Escondido Canyon had lower average alpha diversity than Lopez and Peñasquitos canyons, P =0.05 (Fig. 4). Beta diversities of unweighted and weighted tick microbiomes had small but statistically significant associations with location as measured by analysis of similarity (ANOSIM) of UniFrac distances and visualized on Principal coordinate analysis (PCoA) (Figs. 5A and 5B). When only Rickettsia and Francisella were assessed for association with location, ANOSIM results were not statistically significant (ANOSIM, unweighted UniFrac; R = − 0.06, P = 0.92; ANOSIM, weighted UniFrac R = 0.02, P = 0.13). However, in order to determine if location influenced the non-dominant species separately from the dominant Rickettsia and Francisella endosymbionts, Rickettsia and Francisella were removed from the data and the analysis was repeated. After Rickettsia and Francisella were removed, the remaining microbiome association with location was low but statistically significant (ANOSIM, unweighted UniFrac; R = 0.20, P < 0.01; ANOSIM, weighted UniFrac; R = 0.28, P < 0.01). Procrustes analysis also demonstrated that the beta diversity of microbiomes in which Rickettsia and Francisella were removed had a different association with location than Rickettsia and Francisella endosymbionts (error, M2 = 0.91, P < 0.01). Isolation by distance (IBD) analysis using unweighted UniFrac distances that incorporated all members of the microbiome revealed little geographic IBD (Mantel test, unweighted UniFrac, R = 0.09, P < 0.01). However, a pattern of IBD was significant after excluding Rickettsia and Francisella (Mantel test, unweighted UniFrac, R = 0.14, P < 0.01). (Unlike weighted UniFrac, unweighted UniFrac distances only incorporate the presence or absence of microbial taxa and to not take into account the abundance of the particular taxa. This allowed us to focus on the taxonomic differences among locations rather than the abundance differences of particular taxa. In a separate analysis, we found significant differences in the relative abundances of three bacterial genera, Nevskia, Curtobacterium and Sphingomonas, between locations (Kruskal–Wallis H = 25.7, 24.2, 22.9; Bonferroni corrected P < 0.01, respectively). Ticks in Peñasquitos and Lopez Canyons had higher abundances of Nevskia than ticks collected in Mission Trails. Peñasquitos and Lopez Canyons ticks had higher relative abundances of Curtobacterium and Sphingomonas than ticks in Escondido Creek and Mission Trails (Table 2).