PNNL

Dr. Sneha Couvillion is a Research Scientist in the Earth and Biological Sciences Directorate at the Pacific Northwest National Laboratory (PNNL) and is based at PNNL’s Sequim campus. Her research leverages mass-spectrometry and integrative omics approaches to uncover small molecules that mediate interactions within microbial communities, their hosts (plants, human) and their environment. She is developing the use of lipidomics and metabolomics in soil microbial ecology to characterize the chemodiversity and functional roles of small molecule that drive plant-microbe-soil interactions for productive ecosystems. Dr. Couvillion received the DOE Early Career Research Award in 2024 and is a Thrust Lead on PNNL’s Soil Microbiome Science Focus Area.

Her DOE Early Career research program is advancing molecular and functional understanding of soil lipids and metabolites, clarifying their contributions to soil fertility, plant productivity, and ecosystem processes relevant to DOE missions in energy security and the bioeconomy.

She currently serves as the elected chair of the Microbial Ecology Section of the Ecological Society of America and is an elected member of the Joint Genome Institute’s user executive committee. She is also a National Microbiome Data Collaborative (NMDC) Champion and advocate for well-curated, FAIR data and data sharing in the microbiome research community.

• Root-soil-microbe interactions in deep soils- impacts on nutrient cycling, plant growth and soil productivity
• Root exudate chemodiversity and functional impact on soil microbes
• Soil lipids and metabolites, and their functions
• Microbial ecology and host-microbe interactions
• Interaction networks between plant roots, arbuscular mycorrhizal fungi and bacteria

• Mass-spectrometry based metabolomics, lipidomics and proteomics
• Chemical Ecology
• Microbial ecology
• Integration of sequencing based, and mass-spectrometry based omics data
• Plant-fungal-bacterial interactions

• PhD in Chemical and Biomolecular Engineering, University of Notre Dame
• MS in Chemical and Biomolecular Engineering, University of Notre Dame
• MT in Chemical Engineering, Jawaharlal Nehru Technological University
• BT in Chemical Engineering, Jawaharlal Nehru Technological University

• Chair (elected) of the Microbial Ecology Section- Ecological Society of America
• Elected member of the Joint Genome Institute’s (JGI) user executive committee
• Member of Metabolomics Association of North America (MANA)
• National Microbiome Data Collaborative (NMDC)- Champion

Department of Energy Early Career Award - 2024

PNNL EBSD BESTies 2023- Above and Beyond- Women of Color Community Network

PNNL EBSD BESTies 2023- Core Value – Creativity

PNNL EBSD BESTies 2022- New PI Award

View complete list of publications on Google Scholar

2025

Rodríguez-Ramos, J., Sadler, N., Zegeye, E.K., Farris, Y., Purvine, S., Couvillion, S., Nelson, W.C. and Hofmockel, K.S., 2025. Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation. mSystems, pp.e01616-24.

Alharithi, Y.J., Phillips, E.A., Wilson, T.D., Couvillion, S.P., Nicora, C.D., Darakjian, P., Rakshe, S., Fei, S.S., Counts, B.R., Metz, T.O. and Searles, R.P., 2025. Metabolomic and transcriptomic remodeling of bone marrow myeloid cells in response to maternal obesity. American Journal of Physiology-Endocrinology and Metabolism, 328(2), pp.E254-E271.

2024

Couvillion, S.P., Nakayasu, E.S., Webb-Robertson, B.J.M., Yang, I.H., Eder, J.G., Nicora, C.D., Bramer, L.M., Gao, Y., Fox, A., DeCarlo, C. and Yang, X., 2024. Associations between SARS-CoV-2 Infection or COVID-19 Vaccination and Human Milk Composition: A Multi-Omics Approach. The Journal of Nutrition, 154(12), pp.3566-3574.

Cruz, A.K., Alves, M.A., Andresson, T., Bayless, A.L., Bloodsworth, K.J., Bowden, J.A., Bullock, K., Burnet, M.C., Neto, F.C., Choy, A. and Clish, C.B., 2024. Multiplatform metabolomic interlaboratory study of a whole human stool candidate reference material from omnivore and vegan donors. Metabolomics, 20(6), p.125.

Harrison, A., Eder, J.G., Lalli, P.M., Munoz, N., Gao, Y., Clendinen, C.S., Orton, D.J., Zheng, X., Williams, S.M., Couvillion, S.P. and Chu, R.K., 2024. PeakQC: A Software Tool for Omics-Agnostic Automated Quality Control of Mass Spectrometry Data. Journal of the American Society for Mass Spectrometry, 35(11), pp.2680-2689.

Liu, J., Cao, S., Imbach, K.J., Gritsenko, M.A., Lih, T.S.M., Kyle, J.E., Yaron-Barir, T.M., Binder, Z.A., Li, Y., Strunilin, I. and Wang, Y.T., 2024. Multi-scale signaling and tumor evolution in high-grade gliomas. Cancer cell, 42(7), pp.1217-1238.

2023

Couvillion, S.P., Danczak, R.E., Naylor, D., Smith, M.L., Stratton, K.G., Paurus, V.L., Bloodsworth, K.J., Farris, Y., Schmidt, D.J., Richardson, R.E. and Bramer, L.M., 2023. Rapid remodeling of the soil lipidome in response to a drying-rewetting event. Microbiome, 11(1), pp.1-20.

Naasko, K.I., Naylor, D., Graham, E.B., Couvillion, S.P., Danczak, R., Tolic, N., Nicora, C., Fransen, S., Tao, H., Hofmockel, K.S. and Jansson, J.K., 2023. Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry. Mbio, 14(5), pp.e01758-23.

Tabb, D.L., Jeong, K., Druart, K., Gant, M.S., Brown, K.A., Nicora, C., Zhou, M., Couvillion, S., Nakayasu, E., Williams, J.E. and Peterson, H.K., 2023. Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection. Journal of Proteome Research.

Couvillion, S.P., Danczak, R.E., Cao, X., Yang, Q., Keerthisinghe, T.P., McClure, R.S., Bitounis, D., Burnet, M.C., Fansler, S.J., Richardson, R.E. and Fang, M., 2023. Graphene oxide exposure alters gut microbial community composition and metabolism in an in vitro human model. NanoImpact, 30, p.100463.

Naylor, D., Naasko, K., Smith, M., Couvillion, S., Nicora, C., Trejo, J., Fransen, S., Danczak, R., McClure, R., Hofmockel, K.S. and Jansson, J.K., 2023. Interactive effects of depth and differential irrigation on soil microbiome composition and functioning. Frontiers in Microbiomes, 2, p.1078024. https://doi.org/10.3389/frmbi.2023.1078024

Couvillion, S.P., Mostoller, K.E., Williams, J.E., Pace, R.M., Stohel, I.L., Peterson, H.K., Nicora, C.D., Nakayasu, E.S., Webb-Robertson, B.J.M., McGuire, M.A. and McGuire, M.K., 2023. Interrogating the role of the milk microbiome in mastitis in the multi-omics era. Frontiers in Microbiology, 14, p.1105675. https://doi.org/10.3389/fmicb.2023.1105675

McClure, R., Garcia, M., Couvillion, S., Farris, Y. and Hofmockel, K.S., 2023. Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy. Frontiers in Microbiology, 13, p.1046661. https://doi.org/10.3389/fmicb.2022.1046661

Shaffer, J.P., Nothias, L.F., Thompson, L.R., Sanders, J.G., Salido, R.A., Couvillion, S.P., Brejnrod, A.D., Lejzerowicz, F., Haiminen, N., Huang, S. and Lutz, H.L., 2022. Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity. Nature microbiology, 7(12), pp.2128-2150 https://doi.org/10.1038/s41564-022-01266-x

2022

Zhang, S., Song, W., Nothias, L.F., Couvillion, S.P., Webster, N. and Thomas, T., 2022. Comparative metabolomic analysis reveals shared and unique chemical interactions in sponge holobionts. Microbiome, 10(1), pp.1-14. https://doi.org/10.1186/s40168-021-01220-9

McClure, R., Farris, Y., Danczak, R., Nelson, W., Song, H.S., Kessell, A., Lee, J.Y., Couvillion, S., Henry, C., Jansson, J.K. and Hofmockel, K.S., 2022. Interaction networks are driven by community-responsive phenotypes in a chitin-degrading consortium of soil microbes. Msystems, 7(5), pp.e00372-22. https://doi.org/10.1128/msystems.00372-22

2021

• Cao X, X Pan, SP Couvillion, T Zhang, C Tamez, LM Bramer, JC White, W-J Qian, BD Thrall, KW Ng, X Hu, P Demokritou. "Fate, cytotoxicity and cellular metabolomic impact of ingested nanoscale carbon dots using simulated digestion and a triculture small intestinal epithelial model." NanoImpact 23: 100349 (2021). doi: 10.1016/j.impact.2021.100349 
• Xu C, SP Couvillion, RL Sontag, NG Isern, Y Maezato, SR Lindemann, TR Chowdhury, R Zhao, BR Morton, RK Chu, RJ Moore, JK Jansson, VL Bailey, PJ Mouser, MF Romine, JF Fredrickson, TO Metz. "MetFish: a Metabolomics Pipeline for Studying Microbial Communities in Chemically Extreme Environments." mSystems 6, no. 3:e01058-20 (2021). doi: 10.1128/mSystems.01058-20
• Zamith-Miranda D, RP da Silva, SP Couvillion, EL Bredeweg, MC Burnet, C Coelho, E Camacho, L Nimrichter, R Puccia, IC Almeida, A Casadevall, ML Rodrigues, LR Alves, JD Nosanchuk, ES Nakayasu. "Omics approaches for understanding biogenesis, composition and functions of fungal extracellular vesicles." Frontiers in Genetics 12:641 (2021). doi: 10.3389/fgene.2021.648524
• Wang L-B, A Karpova, MA Gritsenko, JE Kyle, S Cao, Y Li, D Rykunov, A Colaprico, JH Rothstein, R Hong, V Stathias, M Cornwell, F Petralia, Y Wu, B Reva, K Krug, P Pugliese, E Kawaler, LK Olsen, W-W Liang, X Song, Y Dou, MC Wendl, W Caravan, W Liu, DC Zhou, J Ji, C-F Tsai, VA Petyuk, J Moon, W Ma, RK Chu, KK Weitz, RJ Moore, ME Monroe, R Zhao, X Yang, S Yoo, A Krek, A Demopoulos, H Zhu, MA Wyczalkowski, JF McMichael, BL Henderson, CM Lindgren, H Boekweg, S Lu, J Baral, L Yao, KG Stratton, LM Bramer, E Zink, SP Couvillion, KJ Bloodsworth, S Satpathy, W Sieh, SM Boca, S Schürer, F Chen, M Wiznerowicz, KA Ketchum, ES Boja, CR Kinsinger, AI Robles, T Hiltke, M Thiagarajan, AI Nesvizhskii, B Zhang, DR Mani, M Ceccarelli, XS Chen, SL Cottingham, QK Li, AH Kim, D Fenyö, KV Ruggles, H Rodriguez, M Mesri, SH Payne, AC Resnick, P Wang, RD Smith, A Iavarone, MG Chheda, JS Barnholtz-Sloan, KD Rodland, T Liu, L Ding, A Agarwal, M Amin, E An, ML Anderson, DW Andrews, T Bauer, C Birger, MJ Birrer, L Blumenberg, WE Bocik, U Borate, M Borucki, MC Burke, S Cai, AP Calinawan, SA Carr, S Cerda, D W Chan, A Charamut, LS Chen, D Chesla, AM Chinnaiyan, S Chowdhury, MP Cieślik, DJ Clark, H Culpepper, T Czernicki, F D'Angelo, J Day, S De Young, E Demir, SM Dhanasekaran, R Dhir, MJ Domagalski, B Druker, E Duffy, M Dyer, NJ Edwards, R Edwards, K Elburn, M J Ellis, J Eschbacher, A Francis, S Gabriel, N Gabrovski, L Garofano, G Getz, MA Gillette, AK Godwin, D Golbin, Z Hanhan, LI Hannick, P Hariharan, B Hindenach, KA Hoadley, G Hostetter, C Huang, E Jaehnig, SD Jewell, N Ji, CD Jones, A Karz. "Proteogenomic and metabolomic characterization of human glioblastoma." Cancer Cell 39, no. 4:509-528.e20 (2021). doi: 10.1016/j.ccell.2021.01.006
• AA Aksenov, I Laponogov, Z Zhang, SLF Doran, I Belluomo, D Veselkov, Wt Bittremieux, LF Nothias, M Nothias-Esposito, KN Maloney, BB Misra, AV Melnik, A Smirnov, X Du, KL Jones, K Dorrestein, M Panitchpakdi, M Ernst, JJJ van der Hooft, Ml Gonzalez, C Carazzone, A Amézquita, C Callewaert, JT Morton, RA Quinn, A Bouslimani, AA Orio, D Petras, AM Smania, SP Couvillion, MC Burnet, CD Nicora, E Zink, TO Metz, V Artaev, E Humston-Fulmer, R Gregor, MM Meijler, Ik Mizrahi, S Eyal, B Anderson, R Dutton, R Lugan, P Le Boulch, Y Guitton, S Prevost, A Poirier, G Dervilly, B Le Bizec, A Fait, NS Persi, C Song, K Gashu, R Coras, M Guma, J Manasson, JU Scher, DK Barupal, S Alseekh, AR Fernie, R Mirnezami, V Vasiliou, R Schmid, RS Borisov, LN Kulikova, R Knight, M Wang, GB Hanna, PC Dorrestein, K Veselkov. "Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data." Nature Biotechnology 39, no. 2:169-173 (2021). doi: 10.1038/s41587-020-0700-3

2020

• Couvillion SP, Agrawal N, Colby SM, Brandvold KR, Metz TO. “Who Is Metabolizing What? Discovering Novel Biomolecules in the Microbiome and the Organisms Who Make Them.” Frontiers in Cellular and Infection Microbiology 10, 388. (2020). https://doi.org/10.3389/fcimb.2020.00388
• Cleare L.G., D. Zamith-Miranda, H.M. Heyman, S.P. Couvillion, L. Nimrichter, M.L. Rodrigues, and E.S. Nakayasu, et al. 2020. "Media Matters! Alterations in the loading and release of Histoplasma capsulatum extracellular vesicles in response to different nutritional milieus." Cellular Microbiology 22, no. 9:Article No. e13217. PNNL-SA-151908. doi:10.1111/cmi.13217
• Khare S., G.M. Deloid, R.M. Molina, K. Gokulan, S.P. Couvillion, K.J. Bloodsworth, and E.K. Eder, et al. 2020. "Effects of ingested nanocellulose on intestinal microbiota and homeostasis in Wistar Han rats." NanoImpact 18. PNNL-SA-149247. doi:10.1016/j.impact.2020.100216

2019

• Zamith-Miranda D., H.M. Heyman, L.G. Cleare, S.P. Couvillion, G. Clair, E.L. Bredeweg, and A. Gacser, et al. 2019. "Multi-omics signature of Candida Auris, an emerging and multidrug-resistant pathogen." mSystems 4, no. 4:e00257-19. PNNL-SA-140174. doi:10.1128/mSystems.00257-19
• Couvillion, Sneha P., et al. "New mass spectrometry technologies contributing towards comprehensive and high throughput omics analyses of single cells." Analyst 144.3 (2019): 794-807. 10.1039/C8AN01574K

2017

Polisetti, S., Baig, N.F., Morales-Soto, N., Shrout, J.D. and Bohn, P.W., 2017. Spatial mapping of pyocyanin in Pseudomonas aeruginosa bacterial communities using surface enhanced Raman scattering. Applied spectroscopy, 71(2), pp.215-223.

2016

Baig, N., Polisetti, S., Morales-Soto, N., Dunham, S.J., Sweedler, J.V., Shrout, J.D. and Bohn, P.W., 2016, September. Label-free molecular imaging of bacterial communities of the opportunistic pathogen Pseudomonas aeruginosa. In Biosensing and Nanomedicine IX (Vol. 9930, pp. 2-9). SPIE. https://doi.org/10.1117/12.2236695

Bible, A.N., Fletcher, S.J., Pelletier, D.A., Schadt, C.W., Jawdy, S.S., Weston, D.J., Engle, N.L., Tschaplinski, T., Masyuko, R., Polisetti, S. and Bohn, P.W., 2016. A carotenoid-deficient mutant in Pantoea sp. YR343, a bacteria isolated from the rhizosphere of Populus deltoides, is defective in root colonization. Frontiers in microbiology, 7, p.491. https://doi.org/10.3389/fmicb.2016.00491

Polisetti, S., Bible, A.N., Morrell-Falvey, J.L. and Bohn, P.W., 2016. Raman chemical imaging of the rhizosphere bacterium Pantoea sp. YR343 and its co-culture with Arabidopsis thaliana. Analyst, 141(7), pp.2175-2182. https://doi.org/10.1039/C6AN00080K

(Publications prior to 2018 use maiden name Sneha Polisetti)