Our understanding of the contributions of the gut microbiome to human health and disease has expanded dramatically with the development of high-throughput sequencing approaches for measuring microbial community structure. However, the wealth of data produced by these efforts has been limited by its compositional nature that neglects the possibility of changes in the overall size of the microbial community (microbiota density). Here, we present advances in the ability to measure microbiota density with greater throughput and as part of a standard microbiome analysis pipeline. We assayed gut microbiota density across mammals, disease, and therapeutic interventions. We identify microbiota density as an important feature of the microbiota that is shaped by physiologic features of the host (host carrying capacity) and the composition of the gut microbiota itself (gut microbiota fitness). Therapeutic manipulation of microbiota density in mice altered host metabolic and immune homeostasis. In humans, gut microbiota density was reduced in Crohn’s disease, ulcerative colitis, and ileal pouch-anal anastomosis compared to healthy individuals. The gutmicrobiota in recurrent Clostridium difficile infection also had lower density as a result of reduced microbiota fitness that was restored by fecal microbiota transplantation. Understanding the interplay between microbiota and disease through the conceptual framework of microbiota density, host carrying capacity, and microbiota fitness could provide biomarkers to identify candidates for microbiota therapeutics and monitor their responses.