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Type of publication: Journal Article
Type of document: Full Paper

Year: 2015

Authors: Wetzels, SU; Mann, E; Metzler-Zebeli, BU; Wagner, M; Klevenhusen, F; Zebeli, Q; Schmitz-Esser, S

Title: Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats.

Source: J Dairy Sci. 2015; 98(8):5572-5587

Authors Vetmeduni Vienna:

Klevenhusen Fenja
Metzler-Zebeli Barbara
Schmitz-Esser Stephan
Selberherr Evelyne
Wagner Martin
Wetzels Stefanie
Zebeli Qendrim

Vetmed Research Units
Institute of Animal Nutrition and Functional Plant Compounds
Institute of Food Safety, Food Technology and Veterinary Public Health, Unit of Food Microbiology
University Clinic for Swine

Project(s): d-i.INFLACOW: Characterization and prevention of diet-induced inflammation and related immune and metabolic disorders in dairy cows

Ecological balance in the rumen is highly sensitive to concentrate-rich diets. Yet the effects of these feeding practices on the caprine bacterial epimural microbiome (CBEM), a microbial community with putative important physiological functions in the rumen, are largely unexplored. This study aimed to investigate the effect of dietary concentrate amount on ruminal CBEM. Seventeen growing goats were fed diets with 0 [n=5; 6.2MJ of metabolizable energy (ME)/d], 30 (n=6; 7.3MJ of /d), or 60% (n=6; 10.2MJ of ME/d) concentrate for 6 wk. Two hours after their last feeding, goats were euthanized and tissue samples of the ventral rumen wall were collected, washed in phosphate-buffered saline to detach loosely attached bacteria, and stored at -20°C for further processing. Genomic DNA was isolated from thawed rumen mucosa samples and used for Roche/454 Life Science (Branford, CT) 16S rRNA gene amplicon pyrosequencing yielding 122,458 reads. Pyrosequencing data were clustered into 1,879 operational taxonomic units (OTU; 0.03 distance level). Pyrosequencing revealed Proteobacteria, Bacteroidetes, Firmicutes, and Spirochaetes as the most abundant phyla (97.7%). Compared with the 30% group, both the 60 and 0% concentrate groups harbored significantly more Firmicutes and SR1, respectively. On an OTU level, a Bergeriella-related OTU was most abundant in the CBEM, followed by 2 Campylobacter OTU, which responded differently to diets: 1 OTU was significantly increased whereas the other significantly decreased with highest concentrate amount in the diet. At the genus level, the 0% concentrate group harbored increased Kingella-like sequences compared with the other feeding groups. Furthermore, the 0% concentrate group tended to have more Bergeriella than the 30 and 60% concentrate groups. The genus Bergeriella was significantly decreased in the 60% feeding group compared with the other diets. In conclusion, this is the first report of CBEM using deep-sequencing methods on the genus and OTU level, and our study revealed major shifts in the CBEM in response to concentrate-rich diets with potential health relevance in goats.

Keywords Pubmed: Animals
Base Sequence
DNA, Bacterial/analysis
Energy Intake
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/methods

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