Full Shotgun DNA Metagenomics

Abstract

Full DNA metagenomics is the sequencing of all DNA from a sample followed by assembly and annotation and assignment of sequence information to organisms and function. The assembly of DNA sequence reads attempts to reconstruct genome fragments to draft genomes. The bioinformatics pipelines Mothur and QIIME demonstrated in Chap. 8 for 16S rRNA amplicon sequence analysis can also be used for full DNA metagenomics. The focus in the chapter is on MG-RAST that both can handle the information from predicted proteins in metagenomics data for further prediction of function or taxonomic relationships and also can extract the 16S rRNA gene sequence information and provide more detailed taxonomic information from the specialized databases SILVA, Greengenes, and RDP that were presented in Chap. 8. The most serious limitation of full DNA metagenomics is probably the databases which mainly are being based on cultured microorganisms.