Bacterial endophytes colonize the interior of plants without causing disease and can produce beneficial effects to the host. These are transmitted vertically via seed or from soil by colonizing cracks in plant roots. Research is needed to understand what drives endophyte communities and management strategies which promote colonization of beneficial microbes. The benefits of chicken crop-livestock rotations on bacterial microbiomes is unknown. We aim to characterize the endophytic bacteria of tomato seedlings grown in chicken-grazed (CG) soils and determine the impact of soil diversity gradient in endophyte microbiome. Two tomato varieties were grown in the greenhouse in five treatments: 100%, 75%, 50% and 25% CG soil and 100% sterile soil substrate. Five-week-old tomato seedlings were measured for fresh weight and height and endophytes were isolated. Seedlings grown in 100% and 75% treatments had significant lower biomass. 88 bacterial endophytes from 14 genera, were recovered. 50% of the isolates obtained from higher diversity soils were Bacillus sp. and 20% of the isolates obtained from lower diversity soils were Microbacterium sp. Our data suggests that soil diversity gradient affects endophyte richness and plant biomass. Microbiome characterization of stem, root and leaves will be done using next generation sequencing. This project will lead to greater understanding of the impact of sustainable management strategies on the microbiome of this important commodity.