Investigation of the bacterial microbiome of poultry litter
Samples of litter were collected from poultry houses to examine the litter bacterial microbiome and how this changes during the production cycle.  Samples were collected from six farms which used a variety of bedding types.  Samples were collected for two consecutive production cycles from each farm during the early, middle and late parts of the cycle.  Litter samples were transported to the laboratory on ice and thoroughly mixed with sterile phosphate buffered saline (PBS) at a 1:1 ratio (vol:vol). Aliquots of the PBS were frozen until DNA was extracted using Qiagen Powersoil Pro kit (according to manufacturer's instructions).  The v4 region of the 16s rRNA gene was sequenced using an Illumina Miseq (250bp paired end reads).