*. Degradation of host translational machinery drives tRNA acquisition in viruses. Cell Syst. 2021 Aug 18;12(8):771-779.e5. doi: 10.1016/j.cels.2021.05.019. Epub 2021 Jun 17. PMID: 34143976; PMCID: PMC8826309.

Chang WK, VanInsberghe D, Kelly L. Topological analysis reveals state transitions in human gut and marine bacterial communities. NPJ Biofilms Microbiomes. 2020 Oct 14;6(1):41. doi: 10.1038/s41522-020-00145-9. PMID: 33057043; PMCID: PMC7560872.

Guthrie L, Wolfson S, Kelly L. The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs. Elife. 2019 Jun 11;8. doi: 10.7554/eLife.42866. PubMed PMID: 31184303; PMCID:PMC6559788.

Guthrie L, Gupta S, Daily J, Kelly L. Human microbiome signatures of differential colorectal cancer drug metabolism. NPJ Biofilms Microbiomes. 2017 Nov 1;3:27. doi: 10.1038/s41522-017-0034-1. eCollection 2017. PMID:29104759; PMCID: PMC5665930

(†= co-first author; *=co-corresponding author). 

Complete publications list

https://scholar.google.com/citations?user=sg7-rm4AAAAJ&hl=en

https://pubmed.ncbi.nlm.nih.gov/?term=Libusha+Kelly&sort=date