**9. Uncultured microorganisms**

Metagenomics has emerged as a promising field of interest, where identification of uncultured microorganisms is attempted. Since 99% of the microbial population is considered to be uncultivable, metagenomics assumes importance [63]. Next generation Sequencing (NGS) has 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 in their presence [68].

generation times and confounded by genetic exchange between unrelated organisms. These limitations have been largely overcome by modern developments of sequencing technologies and the recognition of rDNA sequences as a cornerstone for identification purposes. Overall, it is important to recognize that microbial diversity is intricately linked to its environment and this correlation has to be established by description of environmental parameters whenever sampling is carried out. It is also important to study the phenotypic characteristics and link them to the observations obtained from genotyping techniques. The link between habitat and

Modern Taxonomy for Microbial Diversity http://dx.doi.org/10.5772/57407 63

and Michael K. Danquah3\*

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

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

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

[1] Vandamme P, Pot B, Gillis M, De Vos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics, Microbiological Reviews 1996; 60 (2):

[2] Fierer N. Microbial biogeography: patterns in microbial diversity across space and time. In: Zengler K. (ed.), Accessing Uncultivated Microorganisms: from the Environ‐ ment to Organisms and Genomes and Back. Washington DC: ASM Press; 2008.

[3] Kassen R, Rainey P. The ecology and genetics of microbial diversity, Annual Review

[4] Zinger L, Gobet A, Pommier T. Two decades of describing the unseen majority of

[5] Madigan MT, Martinko JM, Stahl DA, Clark DP. Brock biology of microorganisms

aquatic microbial diversity, Molecular Ecology 2012; 21(8): 1878–1896.

13th Edition; Ch. 16, pp. 446-474; Benjamin Cummings; 2010.

diversity then becomes easier to understand for future studies.

, Sharadwata Pan2

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

**Author details**

Indira P. Sarethy1

Sarawak, Malaysia

407-438.

p95-115.

of Microbiology 2004; 58: 207 – 231.

**References**

India

India
