The fecal bacterial microbiota of healthy alpacas was analyzed using 16S amplicon sequencing

The microbiota in different alpacas was similar with UniFrac distance averaging between 0.16 and 0.21 across 3 collections. ß diversity between pairs of samples from different collections was significantly correlated, consistent with microbiota stability. This pattern was not affected by time between collections as a similar correlation was found when comparing collection 1 with 2, 2 with 3 and 1 with 3. Consistent with the persistence of ß diversity, a diversity was also correlated between collections. Animals with a more diverse micobiota were likely to harbor a diverse microbiota in subsequent collections. Levamisol did not appear to impact the microbiota, but the survey was not designed to detect such an effect as all animals sampled were treated. The intensity of the infection with HOT complex nematodes appeared to have a minor interaction with the microbiota as the association between HOT egg concentration and the microbiota profile was only detectable in one out of three collections. In contrast to infection with HOT complex, age and weight had a clear and consistent effect on the microbiota.