Diversity and composition of the bacterial community in the feces of cattle and goats

The present study aimed to assess and compare the diversity and composition of the bacterial community of feces of cattle and goats, using advanced method of molecular biology. A total of 17 female goats, Bionda dell’Adamello and 16 female cows, Original “Bruna” (Brown Swiss), were selected for the study, they were fed pasture and hay and they had free access to water. The collection of fresh fecal samples was carried out immediately after defecation and all of the samples were freeze-dried and kept in the fridge until needed for the analysis. The DNA extraction and the amplification of the bacterial variable V4-V5 region of 16S rRNA was performed. The bacterial structure was studied using high-throughput sequencing. The analysis of bacterial diversity was evaluated through alpha diversity, and beta diversity and the taxonomical composition was analyzed using QIIME2 platform. Alpha diversity measurements of the bacterial community revealed significant difference in Pielou Evenness index showing a higher species evenness in cows compared to goats. Other alpha diversity indices showed no statistical differences between the two groups of animals, indicating a similar richness of bacterial species. Beta diversity measurements revealed statistical differences between animals indicating dissimilarities and distinct clustering of bacterial composition of feces between goats and cows. Regarding the taxonomical composition, Firmicutes was dominant phylum both in goats and cows, followed by Bacteroidetes, Proteobacteria and Spirochaetes. Linear discriminant analysis effect size (LEfSe) showed a total of 63 significantly different taxa between goats and cows. Mainly, the relative abundance of Spirochaetales, Christensenellaceae, Spirochaetaceae, Treponema and Ruminococcus was higher in goats compared to cows. In contrary, the relative abundance of Bacillales, Paraprevotellaceae, p-2534-18B5, Peptostreptococcaceae, Planococcaceae and CF231 was higher in cows compared to goats. In conclusion, our findings suggest that host’s species has a significant influence on the composition of fecal bacterial community.