Simple SummaryNecrotic enteritis, a secondary gastrointestinal (GIT) infection in poultry, is a costly burden to the commercialized poultry industry, impacting the welfare of broiler chickens as well as production gains. Many feed supplements have been proposed to alleviate the burden of necrotic enteritis in poultry with varied success. A promising supplement, a microencapsulated blend of organic acids and botanicals, has been demonstrated to modulate the immune system and the gastrointestinal microbial ecology in healthy birds. Therefore, we aimed to test this supplement in the feed of broiler breeder chickens infected with necrotic enteritis. To determine if the supplement improved the microbial ecology of the GIT, where necrotic enteritis resides, the GIT microbiota were elucidated using microbiome sequencing. There were minimal differences in the microbiota diversity; however, the core microorganisms of birds fed the supplement consisted ofLactobacillusandClostridiaceae. The supplemented-fed birds also had a higher abundance of normal microbiome inhabitants, namely,Actinobacteriota,Bacteroidota, andVerrucomicrobiota, than those not fed the supplement. Therefore, the supplementation of a microencapsulated blend supported beneficial and core microorganisms, potentially improving the bird’s response to NE.AbstractPreviously, the supplementation of a microencapsulated blend of organic acids and botanicals improved the health and performance of broiler breeders under non-challenged conditions. This study aimed to determine if the microencapsulated blend impacted dysbiosis and necrotic enteritis (NE) in broiler breeders. Day-of-hatch chicks were assigned to non-challenge and challenge groups, provided a basal diet supplemented with 0 or 500 g/MT of the blend, and subjected to a laboratory model for NE. On d 20–21, jejunum/ileum content were collected for microbiome sequencing (n = 10; V4 region of 16S rRNA gene). The experiment was repeated (n = 3), and data were analyzed in QIIME2 and R. Alpha and beta diversity, core microbiome, and compositional differences were determined (significance atp≤ 0.05; Q ≤ 0.05). There was no difference between richness and evenness of those fed diets containing 0 and 500 g/MT microencapsulated blend, but differences were seen between the non-challenged and challenged groups. Beta diversity of the 0 and 500 g/MT non-challenged groups differed, but no differences existed between the NE-challenged groups. The core microbiome of those fed 500 g/MT similarly consisted ofLactobacillusandClostridiaceae.Furthermore, challenged birds fed diets containing 500 g/MT had a higher abundance of significantly different phyla, namely,Actinobacteriota,Bacteroidota, andVerrucomicrobiota, than the 0 g/MT challenged group. Dietary supplementation of a microencapsulated blend shifted the microbiome by supporting beneficial and core taxa.