Manning Lab Meeting Notes - Friday January 17th 2014

Discussion of strategies for Brian’s Phage study

Need to get better DNA yields for metagenomic sequencing of the Human gut phage community – in some low phage concentration cases he needs up to 500 grams of fecal material

It might be possible to use multiple displacement amplification in increase yields.

Brian will make an spreadsheet with all the samples that we will attempt to sequence for phage metagenomics. I will optimize his metagenomic partitioning and database for phage sequence identification and assembly. I suggested that we do Illumina sequencing of barcoded samples.

Check on the following: look for remnant of phage in metagenome datasets, tail region (or other region) primer design, may be possible to “deactivate” Stx gene and create “tag” to monitor phage in experimental populations – think more about this.

Check on ways of monitoring temperate and lytic/lysogenic phases. Read classic review on this.

Check on DNA sequencing for Phage plaque assays.

Strains to possibly use for experimental study: Salmonella, Shigella, EPEC versus EHAE, E. coli O157 Spinach Strain, EAE Cattle Isolate.

Pan-Genomics – big project of ongoing work.

Read these papers: Development and application of a method for the purification of free shigatoxigenic bacteriophage from environmental samples and Comparative genomics of Shiga toxin encoding bacteriophages.

Don’t forget Cary-Blair Transport Media