16S amplicon sequencing of bacteria in suckler sheep's milk
Milk samples were collected from both mammary gland halves at lambing then weekly for 6 weeks and at week 8. DNA was extracted from 399 milk samples using the hydroxyapatite spin column method (Purdy, Meth Enzymol 397:271-292). An extraction control was processed with every DNA extraction run. PCR with general bacterial primers 27F and 338R-GC. MiSeq adapters were added in subsequent very short PCRS, including PCR and model community (Staphylococcus aureus, E. coli, Streptococcus agalactiae, Streptococcus hyicus and Mannheimia haemolytica) controls in every PCR run. All samples and controls were sequenced in two 200 bp paired end sequence runs.