Comparative Analysis of Gut Microbiome Diversity, Stability, and Predicted Function in Captive Guanacos (Lama...

The gut microbiota plays a vital role in host health. In response to the scarcity of comparative studies examining wild and domesticated South American camelids under identical captive conditions, this study was conducted to compare the gut microbiota of 16 captive guanacos (Lama guanicoe) and 8 alpacas (Vicugna pacos) housed in the same zoo and fed identical diets, using 16S rRNA gene sequencing and multiple ecological metrics for analysis. Alpha diversity indices (Shannon, observed richness, and Shannoneven) did not differ between the two species, but beta diversity (principal component analysis) indicated significant separation (p < 0.05), and the guanacos exhibited significantly lower within-group Bray-Curtis dissimilarity, indicating more consistent microbial communities. Guanacos exhibited a lower average variation degree (AVD), indicating greater community stability, a broader niche, and a co-occurrence network with 81.1% positive edges and high modularity (0.691). In contrast, the alpacas showed a higher AVD (lower stability), a narrower niche, and a network with only 62.2% positive edges and lower modularity (0.534). Linear discriminant analysis effect size analysis revealed that Monoglobus and Bacteroides are enriched in guanacos, while Rikenellaceae_RC9_gut_group is enriched in alpacas. Functional predictions revealed that alpacas had higher predicted abundances of potentially pathogenic taxa and Kyoto Encyclopedia of Genes and Genomes pathways related to Staphylococcus aureus infection (p < 0.05). These findings demonstrate that, despite sharing environments, guanacos have a more stable, generalist-dominated gut microbiota with a higher proportion of positive co-occurrences, whereas alpacas exhibit a less stable, specialist-oriented community with a higher proportion of negative co-occurrences and greater predicted pathogenic potential. These results suggest that domestication may have contributed to the observed divergence in gut microbial ecology between the two species.