Geography and diet determine the cecal microbiota of Cavia porcellus and reveal a fermentative core within its intestinal ecosystem
Cavia porcellus is a small mammal raised as a protein source in several South American countries. Its rapid reproduction and adaptability make it well suited to diverse production systems, supporting a livestock population of over 100 million animals. To meet its high metabolic demands, C. porcellus depends on cecal microbial fermentation for efficient forage digestion; however, the intestinal bacterial microbiota supporting this specialized digestive strategy remains poorly understood. In this study, we characterized the intestinal bacterial communities of C. porcellus using high-throughput amplicon sequencing of the 16S ribosomal RNA gene (V4 region). We analyzed microbial composition across intestinal segments (duodenum, jejunum, ileum, cecum, colon) and feces from a subset of 8 individuals, and conducted a more extensive exploration of the cecal microbiota in 288 animals from various rural districts in southern Colombia. Our results revealed clear compositional differences between the microbiota of the small and large intestines. We also observed a notable similarity among the cecum, colon, and fecal communities, suggesting the presence of a robust microbial core shared in this distal section of the gastrointestinal tract. Moreover, geographic origin, environmental conditions at the production units, and diet emerged as key factors influencing cecal microbial composition. Animals fed a mixed grass-based diet showed an enrichment of bacterial groups associated with the degradation of complex fibers. A comparative analysis of hindgut-fermenting rodents, such as the capybara, allowed us to identify both conserved bacterial groups and host-specific microbial signatures. Our study provides the most comprehensive view to date of the intestinal bacterial microbiota in C. porcellus, a species of growing relevance in sustainable animal production. These findings offer a framework for understanding how environmental, dietary, and host-related variables shape the gut microbiota of small herbivores and highlight the potential of C. porcellus as a model for studying specialized bacterial fermentation systems.
Cavia porcellus is a small mammal raised as a protein source in several South American countries. Its rapid reproduction and adaptability make it well suited to diverse production systems, supporting a livestock population of over 100 million animals. To meet its high metabolic demands, C. porcellus depends on cecal microbial fermentation for efficient forage digestion; however, the intestinal bacterial microbiota supporting this specialized digestive strategy remains poorly understood. In this study, we characterized the intestinal bacterial communities of C. porcellus using high-throughput amplicon sequencing of the 16S ribosomal RNA gene (V4 region). We analyzed microbial composition across intestinal segments (duodenum, jejunum, ileum, cecum, colon) and feces from a subset of 8 individuals, and conducted a more extensive exploration of the cecal microbiota in 288 animals from various rural districts in southern Colombia. Our results revealed clear compositional differences between the microbiota of the small and large intestines. We also observed a notable similarity among the cecum, colon, and fecal communities, suggesting the presence of a robust microbial core shared in this distal section of the gastrointestinal tract. Moreover, geographic origin, environmental conditions at the production units, and diet emerged as key factors influencing cecal microbial composition. Animals fed a mixed grass-based diet showed an enrichment of bacterial groups associated with the degradation of complex fibers. A comparative analysis of hindgut-fermenting rodents, such as the capybara, allowed us to identify both conserved bacterial groups and host-specific microbial signatures. Our study provides the most comprehensive view to date of the intestinal bacterial microbiota in C. porcellus, a species of growing relevance in sustainable animal production. These findings offer a framework for understanding how environmental, dietary, and host-related variables shape the gut microbiota of small herbivores and highlight the potential of C. porcellus as a model for studying specialized bacterial fermentation systems.
Universidad Nacional de Colombia