Microbial Genomics and Metagenomics in India: Explorations and Perspectives

  • Princy Hira
  • Abhay Bajaj
  • Akshita Puri
  • Chandni Talwar
  • Himani Khurana
  • Ram Krishnan Negi
  • Yogendra Singh
  • Rup Lal
  • Mallikarjun Shakarad
Keywords: Genomics; Metagenomics; Microbial Diversity; Next-generation Sequencing


The discipline of genomics and metagenomics has been rapidly growing as an emerging field of research since the last decade.
This development is largely due to the rapid advances in sequencing technologies that generate enormous amount of high
throughput data at low costs. While there is huge information on genomics and metagenomics from different parts of the
world, there have been few studies from India due to the underlying limitation of data analyses. In this review, major
genomic and metagenomic studies to predict the bacterial diversity and their ecological significance, and the functional roles
played by microbes in different environments in India have been summarized. The integration of culture dependent and
culture-independent approaches has expanded our knowledge on the composition and function of microbial communities
in specific niches. However, there still exist challenges and gaps in our understanding about the microbial resource in Indian
subcontinent as their importance is over-looked by the scientific community despite quite a few reports on metagenomics/
genomics from India.


Agarwal L and Purohit HJ (2013) Genome sequence of Rhizobium
lupini HPC (L) isolated from saline desert soil, Kutch
(Gujarat) Genome Announc 1 e00071-12
Ahmed N, Saini V, Raghuvanshi S, Khurana JP, Tyagi AK et al.
(2007) Molecular Analysis of a Leprosy
Immunotherapeutic Bacillus Provides Insights into
Mycobacterium Evolution PLoS One 2 e968
Ahmed V, Verma MK, Gupta S, Mandhan V and Chauhan NS
(2018) Metagenomic Profiling of Soil Microbes to Mine
Salt Stress Tolerance Genes Front Microbiol 9 159
Arjun JK and Harikrishanan K (2011) Metagenomic analysis of
bacterial diversity in the rice rhizosphere soil microbiome
Biotechnol Bioinf Bioeng 1 361-367
Arora SK, Dewan P and Gupta P (2015) Microbiome:
Paediatricians’ perspective Indian J Med Res 142 515
Avasthi TS, Kumar N, Baddam R, Hussain A, Nandanwar N,
Jadhav S, and Ahmed N (2011) Genome of multidrugresistant uropathogenic Escherichia coli strain NA114
from India J Bacteriol 193 4272-4273
Badhai J, Ghosh TS and Das SK (2015) Taxonomic and functional
characteristics of microbial communities and their
correlation with physicochemical properties of four
geothermal springs in Odisha, India Front Microbiol 6
Bairagi A, Ghosh KS, Sen SK and Ray AK (2002) Enzyme
producing bacterial flora isolated from fish digestive tracts
Aquaculture International 10 109-121
Balaji V, Rajenderan S, Anandan S and Biswas I (2015) Genome
sequences of two multidrug-resistant Acinetobacter
baumannii clinical strains isolated from southern India
Genome Announc 3 e01010-15
Banerjee G, Dan S K, Nandi A, Ghosh P and Ray AK (2015)
Autochthonous gut bacteria in two Indian air-breathing
fish, climbing perch (Anabas testudineus) and walking
catfish (Clariasbatrachus) mode of association,
identification, and enzyme producing ability Pol J
Microbiol 64 361-368.
Special Section