Biomedical Scientist
Biomedical Scientist


I am a Staff Scientist in the Earth and Biological Sciences Directorate at the Pacific Northwest National Laboratory (PNNL), Richland, WA. My research leverages mass-spectrometry and integrative omics approaches to uncover small molecules that mediate interactions within microbial communities and their hosts. As a Thrust Lead in PNNL’s Soil Microbiome Science Focus Area, I lead a team investigating the impact of drought on plant root exudate chemodiversity and plant-microbe interactions in the rhizosphere. I am developing the use of lipidomics in soil microbial ecology as a highly sensitive approach to measure the phenotypic responses of soil biota to environmental change and substrate availability. On the human health front, I am investigating the functional roles of small molecules and proteins in gut and milk microbiomes, circadian biology and immunometabolism. My work is helping characterize the chemodiversity and functional roles of small molecule metabolites and lipids driving interkingdom interactions for sustainable energy and human health.

I currently serve as the Secretary for the Microbial Ecology section of Ecological Society of America (ESA). I am an National Microbiome Data Collaborative (NMDC) Champion and advocate for well-curated, FAIR data and data sharing in the microbiome research community. I am on the EBSD Diversity and Inclusion Council at PNNL and have founded the PNNL Women of Color Community to foster a more diverse and inclusive research community in the national laboratories.

Research Interest

  • Microbial ecology and host-microbe interactions
  • Plant-soil-microbe interactions in the rhizosphere
  • Root exudate chemodiversity and impact on microbial community metabolism
  • Microbial lipids


Disciplines and Skills

  • Mass spectrometry based metabolomics, lipidomics and proteomics
  • Microbial ecology
  • Integration of sequencing based, and mass-spectrometry based omics data


  • 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

Affiliations and Professional Service

  • Member of the Ecological Society of America- Secretary of Microbial Ecology Section
  • Member of Metabolomics Association of North America (MANA)
  • National Microbiome Data Collaborative (NMDC)- Champion

Awards and Recognitions

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


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. Microbiome11(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. Mbio14(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. NanoImpact30, 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 Microbiomes2, p.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 Microbiology14, p.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 Microbiology13, p.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 microbiology7(12), pp.2128-2150


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. Microbiome10(1), pp.1-14.

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. Msystems7(5), pp.e00372-22.


  • 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


  • 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).
  • 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


  • 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


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 spectroscopy71(2), pp.215-223.


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.

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 microbiology7, p.491.

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. Analyst141(7), pp.2175-2182.

(Publications prior to 2018 use maiden name Sneha Polisetti)