ruminal fluid and feces raw sequence reads. Ruminal fluid and feces

Indigestion, mastitis and laminitis are common diseases in high producing dairy cows fed grain-based diets. Information on the effects of these challenges on gastrointestinal microbial communities of lactating dairy cows is still limited. In order to study the effects of these challenges on potential gut dysbiosis, 45 Holstein dairy cows that included 10 healthy, 11 with indigestion, 13 with mastitis, and 11 with laminitis were used in the study. Extracted DNA from rumen fluid and feces was analyzed using Illumina MiSeq sequencing of the V3~V4 region of the 16S rRNA gene to compare the bacterial communities between healthy cows and cows with some disease.