Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers

Background:Ruminants rely upon a complex community of microbes in their rumen to convert host-indigestible feed into nutrients.However,little is known about the association between the rumen microbiota and feed efficiency traits in Nellore(Bos indicus)cattle,a breed of major economic importance to the global beef market.Here,we compare the composition of the bacterial,archaeal and fungal communities in the rumen of Nellore steers with high and low feed efficiency(FE)phenotypes,as measured by residual feed intake(RFI).Results:The Firmicutes to Bacteroidetes ratio was significantly higher(P<0.05)in positive-RFI steers(p-RFI,low feed efficiency)than in negative-RFI(n-RFI,high feed efficiency)steers.The differences in bacterial composition from steers with high and low FE were mainly associated with members of the families Lachnospiraceae,Ruminococcaceae and Christensenellaceae,as well as the genus Prevotella.Archaeal community richness was lower(P<0.05)in p-RFI than in n-RFI steers and the genus Methanobrevibacter was either increased or exclusive of p-RFI steers.The fungal genus Buwchfawromyces was more abundant in the rumen solid fraction of n-RFI steers(P<0.05)and a highly abundant OTU belonging to the genus Piromyces was also increased in the rumen microbiota of highefficiency steers.However,analysis of rumen fermentation variables and functional predictions indicated similar metabolic outputs for the microbiota of distinct FE groups.Conclusions:Our results demonstrate that differences in the ruminal microbiota of high and low FE Nellore steers comprise specific taxa from the bacterial,archaeal and fungal communities.Biomarker OTUs belonging to the genus Piromyces were identified in animals showing high feed efficiency,whereas among archaea,Methanobrevibacter was associated with steers classified as p-RFI.The identification of specific RFI-associated microorganisms in Nellore steers could guide further studies targeting the isolation and functional characterization of rumen microbes potentially important for the energy-harvesting efficiency of ruminants.

Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

Background:Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease.Sand can also be efficiently recycled and reused,making it cost-effective.However,some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria,although no studies have yet characterized the total bacterial community composition.Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing.Results:Bacterial community compositions of the sand recycling system differed by both seasons and stage.Summer samples had higher richness and distinct community compositions,relative to winter samples.In both summer and winter samples,the diversity of recycled sand decreased with time drying in the recycling room.Compositionally,summer sand 14 d post-recycling was enriched in operational taxonomic units(OTUs)belonging to the genera Acinetobacter and Pseudomonas,relative to freshly washed sand and sand from cow pens.In contrast,no OTUs were found to be enriched in winter sand.The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45%±10.33%SD of the total bacterial relative abundance at each sampled stage.The 4 most abundant genera in this core microbiota included Acinetobacter,Psychrobacter,Corynebacterium,and Pseudomonas.Acinetobacter was present in greater abundance in summer samples,whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples.Pseudomonas had consistent relative abundances across both seasons.Conclusions:These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.

The ruminal bacterial community in lactating dairy cows has limited variation on a day-to-day basis

Dairy cows rely on a complex ruminal microbiota to digest their host-indigestible feed. Our ability to characterize this microbiota has advanced significantly due to developments in next-generation sequencing. However, efforts to sample the rumen, which typical y involves removing digesta directly from the rumen via a cannula, intubation, or rumenocentesis, is costly and labor intensive. As a result, the majority of studies characterizing the rumen microbiota are conducted on samples col ected at a single time point. Currently, it is unknown whether there is significant day-to-day variation in the rumen microbiota, a factor that could strongly influence conclusion drawn from studies that sample at a single time point. To address this, we examined day-to-day changes in the ruminal microbiota of lactating dairy cows using next-generation sequencing to determine if single-day sampling is representative of sampling across 3 consecutive days. We sequenced single-day solid and liquid fractions of ruminal digesta col ected over 3 consecutive days from 12 cannulated dairy cows during the early, middle, and late stages of a single lactation cycle using the V4 region of the bacterial 16 S r RNA gene. We then generated 97% similarity operational taxonomic units(OTUs) from these sequences and showed that any of the individual samples from a given 3-day sampling period is equivalent to the mean OTUs determined from the combined 3-d data set. This finding was consistent for both solid and liquid fractions of the rumen,and we thus conclude that there is limited day-to-day variability in the rumen microbiota.