Diarrhea-Associated Changes in Fecal Microbiota Composition and Community Structure in Llama Crias

The gastrointestinal microbiota plays a key role in the health and productivity of llama crias, yet its dynamics under disease conditions remain poorly understood. This study aimed to characterize and compare the fecal microbiota of healthy and diseased llama crias. Fecal samples collected from nine llama crias (six with diarrhea and three clinically healthy controls) were analyzed using 16S rRNA gene sequencing targeting the V4 region, followed by bioinformatic processing and statistical analyses, including diversity metrics and generalized linear mixed models. Results showed that microbial communities were dominated by Bacillota and Bacteroidota in both groups; however, diseased animals exhibited increased abundance of Pseudomonadota, particularly Gammaproteobacteria and Enterobacteriaceae. Beta diversity analysis revealed significant differences in community structure between groups, with diseased samples showing higher dispersion. Additionally, a greater number of unique ASVs was observed in diseased individuals, indicating increased microbial heterogeneity. Differential abundance analysis identified distinct microbial signatures associated with health status, with opportunistic taxa enriched in diseased animals and fiber-degrading taxa more prevalent in healthy individuals. Overall, the findings demonstrate an association between diarrhea and differences in the fecal microbiota of llama crias. Because this was a cross-sectional observational study, causal relationships cannot be inferred. These results provide a foundation for future investigations into host–microbiota interactions and gastrointestinal health in South American camelids.