Fig. 5

Shannon indexes of rumen metagenome data for (A) library preparation kits and (B) DNA extraction kits, and (C) principal coordinates analysis. The Australian dataset for sequencing kit analysis only included the data from the PowerFecal kit. The Australian dataset used the ligation kit SQK-LSK109 and the rapid sequencing kit SQK-RBK110.96. The Spanish dataset used the ligation sequencing kit SQK-LSK109 and the rapid sequencing kit SQK-RBK004. The DNA extraction kit dataset only used samples sequenced by the ligation kit SQK-LSK109 from the Australian dataset. Data for sequencing and extraction kit analysis were basecalled under SUP mode. Dotted lines in boxplots link the same DNA sample. Animal ID AUS01 was from the Australian dataset, while the other animals were from the Spanish dataset. A t-test was used to compare the means of different extraction and sequencing protocols (An unpaired t-test for the Australian dataset and a paired t-test for the Spanish dataset). P-values < 0.05: *; P-values < 0.01: **; P-values < 0.001: ***