**Author details**

molecular methods for virus diagnostic purpose are tedious, time-consuming and costly. A recent report from Escobar-Gutierrez et al. described the use of next-generation sequencing (NGS) method in the diagnosis of HCV infection. NGS allows cost-effective analysis of a large number of samples in detail. The study showed low-frequency mutations, genetic variation [68]. Genetic shift and re-assortment viruses are a leading cause of the emergence of a new strain of viruses, especially in RNA viruses. Well a known example is influenza virus, many pandemics and deaths in history. The recent H1N1 virus is a combination of swine, human and avian genomic segments of RNA [69]. The best approach of metagenomics study in 2009 H1N1 pandemic is the use of metagenomics for characterization and detail study of the virus, followed by manufacture of microarray-based virochip for rapid

**4. Evolution of host-virus interaction:** Evolution of RNA viruses is comparatively fast process than DNA viruses. Study of evolution is necessary to understand the source of new variance, spread and keep a check on epidemic initiating variant. In emerging RNA virus, *norovirus* causative agent of gastroenteritis inter-host, intra-host, and transmission of the new variant has been studied. Usually, it is a self-limiting acute disease but in immunecompromised individuals and in newborns it may cause morbidity and mortality. No vaccine or drugs are available for treatment. A report from Bull et al. hypothesized based on metagenomics study that, *norovirus* has multiple mechanisms of evolution. Chronic hosts are a major reservoir of new variants while acute patients generally possess a single variant. NGS approach for use assists in comprehensive study of viral population dynamics [71]. Characterization of cardiovirus genus originally believed to possess two genera, metagenomics study has revealed five new genera with full characterization. Cardioviruses are the causative agent of enteric diseases in mice with multiple symptoms. In humans, it causes encephalitis-like condition and diarrhea in children's [72]. Metagenomics based studies help in designing future approach with these new genotypes and associated diseases.

The metagenomics studies have a huge potential to describe about diversity of microbiome in gut microflora and most importantly directly in infectious samples. Among all pathogens viruses are the ones, who cause severe illness to mankind. With rapid improvement in the genomic sequencing techniques, the overall metagenomics approach is very valuable for discovery of new viruses, novel genes, surveillance of pathogens, discover new pathway, host virus interaction, functional studies. The leads obtained through this exercise may have great impact on early diagnosis and treatment. While metagenomic studies also experience limitations and challenges, which need to overcome in near future to obtain a precise results. Unified genomic extraction techniques and development of improved analysis modules may suffice the needs of metagenomics in future.

detection and differential screening from seasonal virus [70].

**5. Conclusion**

28 Metagenomics for Gut Microbes

**Conflict of interest**

Authors declare no conflict of interest.

Prudhvi Lal Bhukya<sup>1</sup> \* and Renuka Nawadkar<sup>2</sup>

