Extended-spectrum ß-lactamase-producing (ESBLs) Enterobacteriaceae bacteria_ Escherichia coli_edited

SOUMYADEV SARKAR

Postdoctoral Research Scholar,
Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University

ABOUT SOUMYADEV

I was awarded Ph.D. from Jadavpur University on novel insights into the nitrogen stress response of Papiliotrema laurentii strain RY1. As a postdoctoral scientist at Kansas State University, I used metagenomics to dissect the complex microbe-microbe and host-microbe interactions in plant-microbe systems. Currently, at Arizona State University, I am implementing the techniques of microbiology and bioinformatics to elucidate the symbiotic relationship between the cyanobacteria and the heterotrophs residing in the cyanosphere.

Editorial responsibilities:

Editor: Engineering Microbiology

Guest Associate Editor for Frontiers in Fungal Biology, Frontiers in Cellular and Infection Microbiology

Guest Editor for Vaccines, Agronomy,

Journal of Visualized Experiments (JoVE)

Reviewer for Journals:

Food and Humanity; Data in Brief; RSC Advances; Cell Stress and Chaperons; Journal of Biomolecular Structure & Dynamics; Food Research International; Encyclopedia; Genes; Journal of Scientific Research and Reports; Water; Biomolecules; Asian Journal of Agricultural and Horticultural Research; International Journal of Molecular Sciences; Sustainability; Journal of Pharmaceutical Research International; Archives of Current Research International, Life; Applied Food Research; Agronomy; Biomed; Coatings, Plants, Journal of Marine Science and Engineering.

Inducted as an Honored Listee for

Marquis Who's Who Top Scientists 2023

Get in Touch

RESEARCH INTERESTS

SYMBIOSIS OF CYANOBACTERIA-CYANOSPHERE HETEROTROPHS IN BIOLOGICAL CRUSTS

PUBLICATIONS

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. 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)

3. 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.

4. 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.

5. 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, no. 2: 318. https://doi.org/10.3390/microorganisms11020318

6. 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, *Corresponding author)

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.

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. 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

10. 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

11. 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

12. 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

13. 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. https://doi.org/10.1016/j.micpath.2019.103927

14. Mukherjee, Avishek, Soumyadev Sarkar, Suchetana Gupta, Sayanika Banerjee, Sanjib Senapati, Riya Chakrabarty, and Ratan Gachhui. 2019. “DMSO Strengthens Chitin Deacetylase-Chitin Interaction: Physicochemical, Kinetic, Structural and Catalytic Insights.” Carbohydrate Polymers 223 (November): 115032. DOI: https://doi.org/10.1016/j.carbpol.2019.115032

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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/s00284-016-1136-3

22. 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

23. 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

METHODS

24. 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)

25. 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)

PREPRINTS

26. 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

27. 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.