“The comparisons were relatively straightforward,” Tessler said. Shotgun Metagenomic Sequencing July 20, 2020 Shallow Shotgun Sequencing: A Primer September 16, 2019 Introducing the Microbiome Study Guide, a Guide to Microbiome Research June 23, 2020 In genetics, shotgun sequencing is a method used for sequencing random DNA strands. However, even though many people believe that 16S amplicon sequencing will soon be an obsolete technology, under some circumstances 16S sequencing still has an edge over shotgun … It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun.. The method enables microbiologists to evaluate bacterial diversity and detect the abundance of microbes in various environments. Some articles report identifying microbes using only a couple of regions of the gene, which obviously makes the amplicons even smaller and more cost effective. Shotgun metagenomic sequencing allows researchers to comprehensively sample all genes in all organisms present in a given complex sample. SHOTGUN METAGENOMIC SEQUENCING. No viruses were detected in the 16S amplicon sequencing samples while between 0.01% and 0.02% of the reads mapped to viruses in the shotgun metagenomic samples. After gathering a series of samples from four Brazilian river floodplains, they compared shotgun sequencing (random sequencing of whole genomes) with amplicon sequencing from the 16S ribosomal RNA gene on the Illumina and Roche 454 platforms, respectively. While 16S rRNA sequencing utilizes a marker gene approach and does not target the whole genome, metagenomics on the contrary is a culture-independent genomic analysis of microbes taken directly from the environment using a genome-wide shotgun sequencing approach [29, 30]. Compared to whole microbial genome, the 16s rDNA is relatively smaller, which is important as the cost of sequencing goes up and up the larger the libraries. The method enables microbiologists to evaluate bacterial diversity and detect the abundance of microbes in various environments. Shotgun sequencing can be used to profile taxonomic composition and functional potential of microbial communities and to recover whole genome sequences. 16S/ITS SEQUENCING VS. 16S rRNA Gene Sequencing vs. If your study requires genomic analyses beyond taxonomy profiling, such as metabolic pathway analysis, you should consider shotgun metagenomic sequencing due to its greater genomic coverage and data output. Shotgun metagenomic sequencing allows researchers to comprehensively sample all genes in all organisms present in a given complex sample. Resolution of the 16S gene is often too low to differentiate between closely related species As sequencing costs drop, microbiome research is moving from 16S rRNA gene sequencing to more comprehensive functional representations via whole genome or shotgun metagenomics sequencing.