Cow milk and faeces samples Raw sequence reads

Raw milk and fecal samples were collected from 31 dairy cows belonging to Holstein breeds, and the bacterial diversity was explored using 16S rRNA amplicon sequencing. Previous bacteriological screening analysis showed that nine animals were in a healthy status while 22 animals could be classified as affected with subclinical mastitis: 11 by Streptococcus spp. and 11 by Prototheca spp. This study aimed to analyze the dynamic composition of bacterial communities of dairy cow milk samples obtained from healthy and subclinical mastitis affected animals of a Holstein breed cattle, using a microbial approach. In addition, in order to examine the gut inner microbial environment during mastitis, we collected and analysed also faeces samples from all the three cow groups: healthy cows, Streptococcus spp affected cows and finally Prototheca spp affected cows.