Shotgun Metagenomic Sequencing Analysis of Soft-Rot Enterobacteriaceae in Polymicrobial Communities

James Doonan; Sandra Denman; James E McDonald; Peter N Golyshin

doi:10.1007/978-1-4939-6691-2_7

Shotgun Metagenomic Sequencing Analysis of Soft-Rot Enterobacteriaceae in Polymicrobial Communities

Methods Mol Biol. 2017:1539:85-97. doi: 10.1007/978-1-4939-6691-2_7.

Authors

James Doonan¹, Sandra Denman², James E McDonald¹, Peter N Golyshin³

Affiliations

¹ School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK.
² Centre for Ecosystems Society and Biosecurity, Forest Research, Surrey, UK.
³ School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK. p.golyshin@bangor.ac.uk.

PMID: 27900686
DOI: 10.1007/978-1-4939-6691-2_7

Abstract

Shotgun metagenomic sequencing of bacterial communities in necrotic plant lesions allows insights of host-pathogen molecular interactions. Soft-rot Enterobacteriaceae are significant crop pathogens with a wide host range. Reconstructed polymicrobial community DNA from soft-rot affected crops provides details of species relative abundance and functional potential, enabling significant insights into their lifestyle. Here, we describe a workflow for DNA recovery, metagenomic shotgun sequencing and in particular, an in silico analysis of bacterial isolates from affected plant tissue.

Keywords: Host–pathogen molecular interactions; In silico; Polymicrobial; Shotgun metagenomics; Soft-rot Enterobacteriaceae.

MeSH terms

Computational Biology / methods
DNA Barcoding, Taxonomic
Enterobacteriaceae / classification*
Enterobacteriaceae / genetics*
Genome, Bacterial*
Genomic Library
High-Throughput Nucleotide Sequencing* / methods
Metagenomics* / methods
Molecular Sequence Annotation