Fig. 2

Microbial changes in alpha- and beta-diversity and biomarkers before, during, and after S. aureus clinical mastitis (CM) in Group I. Group I consisted of sick cows (n = 7) where Staphylococcus was detected in CM quarters at the time of CM diagnosis (Week 0). Both alpha-diversity (A) and beta-diversity (B) were similar between healthy and mastitic quarters at Week-6 and Week-4. Alpha-diversity in healthy quarters was significantly different from sick quarters two weeks before diagnosis (Week-2). Both alpha- and beta-diversity were significantly dissimilar between healthy and sick quarters at Week 0, which then remained as such while the mastitis continued for a few more weeks. Two weeks after the resolution of S. aureus CM (Week2), alpha- and beta-diversity had recovered, and were similar to the healthy quarters. C LEfSe analysis showed that at the time of diagnosis OTU0002 (Aerococcus) and OTU0001 (Staphylococcus) were highly associated with healthy and mastitic quarters, respectively. Ruminococcaceae unclassified (OTU0009) was highly associated with healthy quarters at Week 0 and Week 2