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, 79 (12), 3744-55

Changes in the Rumen Epimural Bacterial Diversity of Beef Cattle as Affected by Diet and Induced Ruminal Acidosis

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Changes in the Rumen Epimural Bacterial Diversity of Beef Cattle as Affected by Diet and Induced Ruminal Acidosis

R M Petri et al. Appl Environ Microbiol.

Abstract

Little is known about the nature of the rumen epithelial adherent (epimural) microbiome in cattle fed different diets. Using denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and pyrosequencing of the V3 hypervariable coding region of 16S rRNA, epimural bacterial communities of 8 cattle were profiled during the transition from a forage to a high-concentrate diet, during acidosis, and after recovery. A total of 153,621 high-quality gene sequences were obtained, with populations exhibiting less taxonomic variability among individuals than across diets. The bacterial community composition exhibited clustering (P < 0.03) by diet, with only 14 genera, representing >1% of the rumen epimural population, differing (P ≤ 0.05) among diets. During acidosis, levels of Atopobium, Desulfocurvus, Fervidicola, Lactobacillus, and Olsenella increased, while during the recovery, Desulfocurvus, Lactobacillus, and Olsenella reverted to levels similar to those with the high-grain diet and Sharpea and Succinivibrio reverted to levels similar to those with the forage diet. The relative abundances of bacterial populations changed during diet transition for all qPCR targets except Streptococcus spp. Less than 5% of total operational taxonomic units (OTUs) identified exhibited significant variability across diets. Based on DGGE, the community structures of epithelial populations differed (P ≤ 0.10); segregation was most prominent for the mixed forage diet versus the grain, acidotic challenge, and recovery diets. Atopobium, cc142, Lactobacillus, Olsenella, RC39, Sharpea, Solobacterium, Succiniclasticum, and Syntrophococcus were particularly prevalent during acidosis. Determining the metabolic roles of these key genera in the rumens of cattle fed high-grain diets could define a clinical microbial profile associated with ruminal acidosis.

Figures

Fig 1
Fig 1
Cluster analysis of dietary treatments created using Jaccard analysis to show dissimilarity between epithelial populations based on unique OTUs for each treatment. OTUs are estimated at a 10% difference level.
Fig 2
Fig 2
Dendrogram of PCR-DGGE analysis of rumen epithelial samples from cattle fed a progression of dietary treatments (forage, mixed forage, high grain, acidotic challenge, and challenge recovery). Results were clustered with the Dice similarity coefficient (optimization, 1.0%; tolerance, 1.0%) and UPGMA.
Fig 3
Fig 3
Graphical representation of the phylogenetic tree of the rumen epithelial core microbiome. Any OTU present in all samples, for all animals on all treatments, was considered part of the core microbiome. Average percentages of abundance are given in parentheses.
Fig 4
Fig 4
Daily monitored pHs in highly acidotic (animals 7 and 41) and minimally acidotic (animals 143 and 153) heifers. The time of the grain challenge was 0900, and the time of feeding was 1 h postchallenge.
Fig 5
Fig 5
Differences in relative abundances (expressed as percentages) of epithelial bacterial genus populations in clinically acidotic heifers (animals 7 and 41) compared to subclinically acidotic heifers (animals 143 and 153). Acidotic ranking was determined by the area under the curve for a pH of <5.2, adjusted for the dry-matter intake of the animal. IS, incertae sedis.

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