(A) (i) Shannon H’ diversity was decreased (Wilcoxon t-test, two-sided, 95% CI), when fish from both groups were exposed to cold conditions (12°C, blue). (ii) However, in control-warm conditions (24°C, pink) sensitive fish (purple) had a greater diversity of species in their gut microbiomes compared to the resistant fish (green) (Wilcoxon t-test, two-sided, 95% CI). (B) The relative abundance of various orders of microbes in the gut was affected when both resistant and sensitive fish were moved from warm to cold conditions. (C) Comparison of the β-diversity (Bray Curtis) within each of the host groups in (i) warm conditions showed a greater similarity among the resistant individuals compared to that among the sensitive fish, while (ii) comparison in relation to temperature change showed that after exposure to the stressful low-temperature conditions, the microbiomes of cold-resistant fish families were less affected than those of sensitive ones (non-parametric Bonferroni-corrected, using 1000 Monte Carlo permutations). (D) Host-associated species (from indicator species analysis; see 'Materials and methods' section) include several orders that were mostly enriched in either the resistant or the sensitive hosts. (E) (i) Microbial species that were present in >50% of the individuals in both warm and cold conditions (core communities) responded with an increase in their abundance after exposure to cold conditions in the sensitive group, and remained stable in the resistant fish (fold change in abundance from warm to cold shown in (ii)). (iii) These results were also validated by quantitative PCR analysis of the most abundant core species (Pseudomonas veronii and Janthinobacterium lividum). In the box plots, horizontal line in the box represents the median and whiskers indicate the lowest and highest point within 1.5 interquartile ranges of the lower or upper quartile, respectively. Bar plots show the mean copy number per group and whiskers the standard error of the mean.