Deciphering the microbiome by next generation sequencing technologies

Author: Dr. Sheetal Ambardar, Post-Doctoral Fellow,
Centre for Functional Genomics & Bio-informatics.

‘Microbiomics’ is a fast-growing field in which all the microorganisms of a given community are investigated together. High throughput next sequencing approaches have revolutionised the study of microbial diversity and function by metagenomics approaches. This could be the microbiota of an environmental sample (e.g. soil or water), a particular body site (e.g. the gut or the mouth) or from a particular organism (e.g. farm or zoo animals). Microbiomics helps in understanding of microbial diversity, the functional roles that microorganisms have in that particular environment.

I have been studying the microbiomics of world’s economical important spice ‘Crocus sativus’ (Saffron) grown in only Jammu and Kashmir state of India from last 9 years. Microbial diversity can be studied using 16S profiling using next generation sequencing technology wherein multiple samples can be analysed in less time and cost effective.

With the recent advent in next generation sequencing, third generation sequencer are able to sequence full length 16S rRNA gene and thus able to characterise the bacterial community upto species level. The 16S profiling gives a ‘snapshot’ of the bacterial communities present in a sample at any given time, and can be used to compare the communities in different samples, or follow changes in the communities of a particular sample site over time.

In saffron, the microbial community was found specific to niche, growth stages as well as geographical locations (Ambardar and Vakhlu 2013; Ambardar et al. 2014; Ambardar et al., 2016). Moreover, the bacterial community associated with saffron rhizosphere was able to identified upto species level using Nanopore sequencing technology (third generation sequencer). The knowledge gained from studying microbiota can potentially be exploited in the context of global change, food security, biotechnology and human health.

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