Gaurav Sharma

Research Focus Keywords:

Microbial Genomics, Microbiome, Metagenomics, Plants, Myxobacteria, Computational Biology, Microbes, Microbial evolution, Sequencing

Background:

Dr. Sharma completed his Masters in Biotechnology from School of Biotechnology, Jawaharlal Nehru University, New Delhi, India and worked with Dr. Swati Tiwari on in silico Entamoeba Ubiquitin-Proteasome Pathway categorization. With a research fellowship from CSIR, he obtained his Ph.D. in Microbial Genomics with Dr. Srikrishna Subramanian from Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India. During his Ph.D., he sequenced 15 novel myxobacterial strains and did some interesting comparative genomic work in the field of myxobacterial biology. Later he worked with Prof. Mitchell Singer at the University of California, Davis to understand more about myxobacterial evolution using genomics, transcriptomics and molecular genetics. Dr. Sharma has joined IBAB on August 2019 to start his lab focused on plant microbiome and microbial genomics. He has been awarded INSPIRE Faculty Fellowship from Department of Science and Technology (DST), India for 2019-2024.

Education:

• Postdoc: Dept. of Microbiology and Molecular Genetics, University of California, Davis, USA (2016-2019)
• Ph.D.: Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India (2011-16)
• M.Sc. (Biotech): School of Biotechnology, Jawaharlal Nehru University, India (2009-11)
• B.Sc. (Life Science): DAV Degree College, Muzaffarnagar, CCS University, Meerut, UP, India (2006-09)

Professional Career:

DST-INSPIRE Faculty Scientist at IBAB, Bengaluru, Karnataka, India (2019-onwards)

Research Interests:

With the boom in sequencing technologies, an enormous amount of data is being generated and continuously heaping up. It can be used to infer interesting theories about the physiology, behavior, and putative lifestyle (pathogenicity/symbiosis/parasitism) of the respective organism. My lab will use computational biology tools to bridge this gap between sequencing data and biological function prediction.

Broadly, my lab will be focused on two major microbial aspects:

1. Exploration of the Plant microbiome to understand the host-microbe interactions
2. Genomic/Transcriptomic data mining of myxobacteria to understand the evolution of their physiological characteristics

Current opportunities:

Open Ph.D. positions in “Microbial Genomics and Plant Microbiome”

We are actively seeking applications from motivated students for two Ph.D. positions in the group of Dr. Gaurav Sharma (https://sites.google.com/view/sharmaglab) at IBAB, Bengaluru. The selected candidates will work in the frontier areas of Plant and Microbial genomics using next-generation sequencing data. The candidate would be assisted with specialized training including data handling, opportunities to learn programming, and data analysis. The candidate will also have opportunities to attend national/international workshops/ symposiums/ conferences to learn and present their work. If you are interested, feel free to write an email, and we can discuss the opportunities and relevant projects. 

The candidate must have a master’s degree (M.Sc. or equivalent) in Bioinformatics/ Computational Biology/ Biotechnology or related subjects with at least 60% marks or 6.50 CGPA from a recognized university along with a Research Fellowship from any central/state government agencies such as CSIR, UGC, DBT, or ICMR. Candidates with a previous working experience in any project related to Bioinformatics/computational biology and handling NGS/genomics data would be preferred. 

Group Members:

Vaishnavi Kolte
Project Assistant: IBAB, Bengaluru (Nov 2019-Present)
M.Sc. (Bioinformatics): Savitribai Phule Pune University, Pune, Maharashtra, India
B.Sc. (Biotechnology): Savitribai Phule Pune University, Pune, Maharashtra, India

Shenu Hudson B.
Project Assistant: IBAB, Bengaluru (Nov 2019-Present)
B.Tech. (Bioinformatics): Sathyabama University, Chennai, Tamil Nadu, India

Shruti Sinha
MSc Dissertation Student: IBAB, Bengaluru (Jan 2021-June 2021)
IBAB MSc (Biotechnology & Bioinformatics): (2019-2021)
BSc Life Sciences: Ramjas College, University of Delhi, Delhi

Kishan Kalia
MSc Dissertation Student: IBAB, Bengaluru (Jan 2021-June 2021)
IBAB MSc (Biotechnology & Bioinformatics): (2019-2021)
BSc Bioinformatics (Hons.): DAV College (Punjab University), Chandigarh.

Niharika Saraf
MSc Dissertation Student: IBAB, Bengaluru (Jan 2021-June 2021)
IBAB MSc (Biotechnology & Bioinformatics): (2019-2021)
BSc (Biotechnology, Chemistry, Zoology): Mount Carmel College, Bangalore

Past group members:

Drishti Singh
M.Sc. (Biotechnology & Bioinformatics) Project Intern: IBAB, Bengaluru (Jan 2020-Present)
B.Sc. (Biotechnology): Shri Murli Manohar Town Post Graduate College, Ballia (Affiliated with Mahatma Gandhi Kashi Vidyapith, Varanasi), Uttar Pradesh, India

Azra Khan
M.Sc. (Biotechnology & Bioinformatics) Project Intern: IBAB, Bengaluru (Jan 2020-Present)
B.Sc. (Bioinformatics): Govt. Holkar Science College, Indore, Madhya Pradesh, India

We are actively looking for students with CSIR, DBT, INSPIRE or any other national fellowships who have an interest in Computational Biology/Bioinformatics.

If you are interested in learning and using computational biology to understand the diverse nature and evolution of microbes, feel free to email me at gauravsharma@ibab.ac.in.

Collaborations:

I am open to discuss new ideas for research and collaboration. Feel free to email me at gauravsharma@ibab.ac.in. At Present, I am having active collaboration with several people, such as:

1. Dr. Salim Timo Islam, INRS-Institut Armand-Frappier Center, Quebec, Canada
2. Dr. Rebecca Parales, Dept. of Microbiology and Molecular Genetics, University of California, Davis, USA
3. Prof. Mitchell Singer, Dept. of Microbiology and Molecular Genetics, University of California, Davis, USA
4. Prof. Edward Ruby, Pacific Biosciences Research Center, University of Hawai‘i at Mānoa, Honolulu, USA
5. Dr. Pia H. Moisander, Department of Biology, University of Massachusetts Dartmouth, Massachusetts, USA
6. Prof. Karaba N Nataraja, Department of Crop Physiology, University of Agricultural Sciences, Bangalore, India
7. Dr. Gunjan Goel, Department of Microbiology, Central University of Haryana, Mahendragarh, Haryana, India
8. Prof. Malali Gowda, Dean and Professor, Faculty of Life and Allied Health Sciences, M. S. Ramaiah University of Applied Sciences, Bengaluru, India
9. Dr. Megha, The University of Trans-Disciplinary Health Sciences and Technology, Bengaluru, India
10. Dr. Srikrishna Subramanian, Institute of Microbial Technology, Chandigarh, India

Publications:

^# As Corresponding author

^* As co-first author

• Gaurav Sharma^, Andrew I. Yao, Gregory T. Smaldone, Jennifer Liang, Matt Long, Marc T. Facciotti, Mitchell Singer.
  Global gene expression analysis of the Myxococcus xanthus developmental time course.
  Genomics, doi: https://doi.org/10.1016/j.ygeno.2020.11.030 (2021)  ^ Equal author
• Shenu B Hudson, Vaishnavi Kolte, Azra Khan and Gaurav Sharma*
  Dynamic tracking of variant frequencies depicts the evolution of mutation sites amongst SARS-CoV-2 genomes from India.
  Journal of Medical Virology, doi:  https://doi.org/10.1002/jmv.26756 (2020) *Corresponding Author
• Parlikar A, Kalia K, Sinha S, Patnaik S, Sharma N, Vemuri SG, Sharma G*.
  Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2.
  PeerJ. doi:https://doi.org/10.7717/peerj.9576 (2020) *Corresponding Author
• Islam ST, My L, Jolivet NY, Belgrave AM, Fleuchot B, Brasseur G, Faure LM, Sharma G, Lemon DJ, Saidi F, Fiche JB, Bratton BP, Singer M, Garza AG, Nollmann M, Shaevitz JW, Mignot T.
  CglB adhesins secreted at bacterial focal adhesions mediate gliding motility.
  bioRxiv. doi: https://doi.org/10.1101/2020.07.22.216333 (2020)
• Islam ST, Vergara Alvarez I, Saïdi F, Guiseppi A, Vinogradov E, Sharma G, Espinosa L, Morrone C, Brasseur G, Guillemot JF, Benarouche A, Bridot JL, Ravicoularamin G, Cagna A, Gauthier C, Singer M, Fierobe HP, Mignot T, Mauriello EMF.
  Modulation of bacterial multicellularity via spatio-specific polysaccharide secretion.
  PLoS Biology. doi: https://doi.org/10.1371/journal.pbio.3000728 (2020)
• Nuttall RA, Sharma G, Moisander PH.
  Draft Genome Sequence of Marinobacter hydrocarbonoclasticus NCT7M, Obtained from the Microbiome of a Marine Copepod.
  Microbiol Resource Announcement. doi: https://doi.org/10.1128/mra.01459-19 (2020)
• Khatri I*, Sharma G*, Subramanian S. Composite genome sequence of Bacillus clausii, a probiotic commercially available as Enterogermina^®, and insights into its probiotic properties. 
  BMC Microbiology. 2019 Dec 30;19(1):307. doi:10.1186/ s12866-019-1680-7.
• Parales RE, Sharma G, Zhang X, Subuyuj GA, Langner JT, Wright ME, Ditty JL, Dawson SC. Draft Genome Sequence of the Caffeine-Degrading Methylotroph Methylorubrum populi Pinkel. 
  Microbiology Resource Announcements. 2019 Nov 21;8(47). doi: 10.1128/MRA.01300-19.
• Nuttall R, Sharma G, Moisander PH. Draft Genome Sequence of Vibrio cyclitrophicus NCT10V, Cultivated from the Microbiome of a Marine Copepod. 
  Microbiology Resource Announcements. 2019 Oct 31;8(44). doi: 10.1128/MRA.01208-19. 
• Whitfield DL*, Sharma G*, Smaldone GT, Singer M. Peripheral rods: a specialized developmental cell type in Myxococcus xanthus. 
  Genomics. 2019 Oct 9;. doi: 10.1016/j.ygeno.2019.09.008. 
• Sharma G^#, Parales R, Singer M^#. In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides. 
  BMC Genomics. 2018 Oct 19;19(1):757. doi: 10.1186/s12864-018-5151-6. 
• Sharma G^#, Burrows LL, Singer M^#. Diversity and Evolution of Myxobacterial Type IV Pilus Systems. 
  Frontiers in Microbiology. 2018; 9:1630. doi: 10.3389/ fmicb.2018.01630. eCollection 2018. 
• Islam ST, Belgrave AM, Fleuchot B, Jolivet NY, My L, Faure LM, Sharma G, Lemon DJ, Fiche JB, Bratton BT, Singer M, Garza AG, Shaevitz JW, Mignot T. Integrin-Like Tethering of Motility Complexes at Bacterial Focal Adhesions.
  Preprint available at SSRN. http://dx.doi.org/10.2139/ssrn.3188409
• Sharma G, Khatri I, Subramanian S. Comparative Genomics of Myxobacterial Chemosensory Systems. 
  Journal of Bacteriology. 2018 Feb 1;200(3). doi: 10.1128/ JB.00620-17. Print 2018 Feb 1. Journal Cover Page
• Sharma G, Subramanian S. Unravelling the Complete Genome of Archangium gephyra DSM 2261T and Evolutionary Insights into Myxobacterial Chitinases. 
  Genome Biology and Evolution. 2017 May 1;9(5):1304-1311. doi: 10.1093/gbe/evx066. 
• Sharma G, Khatri I, Subramanian S. Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668T. 
  Genome Biology and Evolution. 2016 Aug 29; 8(8): 2520-9. doi: 10.1093/gbe/evw151. 
• Sharma G, Narwani T, Subramanian S. Complete Genome Sequence and Comparative Genomics of a Novel Myxobacterium Myxococcus hansupus. 
  PLoS One. 2016; 11(2):e0148593. doi: 10.1371/journal.pone.0148593. eCollection 2016. 
• Sharma G, Khatri I, Subramanian S. Draft Genome Sequence of Kocuria palustris PEL.
  Genome Announcement. 2014 Feb 6; 2(1). doi: 10.1128/ genomeA.01261-13. 
• Arya S*, Sharma G*, Gupta P, Tiwari S. In silico analysis of ubiquitin/ubiquitin-like modifiers and their conjugating enzymes in Entamoeba species. 
  Parasitology Research. 2012 Jul;111(1):37-51. doi: 10.1007/ s00436-011-2799-0. Epub 2012 Jan 13. 

Awards:

• 2019               European Molecular Biology Organization (EMBO) Travel fellowship
• 2019               University of California Davis Postdoctoral Scholar Association (UCDavis PSA) Travel Award
• 2019               Department of Science and Technology- INSPIRE Faculty Award
• 2018               ASM Postdoctoral Travel Award
• 2017               Science Communication Fellowship, awarded by UC Davis Clinical and Translational Science Center (CTSC) FUTURE Program and Powerhouse Science Center, Sacramento, CA
• 2016               DBT International Travel Fellowship
• 2013-2016      Senior Research fellowship from Council of Scientific & Industrial Research (CSIR), India
• 2011-2013      Junior Research fellowship from Council of Scientific & Industrial Research (CSIR), India
• 2009-2011      Department of Biotechnology (DBT) scholarship

Research Grants

DST-INSPIRE Research Grant = 2019-2024 (5 Years)