Dietary crude protein modifies fecal microbial populations independent of feed efficiency status in dairy cows

Abstract Understanding the composition and structure of the fecal microbial community may provide insight into bacterial adaptation to dietary changes in cattle. The aim of this study was to determine relationships among the fecal microbiome, residual feed intake (RFI) and residual net energy intake (REI) with diets varying in crude protein (CP). Four Holstein lactating cows (806 ± 38 kg of BW) were randomly assigned to one of two treatments (LOW: 13.2% and BASE:16.6% CP) in a crossover design (2 periods of 18 d each). Cows were 260 ± 62 days in milk (DIM) and averaged 26.5 ± 12.0 kg milk yield (MY). Diets were formulated to meet animal needs. Individual feed intake measured by a Calan Gate system was used to calculate daily dry matter intake (DMI). BW, MY and milk components were also measured daily. A linear mixed model with repeated measurements over time was used to evaluate diet effect on DMI, MY, RFI and REI in SAS. Individual fecal samples were collected at the end of each period and extracted DNA was subject to 16S rRNA gene deep amplicon sequencing. Operational Taxonomic Units (OTU) were obtained using ≥97% similarity (SILVA database) and microbial community structure was assessed using alpha and beta diversity measures. No significant differences in phenotypic variables evaluated were observed between treatments or periods. We identified 927 concordant OTU among all cows, with 505 novel OTU identified in BASE cows and 403 in LOW cows. Microbial community structure was similar between treatments and feed efficiency measures. One OTU class, Erysipelotrichi, increased in abundance (P = 0.014) in BASE compared to LOW treatment. Findings reflect previous literature in which Erysipelotrichi was associated with high energy or high fat diets. Although no differences were observed in the phenotypic measurements between treatments, metagenomics analyses indicated differences in specific fecal microbial abundance.