Microbial communities play an important role in ecosystem functionality and health but remain poorly characterized in wild ecosystems. The sagebrush steppe is one of the largest terrestrial ecosystems in North America and is composed of several sagebrush (Artemesia spp.) species. An understanding of the microbial communities may help scientists better understand multi-species interactions and ecosystem functionality. During the Spring semester of 2023, we—a group of researchers from three institutions representing multiple career stages— embarked on a project to characterize these complex bacterial communities from soil communities of the sagebrush steppe and fecal samples from a sagebrush obligate herbivore (the Greater Sage-grouse, Centrocercus urophasianellus). As undergraduate researchers in the Characterizing Complex Communities (C3) VIP Course, we were upskilled in the linux/unix coding language, high-performance computing, and the QIIME2 pipeline to analyze millions of 16S reads from these samples to understand the complex communities. Preliminary results indicate differences between sample types, with some overlap in bacterial communities between soil and fecal samples. In addition to identifying communities, this semester provided an opportunity to explore the skills needed to build and maintain a multi-institutional collaborative research project, including frequent communication, active listening, and team building.