Abstract
The aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups.
Highlights
The fecal microbiome consists of a complex community of microorganisms and represents a central issue in relation to cattle welfare and feed efficiency
The aim of this study was to characterize and analyze the difference of the fecal microbiome community of heifers and cows of dairy and dual-purpose cattle breeds, targeting the hypervariable regions of the bacterial 16S; we evaluated if the microbiome composition is conserved between the breeds that underwent to different management and diet composition
The total operational taxonomic units (OTUs) obtained (2,302) were clustered trough SILVA and Geengenes for the taxonomic analysis; this identified the presence of 2 kingdoms, 14 phyla, 22 classes, 34 orders, 74 families, 212 genera, and 350 species, while the remaining sequences were not assigned to known phyla (Table 2)
Summary
The fecal microbiome consists of a complex community of microorganisms and represents a central issue in relation to cattle welfare and feed efficiency. The aim of this study was to characterize and analyze the difference of the fecal microbiome community of heifers and cows of dairy and dual-purpose cattle breeds, targeting the hypervariable regions of the bacterial 16S; we evaluated if the microbiome composition is conserved between the breeds that underwent to different management and diet composition. Gaining knowledge on these aspects is expected to be beneficial to investigate changes in methane emissions and variation of feed efficiency, as well as to develop non-invasive routine controls to evaluate animal welfare and health
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