**Author details**

fuelled interest in this field. Classical metagenomics analyses samples by extracting environ‐ mental DNA followed by *de novo* sequencing, or amplification of 16S/18S rDNA using specific primers while functional metagenomics focuses on amplification of genes of interest (generally antibiotics, enzymes etc.) and their cloning into select target microorganisms to produce the metabolite of interest. Roche 454 pyrosequencing and Illumina are the most widely used NGS technologies [4]. DNA bar-coding approach is gaining popularity for assessing microbial diversity [64]. Though only limited datasets (especially for eukaryotic microbes) are currently available, the scenario is improving due to faster and cheaper sequencing methods. Inherent differences in microbial evolution rates, chimeric DNA sequences, artefacts generated during PCR or sequencing and non-universality of primers preclude derivation of a common threshold for taxonomic units [65]. However, bioinformatics handles some of these issues. Sequence quality is checked for series of Ns (nucleotides that are unresolved), errors in primer sequences are checked and verified, and sequences where length varies from the expected length [66] are assessed. Programs have been developed to remove pyrosequencing as well as PCR errors ([4] and references therein). After error-checking and trimming, the sequences are aligned, distance matrices calculated and used for clustering the Operational Taxonomic Units (OTUs) using programs such as MOTHUR [67]. OTUs represented by single sequences (singletons) are also documented and can overestimate diversity. Removal of singletons has not been shown to affect alpha diversity much [4] though more studies are required in this regard. Beta diversity remains conserved without singletons but diversity patterns may change

The definition of a virus 'species' is: "A virus species is a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche" [69]. A virus isolate can refer to any virus as long as the virus has existed for some time. Viruses are not considered to be either prokaryotes or eukaryotes but have implication from health point of view; hence characterization of viruses has increased considerably. Where earlier, only electron microsco‐ py was used, today sequencing of viral genomes constitutes advancements and the database is increasing. According to International Committee on Taxonomy of Viruses (ICTV), propos‐ als are afoot to accept online descriptions of viral taxa based on taxonomical details such as : dsDNA, ssDNA, rtDNA, rtRNA, dsRNA, ssNRNA, ssPRNA, SAT (Satellites), VIR (Viroids),

Zinger et al. state (see Pg. 2 of Ref. [4]): "In its broadest meaning, measuring biodiversity consists of characterizing the number, composition and variation in taxonomic or functional units over a wide range of biological organizations (from genes to communities)". The taxonomical classification of microorganisms has been difficult due to their small size, short

in their presence [68].

UN (unassigned).

**11. Conclusions & perspectives**

**10. Taxonomy of viruses**

62 Biodiversity - The Dynamic Balance of the Planet

Indira P. Sarethy1 , Sharadwata Pan2 and Michael K. Danquah3\*

\*Address all correspondence to: mkdanquah@curtin.edu.my

1 Department of Biotechnology, Jaypee Institute of Information Technology, Noida (U.P.), India

2 Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India

3 Department of Chemical and Petroleum Engineering, Curtin University of Technology, Sarawak, Malaysia
