Fig. 1

Experimental design for the comparison between field collected and lab-reared ticks. Ticks were collected from the field in Burns, OR and Lake Como, MT each spring during 2012–2014 (F0) and reared one generation (F1) in the lab. In this study we focused on the F1 generation as it is considered to most closely represent field collected ticks, with the exception that the microbiome contains only those endosymbionts that are transovarially passaged. The initial cohort that was collected in 2012 was used to establish a laboratory colony that was perpetuated for three generations. In 2013 and 2014, the field collected ticks were only reared to the F1 stage for microbiome sampling and comparison to the 2012 cohort; these lines were not continued. All ticks were dissected and MG and SG were assayed for bacterial microbiome resulting in seven (×2 for each tissue) sequence sets. a, d, and e correspond to the F1 microbiome from 2012, 2013 and 2014, respectively, and are considered as field collected microbiome data. b and c correspond to the F2 and F3 microbiome from the 2012 laboratory colonized ticks. Data for groups A-E was acquired by pooling tissues (MG or SG) from 30 ticks, and 3 biological replicates were performed—i.e., in all, 90 ticks were analyzed per group. In 2014, we analyzed individual ticks at the F0 and F1 stage resulting in data set f (F1) and g (F0). Each horizontal arrow indicates a generational rearing which takes approximately 1 year to complete