Figure 3. Taxonomy bar plot of microbial composition in control and patient (“no drops” and “drops”) eye samples. Patient samples are divided into “Drops” for samples obtained from eyes receiving topical glaucoma medications and “No Drops” for samples obtained from contralateral eyes not receiving topical eyedrops. Only species with relative abundance >1.0% were represented in the figure and considered in pairwise comparisons. Relative abundance values for each individual sample were first calculated by dividing the number of read counts assigned to the amplicon sequence variants corresponding to individual microbes by the total read count of the sample. The relative abundance values represented in the figure are averages across all samples of the respective category (“Controls,” “No Drops,” “Drops”). ( A ) Composition of organisms based on relative abundance at the phyla level. Patient samples contained higher abundance of  Firmicutes ,  Verrucomicrobiota ,  Proteobacteria ,  Patescibacteria ,  Bacteroidota ,  Fusobacteriota , and  Cyanobacteria  ( P  < 0.05, LDA > 2) compared to control samples. Control samples contained higher abundance of  Actinobacteriota  ( P  < 0.05, LDA > 2). ( B ) Composition of organisms based on relative abundance at the genus level. Patient samples had higher abundance of  Akkermansia ,  Faecalibacterium ,  Lachnospiraceae  genus,  Lachnospiraceae  NK4A136 group,  Clostridia  UCG-014,  Gluconobacter ,  Ruminococcus torques  group,  Bifidobacterium, Clostridia vadin  B860 group,  Oscillospiraceae  UCG-002,  Peptoniphilus , and  Rothia  compared to control samples ( P  < 0.05, LDA > 2). Control samples had increased abundance in  Corynebacterium  and  Propionibacteriaceae  Cutibacterium ( P  < 0.05, LDA > 2). No differences in relative abundance were found between eyes treated with drops and untreated patient eye samples at both the phyla ( A ) and genus ( B ) level. LDA - linear discriminant analysis, statistical test used after performing centered log-ratio (CLR) transformation of raw read counts.