Soumyadev SARKAR

Citation Number: 780+; h-index: 12; Total publications: 32; First author publications: 12; Corresponding Author Publications: 4

Peer-Reviewed Articles

1. Kazarina, Anna, Soumyadev Sarkar, Bryttan Adams, Brooke Vogt, Leslie Rodela, Sophia Pogranichny, Summer Powell, et al. 2025. “Interaction of Plant-Derived Metabolites and Rhizobiome Functions Enhances Drought Stress Tolerance.” Genome Biology 26 (1). https://doi.org/10.1186/s13059-025-03778-1.
2. Kazarina, Anna, Hallie Wiechman, Soumyadev Sarkar, Tanner Richie, and Sonny T. M. Lee. 2025. “Recovery of 679 Metagenome-Assembled Genomes from Different Soil Depths along a Precipitation Gradient.” Scientific Data 12 (1): 521.  DOI: https://www.nature.com/articles/s41597-025-04884-2
3. Sarkar, Soumyadev, Anna Kazarina, Paige M. Hansen, Kaitlyn Ward, Christopher Hargreaves, Nicholas Reese, Qinghong Ran, et al. 2025. “Metabolism Diversification of Ammonia-Oxidizing Archaea and Bacteria under Different Precipitation Gradients and Land Legacies.” Applied Soil Ecology: A Section of Agriculture, Ecosystems & Environment 206 (105831): 105831. DOI: https://www.sciencedirect.com/science/article/pii/S0929139324005626
4. HerediaVelásquez, Ana Mercedes*, Soumyadev Sarkar*, Finlay Warsop Thomas, Ariadna Cairó Baza, and Ferran Garcia-Pichel. 2024. “Urea-Based Mutualistic Transfer of Nitrogen in Biological Soil Crusts.” The ISME Journal, December, wrae246. DOI: https://doi.org/10.1093/ismejo/wrae246 (*Co-first authors)
5. Richie, Tanner G., Leah Heeren, Abigail Kamke, Kourtney Monk, Sophia Pogranichniy, Trey Summers, Hallie Wiechman, Qinghong Ran, Soumyadev Sarkar, Brandon L Plattner, Sonny TM Lee 2023. “Limitation of Amino Acid Availability by Bacterial Populations during Enhanced Colitis in IBD Mouse Model.” MSystems, November, e0070323.
6. Kazarina, Anna, Soumyadev Sarkar, Shiva Thapa, Leah Heeren, Abgail Kamke, Kaitlyn Ward, Eli Hartung, et al. 2023. “Home-Field Advantage Affects the Local Adaptive Interaction between Andropogon Gerardii Ecotypes and Root-Associated Bacterial Communities.” Microbiology Spectrum, August, e0020823.
7. Sarkar, Soumyadev, Abigail Kamke, Kaitlyn Ward, Eli Hartung, Qinghong Ran, Brandi Feehan, Matthew Galliart, Ari Jumpponen, Loretta Johnson, and Sonny T. M. Lee. 2022. “Pseudomonas Cultivated from Andropogon Gerardii Rhizosphere Show Functional Potential for Promoting Plant Host Growth and Drought Resilience.” BMC Genomics 23 (1): 784. https://doi.org/10.1186/s12864-022-09019-0
8. Sarkar, Soumyadev, Abigail Kamke, Kaitlyn Ward, Aoesta K. Rudick, Sara G. Baer, Qinghong Ran, Brandi Feehan, et al. 2022. “Bacterial but Not Fungal Rhizosphere Community Composition Differ among Perennial Grass Ecotypes under Abiotic Environmental Stress.” Microbiology Spectrum,        April,   e0239121.  https://journals.asm.org/doi/full/10.1128/spectrum.02391-21
9. Gupta, Suchetana, Ditipriya Mallick, Kumarjeet Banerjee, Shrimon Mukherjee, Soumyadev Sarkar, Sonny Tm Lee, Partha Basuchowdhuri, and Siddhartha S. Jana. 2022. “D155Y Substitution of SARS-CoV-2 ORF3a Weakens Binding with Caveolin-1.” Computational and Structural             Biotechnology             Journal            20        (January):        766–78. https://doi.org/10.1016/j.csbj.2022.01.017
10. Mukherjee, Avishek, Soumyadev Sarkar, Rubia Parvin, Debbethi Bera, Uttariya Roy, and Ratan Gachhui. 2020. “Remarkably High Pb2+ Binding Capacity of a Novel, Regenerable Bioremediator Papiliotrema Laurentii RY1: Functional in Both Alkaline and Neutral Environments.” Ecotoxicology and Environmental Safety 195 (June): 110439. DOI: https://doi.org/10.1016/j.ecoenv.2020.110439
11. Bhattacharya, Debanjana, Ritam Sinha, Priyadarshini Mukherjee, Debaki Ranjan Howlader, Dhrubajyoti Nag, Soumyadev Sarkar, Hemanta Koley, Jeffrey H. Withey, and Ratan Gachhui. 2020. “Anti-Virulence Activity of Polyphenolic Fraction Isolated from Kombucha against Vibrio Cholerae.”  Microbial Pathogenesis 140 (March):          103927. DOI https://doi.org/10.1016/j.micpath.2019.103927
12. Mukherjee, Avishek, Soumyadev Sarkar, Suchetana Gupta, Sayanika Banerjee, Sanjib Senapati, Riya Chakrabarty, and Ratan Gachhui. 2019. “DMSO Strengthens Chitin DeacetylaseChitin Interaction: Physicochemical, Kinetic, Structural and Catalytic Insights.” Carbohydrate Polymers 223 (November): 115032. DOI: https://doi.org/10.1016/j.carbpol.2019.115032
13. Sarkar, Soumyadev, Avishek Mukherjee, Subhadeep Das, Bidisha Ghosh, Shouvik Chaudhuri, Debanjana Bhattacharya, Arpita Sarbajna, and Ratan Gachhui. 2019. “Nitrogen Deprivation Elicits Dimorphism, Capsule Biosynthesis and Autophagy in Papiliotrema Laurentii Strain RY1.”  Micron 124 (September) 102708.  DOI https://doi.org/10.1016/j.micron.2019.102708
14. Sarkar, Soumyadev, Avishek Mukherjee, Rubia Parvin, Subhadeep Das, Uttariya Roy, Somdeep Ghosh, Punarbasu Chaudhuri, et al. 2019. “Removal of Pb (II), As (III), and Cr (VI) by Nitrogen-Starved Papiliotrema Laurentii Strain RY1.” Journal of Basic Microbiology 59 (10): 1016–30. DOI: https://doi.org/10.1002/jobm.201900222
15. Sarkar, Soumyadev, Somnath Chakravorty, Avishek Mukherjee, Debanjana Bhattacharya, Semantee Bhattacharya, and Ratan Gachhui. 2018. “De Novo RNA-Seq Based Transcriptome Analysis of Papiliotrema Laurentii Strain RY1 under Nitrogen Starvation.” Gene 645 (March): 146–56. DOI:  https://doi.org/10.1016/j.gene.2017.12.014
16. Sarkar, Soumyadev, Suchetana Gupta, Writachit Chakraborty, Sanjib Senapati, and Ratan Gachhui. 2017. “Homology Modeling, Molecular Docking and Molecular Dynamics Studies of the Catalytic Domain of Chitin Deacetylase from Cryptococcus Laurentii Strain RY1.” International Journal of Biological Macromolecules 104 (Pt B): 1682–91. DOI:https://doi.org/10.1016/j.ijbiomac.2017.03.057
17. Bhattacharya, Debanjana, Deblina Ghosh, Semantee Bhattacharya, Soumyadev Sarkar, Parimal Karmakar, Hemanta Koley, and Ratan Gachhui. 2018. “Antibacterial Activity of Polyphenolic Fraction of Kombucha against Vibrio Cholerae: Targeting Cell Membrane.” Letters in Applied Microbiology 66 (2): 145–52. DOI: https://doi.org/10.1111/lam.12829
18. Chakraborty, Writachit, Soumyadev Sarkar, Somnath Chakravorty, Semantee Bhattacharya, Debanjana Bhattacharya, and Ratan Gachhui. 2016. “Expression of a Chitin Deacetylase Gene, up-Regulated in Cryptococcus Laurentii Strain RY1, under Nitrogen Limitation.” Journal of Basic Microbiology 56 (5): 576–79. DOI: https://doi.org/10.1002/jobm.201500596
19. Bhattacharya, Debanjana, Semantee Bhattacharya, Madhu Manti Patra, Somnath Chakravorty, Soumyadev Sarkar, Writachit Chakraborty, Hemanta Koley, and Ratan Gachhui. 2016. “Antibacterial Activity of Polyphenolic Fraction of Kombucha Against Enteric Bacterial Pathogens.” Current Microbiology 73 (6): 885–96. DOI: https://doi.org/10.1007/s00284-0161136-3
20. Chakravorty, Somnath, Soumyadev Sarkar, and Ratan Gachhui. 2015. “Identification of New Conserved and Variable Regions in the 16S rRNA Gene of Acetic Acid Bacteria and Acetobacteraceae Family.” Molecular Biology.   DOI:https://link.springer.com/article/10.1134/S0026893315050052

Reviews

1. Das, Subhadeep, Sampad Basak, and Soumyadev Sarkar*. 2025. "Decoding salivary ncRNAomes as novel biomarkers for oral cancer detection and prognosis." Noncoding RNA 11, (2025). (*Corresponding author).  
2. Morrison, Austin Gregory, Soumyadev Sarkar, Shahid Umar, Sonny T. M. Lee, and Sufi Mary Thomas. 2023. “The Contribution of the Human Oral Microbiome to Oral Disease: A Review.” Microorganisms 11 (2): 318. https://doi.org/10.3390/microorganisms11020318
3. Sarkar, Soumyadev. 2023. "Proteogenomic Approaches to Understand Gene Mutations and Protein Structural Alterations in Colon Cancer" Physiologia 3, no. 1: 11-29. https://doi.org/10.3390/physiologia3010002 (Feature Paper, Invited)
4. Ghosh, Bidisha, Soumyadev Sarkar, Nayim Sepay, Kaustuv Das, Sukhen Das, and Sujata Ghosh Dastidar. 2021. “Factors for COVID-19 Infection That Govern the Severity of Illness.” SciMedicine Journal 3 (2): 177–97. https:// 10.28991/SciMedJ-2021-0302-9

Mini-Review

1. Das, Subhadeep, and Soumyadev Sarkar*. 2024. “Arbuscular Mycorrhizal Fungal Contribution towards Plant Resilience to Drought Conditions.” Frontiers in Fungal Biology 5 (February): 1355999. (*Corresponding author)

Perspective

1. Sarkar, Soumyadev, Kaitlyn Ward, Abigail Kamke, Qinghong Ran, Brandi Feehan, Tanner Richie, Nicholas Reese, and Sonny T. M. Lee. 2022. “Perspective: Simple State Communities to Study Microbial Interactions: Examples and Future Directions.” Frontiers in Microbiology 13 (January): 801864. https://doi.org/10.3389/fmicb.2022.801864  

Methods

1. Sarkar, Soumyadev, Tanner Richie, and Sonny Lee. 2023. “Visualizing, Binning, and Refining of Metagenome-Assembled Genomes (MAGs) with Anvi’o.” Bio-Protocol 13 (9). https://doi.org/10.21769/bioprotoc.4684. (Invited)
2. Sarkar, Soumyadev, Tanner Richie, and Sonny Lee. 2023a. “Metagenomic Protocol (from Quality Control to Mapping) for Metagenome-Assembled Genomes Using Anvi’o.” Bio-Protocol 13 (9). https://doi.org/10.21769/bioprotoc.4683. (Invited)

Book-Chapters

1. Das, Rajarshi, and Soumyadev Sarkar*. 2024. “Chapter Twelve - Exosomal RNA in Bacterial Infections.” In Exosomal RNA, edited by Debalina Bhattacharya, Mainak Mukhopadhyay, and Kursad Turksen, 271–94. Academic Press. (*Corresponding author)
2. Chakravorty, Somnath, Semantee Bhattacharya, Debanjana Bhattacharya, Soumyadev Sarkar, and Ratan Gachhui. 2019. “10 - Kombucha: A Promising Functional Beverage Prepared From Tea.” In Non-Alcoholic Beverages, edited by Alexandru Mihai Grumezescu and Alina Maria Holban, 285–327. Woodhead Publishing. DOI: https://doi.org/10.1016/B978-0-12-815270-6.00010-4

Preprints

1. Richie, Tanner G., Hallie Wiechman, Carson Ingold, Leah Heeren, Abigail Kamke, Sophia Pogranichniy, Kourtney Monk, Trey Summers, Qinghong Ran, Soumyadev Sarkar, Brandon L. Plattner, Ashley Sidebottom, Eugene Chang, Sonny T.M. Lee 2024. “Eubacterium Rectale Detoxification Mechanism Increases Resilience of the Gut Environment.” bioRxiv : The Preprint Server for Biology, May. https://doi.org/10.1101/2024.05.09.593360.
2.      Sarkar, Soumyadev, Anna Kazarina, Paige M. Hansen, Kaitlyn Ward, Christopher Hargreaves, Nicholas Reese, Qinghong Ran, et al. 2023. “Ammonia-Oxidizing Archaea and Bacteria Differentially Contribute to Ammonia Oxidation in Soil under Precipitation Gradients and Land Legacy.” BioRxiv. https://doi.org/10.1101/2023.11.08.566028.