Table 1.
Primer Sequences Used in This Study.
Fig 1.
Visualization of alpha and beta diversity in the fecal microbiota of pet and stray dogs.
(A) Shannon Index: Box plot comparing the Shannon index of microbial diversity between pet and stray dogs. The Shannon index measures alpha diversity, reflecting both the richness and evenness of species in a community. (B) Observed Features: Box plot comparing the number of observed features (Amplicon Sequence Variants, ASVs) between the two groups. This metric represents alpha diversity by counting the unique ASVs present in each sample, indicating species richness. (C) Faith’s Phylogenetic Diversity: Box plot comparing Faith’s phylogenetic diversity between pet and stray dogs. Faith’s phylogenetic diversity is an alpha diversity measure that considers the branch lengths of a phylogenetic tree, encompassing the evolutionary relationships between species. (D) Jaccard Index: PCoA plot illustrating the beta diversity based on the Jaccard index between pet and stray dogs. The Jaccard index measures beta diversity by comparing the presence or absence of species between samples, indicating community composition differences. (E) Bray–Curtis Index: PCoA plot showing the beta diversity based on the Bray–Curtis distance. The Bray–Curtis index assesses beta diversity by considering the abundance of species between samples, indicating community structure and dissimilarity. (F) Weighted UniFrac: PCoA plot representing the beta diversity based on the Weighted UniFrac distance. Weighted UniFrac is a beta diversity measure that accounts for both the presence/absence and the phylogenetic distances of species, indicating differences in community composition and evolutionary relationships. The statistical test conducted for alpha diversity indices (Shannon Index, Observed Features, Faith’s Phylogenetic Diversity) was the Wilcoxon rank-sum test. The statistical test conducted for beta diversity indices (Jaccard Index, Bray–Curtis Index, Weighted UniFrac) was PERMANOVA (Permutational Multivariate Analysis of Variance).
Fig 2.
Average relative abundance of bacterial taxa in fecal samples.
Bar plot showing the average relative abundance of bacterial phyla (A) and genera (B) in pet and stray dogs. Stacked bar plot illustrating the relative abundance of bacterial phyla (C) and genera (D) in individual fecal samples.
Fig 3.
Differentially abundant microbial taxa between pet and stray dogs.
(A) ANCOM Volcano Plot: Volcano plot illustrating differentially abundant taxa between pet and stray dogs. The red dot represents Faecalitalea with the highest W-statistic value of 185, indicating its significant differential abundance. (B) LEfSe Bar Plot: Bar plot showing taxa with LDA scores greater than 3, indicating significant differential abundance between pet and stray dogs.
Table 2.
Positivity differences in putative bacterial pathogens between the stray and pet dog groups.
Table 3.
Positivity differences in putative eukaryotic pathogens between the stray and pet groups based on 18S rRNA sequencing results.
Fig 4.
LEfSe analysis of differentially abundant taxa based on the presence or absence of Giardia and Pentatrichomonas in the feces.
(A) Bar plot comparing the abundance of bacterial taxa between Giardia-present and Giardia-absent samples from both pet and stray dogs. (B) Bar plot comparing the abundance of bacterial taxa between Pentatrichomonas-present and Pentatrichomonas-absent samples from both pet and stray dogs. (C) Bar plot showing the differential abundance of bacterial taxa between Giardia-present and Giardia-absent samples within only stray dogs. Only genera with LDA scores more than 3 were selected. (D) Bar plot depicting the differential abundance of bacterial taxa between Pentatrichomonas-present and Pentatrichomonas-absent samples within only stray dogs. Only genera with LDA scores more than 3 were selected.