ABSTRACTThe objective of this study was to evaluate the progression of the uterine microbiota from calving until establishment of metritis. Uterine swabs (n= 72) collected at 0, 2, and 6 ± 2 days postpartum (dpp) from 12 metritic and 12 healthy cows were used for metagenomic sequencing of the 16S rRNA gene on the Illumina MiSeq platform. A heat map showed that uterine microbiota was established at calving. The microbiota changed rapidly from 0 to 6 ± 2 dpp, with a decrease in the abundance ofProteobacteriaand an increase in the abundance ofBacteroidetesandFusobacteria, which were dominant in metritic cows. Uterine microbiota composition was shared; however, metritic and healthy cows could be discriminated using relative abundance of bacterial genera at 0, 2, and 6 ± 2 dpp.Bacteroideswas the main genus associated with metritis because it was the only genus that showed significantly greater abundance in cows with metritis. As the abundance ofBacteroidesorganisms increased, the uterine discharge score, a measure of uterine health, worsened.Fusobacteriumwas also an important genus associated with metritis becauseFusobacteriumabundance increased asBacteroidesabundance increased and the uterine discharge score worsened as the abundance increased. The correlation with uterine discharge score and the correlation withBacteroidesorFusobacteriumshowed that other bacteria, such asHelcoccocus,Filifactor, andPorphyromonas, were also associated with metritis. There were also bacteria associated with uterine health, such as “CandidatusBlochmannia,”Escherichia,Sneathia, andPedobacter.
Optimized Protocol for Simple Extraction of High-Quality Genomic DNA from Clostridium difficile for Whole-Genome Sequencing
