There have been significant advancements made in next-generation, high through-put sequencing, making this technology very affordable in its applications to strain typing. More importantly, this technology has made it possible to rapidly sequence whole genomes, and perform transcriptomics from single organisms to microbial communities. Advances in bioinformatics, especially annotation pipelines, has made it easier and quicker to identify the genetic underpinnings behind the emergence or re-emergence of pathogens, serovars, or strains, and identify metabolic differences between diseased and healthy microbiomes. The underlying genetics of a microorganism dictates whether it causes disease, or not, and its behavior in response to its host and other community species. As bacteria have a rapid growth rate, producing many generations within a short time span, genetic changes accumulate rapidly over time.Our goal is to assist the poultry industry with bacterial disease-related issues requiring molecular expertise in identifying pathogens, determining source of infection or contamination, or identifying indicators of healthy vs. diseased microbiome. Specifically, we will use a combination of molecular techniques to: 1) detect specific pathogen, serovar, or strain types in epidemiological investigation; 2) identify intestinal member species associated with healthy vs. diseased or pathogen permissive vs. exclusive intestinal communities.