Figure 3
The species and/or strain level taxonomic profile microbiota associated with bovine clinical mastitis (CM). Sequences are assigned to different taxonomic index in PathoScope (PS) analysis using minimum identity of 95% and minimum alignment length 20 as cutoff parameters and the circular phylogenetic tree is constructed based on the neighbor-joining algorithm using FigTree. The round tree illustrates 363 unique strains of bacteria in CM milk metagenomes. The inner circle represents the root of the microbiome defined as bacteria present in all samples. The outer circles represent different strains of bacteria is defined as species (with different strains) present in >50% of samples of the corresponding groups. For the outer circles, the width of a segment is proportional to the observed incidence for that species. Different colors are assigned according to the taxonomic ranks of the bacteria. The species and/or strains in the phylogenetic tree are also available in Supplementary Data 2.
