Additional file 2 of Rumen microbiome structure and metabolites activity in dairy cows with clinical and subclinical mastitis
Creators: name: Wang, Yue
name: Nan, Xuemei
name: Zhao, Yiguang
name: Jiang, Linshu
name: Wang, Mengling
name: Wang, Hui
name: Zhang, Fan
name: Xue, Fuguang
name: Hua, Dengke
name: Liu, Jun
name: Yao, Junhu
name: Xiong, Benhai
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified

description: Additional file 2 Fig. S1 Pan-Species curve of OTU number in the cows with different udder health status. Pan species was the sum of all the species in a sample, which was used to observe the increase in the total number of species as the number of samples increases. H, healthy; SM, subclinical mastitis; CM, clinical mastitis. Fig. S2 Rarefaction curve of OUT number in the cows with different udder health status. H, healthy; SM, subclinical mastiti; CM, clinical mastitis. Fig. S3 Rumen microbial community composition analysis. a At phylum level. b At genus level. H, healthy; SM, subclinical mastitis; CM, clinical mastitis. Fig.S4 Hierarchical cluster analysis (HCA) of rumen bacteria at genus level. Each row in the figure represents a sample, each column represents a genus, and the color indicates the relative abundance of bacteria measured in the group. Red indicates the high relative abundance, and the green indicates low relative abundance. H, healthy; SM, subclinical mastitis; CM, clinical mastitis. Fig. S5 Linear discriminant analysis effect size (LEfse) analysis of multilevel species differences in ruminal microbiota. a Cladogram; b LEfSe Bar graph. H, healthy; SM, subclinical mastitis; CM, clinical mastitis; LDA, linear discriminant analysis. Fig. S6 The total ion chromatograms (TIC) plot of quality control (QC) samples in a positive ion mode and b negative ion mode. Fig. S7 Orthogonal partial least squares discriminant analysis (OPLS-DA) (a, c, e) and response permutation testing (RPT) (b, d, f) of rumen metabolites between H, SM and CM groups in positive ion mode. H, healthy; SM, subclinical mastitis; CM, clinical mastitis. R2X and R2Y represent the interpretation rate of the built model to the X and Y matrix, R2X (cum) and R2Y (cum) represent the cumulative interpretation rate; Q2 indicates the predictive power of the model. Fig. S8 Orthogonal partial least squares discriminant analysis (OPLS-DA) (a, c, e) and response permutation testing (RPT) (b, d, f) plots of rumen metabolites between H, SM and CM groups in negative ion mode. H, healthy; SM, subclinical mastitis; CM, clinical mastitis. R2X and R2Y represent the interpretation rate of the built model to the X and Y matrix, R2X (cum) and R2Y (cum) represent the cumulative interpretation rate; Q2 indicates the predictive power of the model. Fig. S9 HMDB compound classification (Superclass level) of significantly differential metabolites between a CM and H groups, b SM and H groups and c CM and SM groups. HMDB, Human Metabolome Database; H, healthy; SM, subclinical mastitis; CM, clinical mastitis.