However, despite the small sample size, bacterial community composition differed by farm when using Bray–Curtis ( p = 0.03, PERMANOVA) ( Figure S3C ) and unweighted UniFrac ( p = 0.03, PERMANOVA) but was only a strong trend when using weighted UniFrac distances ( p = 0.08, PERMANOVA).
When using the mg/kg metric to evaluate bacterial community differences by AMU, similar results were found for both alpha (Chao: p < 0.01, Shannon: p = 0.01, Wald) and beta (Bray–Curtis: R 2 : 7.7%, p = 0.005, PERMANOVA, Unweighted UniFrac: R 2 : 5.4%, p = 0.03, PERMANOVA) diversity with the exception of weighted UniFrac (R 2 : 6.2%, p = 0.08, PERMANOVA), which had a lower p -value, trending toward significance, and explained a larger proportion of variance than with DDD. 3.8.3.