Diseases are the major factor affecting economic viability and hampering sustained growth of the aquaculture industry. Over a 16 year period, the University of Idaho and the USDA-Agriculture Research Service have selectively bred rainbow trout that flourish when fed an all plant protein (high soy) diet. After eight generations, the selected strain exhibits rapid growth, altered intestinal morphology and higher survival in bacterial and viral challenge tests while fed an all plant protein diet compared to commercial strains of trout. Here we exploit this unique trout strain to identify genetic mechanisms and to assess the influence of intestinal microbiota (IM) on disease resistance using high-throughput sequencing technologies and standard immunological assays. We analyzed the IM under homeostatic, as well as disease challenged conditions, during early developmental stages that are critical for disease susceptibility and development of host-microbiota interactions. From this, we are able to discern whether the IM and host gastrointestinal associated lymphatic tissue (GALT) are unique, in the absence of the diet-type and intestinal enteritis effects which confounded our previous results. In addition, we evaluated the IM and host intestinal gene expression in the context of both viral and bacterial disease challenges, to investigate the resilience of the selected strains' gut microbial ecology to the perturbation of exposure to virulent pathogens.