Journal of Microbial & Biochemical Technology

Abstract

A Return to Microbial Genomes in the Metagenome Age

Eric Altermann

Metagenomics has broadened significantly in microbial ecosystems, phylogenetic diversity and genetic complexity. In the course of only a few years microbial genomics has seen a dramatic rise from the 1.8 Megabase pair (Mbp) genome of the first free-living organism sequenced (Haemophilus influenzae Rd in 1995 [1]) to (meta) genome programmes now generating more than a Terabase pair of sequence data each. These advances have been made possible by increasingly more powerful sequencing technologies. Fluorescent slab-gel electrophoresis methods were replaced by capillary-based systems, which brought a significant increase in the level of throughput and automation. A step change came with the introduction of “sequencing by synthesis”. This technology was commercialised as ‘pyrosequencing’, notably by 454 Life Sciences. While initially providing only shorter read lengths of 100-200 nucleotides (nt), and having a lower base call quality and problems with homopolymeric stretches of nucleotides, it also delivered a leap in sequencing capacity (up to 400 Mbp per run) from capillary Sanger-based sequencing technologies. Since then a number of other next-generation sequencing platforms have been commercialised (such as Illumina, SOLID, Ion Torrent), each increasing the amount of sequence information gained per run (Illumina HiSeq2500 currently delivers up to 600 Gbp per run). While single molecule real time (SMRT) sequencing is still in its infancy, it is likely to be the “next big thing” and prototypes (mainly from Pacific Biosciences) are currently being trialled.