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:

Utkarsha Mahanta
Ph.D. Researcher: IBAB, Bengaluru (March 2021- Present)
M.Tech (Computational Biology): Pondicherry University, Puducherry
M.Sc. (Mathematics): Tezpur University, Assam
B.Sc. (Mathematics Honours): Cotton College, Gauhati University, Assam

Richa Kakkar
Ph.D. Researcher: IBAB, Bengaluru (Aug 2021- Present)
UGC Junior Research Fellow
M.Sc. (Biochemistry): Padmashree Institute of Management and Sciences, Bengaluru [Bangalore University]
B.Sc. (Biotechnology): Smt. C.H.M. College, Ulhasnagar, Maharashtra, India [University of Mumbai]

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

Mariam Azeezuddin Haneen
Project Assistant: IBAB, Bengaluru (Aug 2021-Present)
M.Sc. (Microbiology): Dayananda Sagar University (DSU), Bangalore
B.Sc. (Microbiology, Chemistry, Zoology): St. Joseph’s College (Autonomous), Bangalore

Sneha S Murthy
Project Assistant: IBAB, Bengaluru (March 2020-Present) (Jointly with BioIT and Dr. Vembar)
Bioinformatics Analyst: Leucine Rich Bio Pvt Ltd, Bengaluru
M. Tech BioInformatics : RV College of Engineering, Bengaluru
BE Biotechnology: PES Institute of Technology, Bengalurue Pune University, Pune, Maharashtra, India

Adyasha Panda
Project Assistant: IBAB, Bengaluru (June 2021-Present)
Research Associate: Kidwai Memorial Institute of Oncology (KMIO), Bangalore, Karnataka, India
M.Sc. (Bioinformatics): Odisha University of Agriculture & Technology, Bhubaneswar, Odisha, India
B.Sc. (Biotechnology): Utkal University, Odisha, India

Akash Chandra Parida
Project Assistant: IBAB, Bengaluru (Aug 2021-Present)
PG Diploma (Advanced Life Science Technologies): SRM Institute of Science and Technology, Chennai, Tamil Nadu
M.Sc. (Plant Science): Central University of Kerala, Kasaragod, Kerala
B.Sc. (Life Sciences): Kendrapara Autonomous College, Kendrapara, Odisha

Past group members:

Kishan Kalia
Present Role: Junior Research Fellow, Institute For Stem Cell Science and Regenerative Medicine (inStem), Bengaluru
MSc Dissertation Student: IBAB, Bengaluru (Jan 2021-June 2021)
IBAB MSc (Biotechnology & Bioinformatics): (2019-2021)
BSc Bioinformatics (Hons.): DAV College (Punjab University), Chandigarh.

Shruti Sinha
Present Role: RWE- Research Analyst 1, Novartis, Hyderabad
MSc Dissertation Student: IBAB, Bengaluru (Jan 2021-July 2021)
IBAB MSc (Biotechnology & Bioinformatics): (2019-2021)
BSc Life Sciences: Ramjas College, University of Delhi, Delhi

Kevin Gohel
Present Role: In Progress
M.Sc Dissertation Student: IBAB, Bengaluru (Jan 2021 – Aug 2021)
M.Sc. Bioinformatics from Sardar Patel University, Anand, Gujarat (2019-2021)
B.Sc. Bioinformatics from N. V. Patel College of Pure and Applied Sciences, Sardar Patel University, Anand, Gujarat (2016-2019)

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

Shenu Hudson B.
Present Role: Junior Bioinformatician, Nucleome Informatics Pvt Ltd
Project Assistant: IBAB, Bengaluru (Nov 2019-May 2021)
B.Tech. (Bioinformatics): Sathyabama University, Chennai, Tamil Nadu, India

Animesh Awasthi
Remote Project Intern: IBAB, Bengaluru (July 2020-Dec 2020)
Third Year of Dual Degree (B.Tech.+M.Tech.) in Biotechnology (2018 – 2023): Indian Institute of Technology, Kharagpur

Shradha Sharma
Present Role: M.Sc. in Bioengineering and Biomedical Engineering (Indian Institute of Engineering Science and Technology (IIEST), Shibpur, West Bengal)
Project Intern: IBAB, Bengaluru (Feb 2020-October 2020)
B. Tech (Biotechnology): G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India

Azra Khan
Present Role: Junior Programmer (GSK)
MSc Dissertation Student: IBAB, Bengaluru (Jan 2020-June 2020)
IBAB MSc (Biotechnology & Bioinformatics): (2018-2020)
M.Sc. (Biotechnology & Bioinformatics) Project Intern: IBAB, Bengaluru (Jan 2020-Present)
B.Sc. (Bioinformatics): Govt. Holkar Science College, Indore, Madhya Pradesh, India

Drishti Singh
Present Role: Intern at Nference
MSc Dissertation Student: IBAB, Bengaluru (Jan 2020-June 2020)
IBAB MSc (Biotechnology & Bioinformatics): (2018-2020)
B.Sc. (Biotechnology): Shri Murli Manohar Town Post Graduate College, Ballia (Affiliated with Mahatma Gandhi Kashi Vidyapith, Varanasi), Uttar 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

• Adyasha Panda, Salim T. Islam, and Gaurav Sharma*.
  Harmonizing Prokaryotic Nomenclature: Fixing the Fuss over Phylum Name Flipping.
  mBio. https://journals.asm.org/doi/10.1128/mbio.00970-22 (2022)
• Utkarsha Mahanta, Gayatri Saberwal, and Gaurav Sharma*.
  Are countries becoming better at SARS-CoV-2 genomic surveillance?
  Frontiers in Public Health. https://www.frontiersin.org/articles/10.3389/fpubh.2022.887955/full (2022)
  Media coverage: India’s Genome-Sequencing Performance Through the Pandemic, in 4 Charts, The Wire Science
  Media coverage: COVID-19: INSACOG shares genome sequencing data after a gap of 3 months, Down To Earth
  Media coverage: India now ranks tenth in genome sequencing; 176% rise in numbers, The Times of India 
• Kapudeep Karmakar, Rohan Bhattacharya, Abhishek Sharma, Kirti Parmar, Utpal Nath, Karaba N Nataraj, Earanna N, Gaurav Sharma, Dipshikha Chakravortty.
  Lysinibacillus macroides mediated control of cellulose producing morphotype of Salmonella.
  Journal of the Science of Food and Agriculture. https://onlinelibrary.wiley.com/doi/abs/10.1002/jsfa.12016 (2022)
• Fares Saïdi†, Utkarsha Mahanta†, Adyasha Panda, Nicolas Y. Jolivet, Razieh Bitazar, Gavin John, Matthew Martinez, Abdelkader Mellouk, Charles Calmettes, Yi-Wei Chang, Gaurav Sharma*, Salim T. Islam*
  Bacterial outer-membrane polysaccharide export (OPX) proteins occupy three structural classes with selective β-barrel porin requirements for polymer secretion.
  bioRxiv. https://www.biorxiv.org/content/10.1101/2022.02.11.480155v1 (2022)
• Pia Moisander, Meaghan Daley, Katyanne Shoemaker, Vaishnavi Kolte, Gaurav Sharma, Kelsey Garlick.
  Nitrogen fixation influenced by phosphorus and nitrogen availability in the benthic bloom-forming cyanobacterium Hydrocoleum sp. identified in a temperate marine lagoon.
  Journal of Phycology. https://onlinelibrary.wiley.com/doi/10.1111/jpy.13244 (2022)
• Kishan Kalia, Gayatri Saberwal, and Gaurav Sharma*.
  The lag in SARS-CoV-2 genome submissions to GISAID.
  Nature Biotechnology. https://www.nature.com/articles/s41587-021-01040-0*Corresponding Author
  Media coverage: COVID-19 control needs faster submission of genome sequence to public portal, Nature India, https://www.natureasia.com/en/nindia/article/10.1038/nindia.2021.111
  Media coverage: Scientist flags India’s slowing rate of genome sequencing, The New Indian Express,https://www.newindianexpress.com/nation/2021/aug/13/scientist-flags-indias-slowing-rate-of-genome-sequencing-2344056.html
  Preprint: Country-wide genomic surveillance of SARS-CoV-2 strains.
  bioRxiv. https://www.biorxiv.org/content/10.1101/2021.06.08.447365v1 (2021). PDF
  Media coverage: Covid: Worrying shortfall, lag in genome sequencing, The Telegraph Online, https://www.telegraphindia.com/india/covid-worrying-shortfall-lag-in-genome-sequencing/cid/1818705
  Media coverage: India falters on virus genome study. The Telegraph. https://epaper.telegraphindia.com/imageview_363573_193959930_4_71_14-06-2021_4_i_1_sf.html
  Media coverage: Delays and shortages hit SARS-CoV-2 genomic surveillance program. in “News Medical” by Dr. Liji Thomas, MD. https://www.news-medical.net/news/20210614/Delays-and-shortages-hit-SARS-CoV-2-genomic-surveillance-program.aspx
• Shilpee Pal^, Gaurav Sharma^, and Srikrishna Subramanian.
  Complete genome sequence and identification of polyunsaturated fatty acid biosynthesis genes of the myxobacterium Minicystis rosea DSM 24000T. BMC Genomics (Accepted). (2021). ^First Author
• Animesh Awasthi, Gaurav Sharma*, Piyush Agrawal*.
  Chapter 20: Computational approaches for vaccine designing. Book Name “Bioinformatics: Methods and Applications” by Elsevier Publications. https://www.elsevier.com/books/bioinformatics/singh/978-0-323-89775-4(2021). *Corresponding Author
• Sunita Gupta, Parul Kulshreshtha, Deuvshree Sharma, Divya Aggarwal, Gitanjali Jiwani, and Gaurav Sharma.
  Microstructure observations of Lemna aequinoctialis ecotype. Journal of Scientific Research (in Press). (2021).
• 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
• 2021 AMI Best ‘Faculty Oral Presentation’ Award in the 61st Association of Microbiologists of India (AMI)-INSCR 2021 International Conference.

Scientific Services:

Editorial Board member:

• Editor at Microbiology Spectrum, an American Society for Microbiology Publication
• Associate Editor at Genomics, an Elsevier Publication

Reviewer for funding agencies:

• Research Grants Council (RGC) of Hong Kong
• Agence Nationale de la Recherche (ANR), French National Research Agency

Reviewer: as verified on Publons:

Applied and Environmental Microbiology (AEM), BMC Genomics, Front. Microbiol., Front. Plant Sci., Genomics, Archives of Microbiology (AOMI), Genomics Data, Marine Genomics, etc

TEACHING COURSES:

• SEMESTER I (IBAB M.Sc. Students)
  BTBIH-105: BASIC BIOINFORMATICS 
  • Unit 1: Biological sequences
  • Unit 2: Database resources
  • Unit 3: Sequence analysis
• SEMESTER II (IBAB M.Sc. Students)
  BTBIP-207: ADVANCED BIOINFORMATICS – LABORATORY
• SEMESTER III (IBAB M.Sc. Students)
  BTBIH-301: GENOMICS, TRANSCRIPTOMICS AND PROTEOMICS
  • Unit 1: Concepts of genomics

ORGANIZED WORKSHOPS:

1. Hands-on Online Workshop on “Fundamentals of NGS Analysis & Drug Discovery” organized by the Bio-IT Centre, IBAB, Bengaluru. #WorkshopFromHome 25-28 Aug 2021
2. 3rd online hands-on workshop on “Introductory Genomic and NGS Analysis” organized by the Bio-IT Centre, IBAB, Bengaluru. #WorkshopFromHome 22-24 Apr 2021
3. “International Metabarcoding and Metagenomics Workshop”: A 3-day online hands-on workshop organized by DAFNAE, University of Padova, Italy and the Bio-IT Centre, IBAB, Bengaluru. #WorkshopFromHome 15-17 December 2020
4. 2nd online hands-on workshop on “Introductory Genomic and NGS Analysis” organized by the Bio-IT Centre, IBAB, Bengaluru. #WorkshopFromHome 9-11 Nov 2020
5. Ist online hands-on workshop on “Introductory Genomic and NGS Analysis” organized by the Bio-IT Centre, IBAB, Bengaluru. #WorkshopFromHome 21-23 Sep 2020

Research Grants

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