title: Epimural Indicator Phylotypes of Transiently-Induced Subacute Ruminal Acidosis in Dairy Cattle.
abstract: The impact of a long-term subacute rumen acidosis (SARA) on the bovine epimural bacterial microbiome (BEBM) and its consequences for rumen health is poorly understood. This study aimed to investigate shifts in the BEBM during a long-term transient SARA model consisting of two concentrate-diet-induced SARA challenges separated by a 1-week challenge break. Eight cows were fed forage and varying concentrate amounts throughout the experiment. In total, 32 rumen papilla biopsies were taken for DNA isolation (4 sampling time points per cow: at the baseline before concentrate was fed, after the first SARA challenge, after the challenge break, and after the second SARA challenge). Ruminal pH was continuously monitored. The microbiome was determined using Illumina MiSeq sequencing of the 16S rRNA gene (V345 region). In total 1,215,618 sequences were obtained and clustered into 6833 operational taxonomic units (OTUs). Campylobacter and Kingella were the most abundant OTUs (16.5 and 7.1%). According to ruminal pH dynamics, the second challenge was more severe than the first challenge. Species diversity estimates and evenness increased during the challenge break compared to all other sampling time points (P < 0.05). During both SARA challenges, Kingella- and Azoarcus-OTUs decreased (0.5 and 0.4 fold-change) and a dominant Ruminobacter-OTU increased during the challenge break (18.9 fold-change; P < 0.05). qPCR confirmed SARA-related shifts. During the challenge break noticeably more OTUs increased compared to other sampling time points. Our results show that the BEBM re-establishes the baseline conditions slower after a SARA challenge than ruminal pH. Key phylotypes that were reduced during both challenges may help to establish a bacterial fingerprint to facilitate understanding effects of SARA conditions on the BEBM and their consequences for the ruminant host.
authors.affiliation: Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria.
authors.forename: Stefanie U
authors.initials: SU
authors.lastname: Wetzels
authors.affiliation: Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria.
authors.forename: Evelyne
authors.initials: E
authors.lastname: Mann
authors.affiliation: Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, University Clinic for Swine, University of Veterinary Medicine ViennaVienna, Austria.
authors.forename: Barbara U
authors.initials: BU
authors.lastname: Metzler-Zebeli
authors.affiliation: Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna Vienna, Austria.
authors.forename: Poulad
authors.initials: P
authors.lastname: Pourazad
authors.affiliation: Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine Vienna Vienna, Austria.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Qumar
authors.affiliation: Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria.
authors.forename: Fenja
authors.initials: F
authors.lastname: Klevenhusen
authors.affiliation: Department for Farm Animals and Veterinary Public Health, Institute for Veterinary Public Health, University of Veterinary Medicine Vienna Vienna, Austria.
authors.forename: Beate
authors.initials: B
authors.lastname: Pinior
authors.affiliation: Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria.
authors.forename: Martin
authors.initials: M
authors.lastname: Wagner
authors.affiliation: Department for Farm Animals and Veterinary Public Health, Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria.
authors.forename: Qendrim
authors.initials: Q
authors.lastname: Zebeli
authors.affiliation: Department of Farm Animal and Public Health in Veterinary Medicine, Institute for Milk Hygiene, Milk Technology and Food Science, University of Veterinary Medicine ViennaVienna, Austria; Department for Farm Animals and Veterinary Public Health, Research Cluster Animal Gut Health, University of Veterinary Medicine ViennaVienna, Austria; Department of Animal Science, Iowa State UniversityAmes, IA, USA.
authors.forename: Stephan
authors.initials: S
authors.lastname: Schmitz-Esser
keywords: 16S rRNA gene amplicon sequencing; Campylobacter; Kingella; cattle; feeding; long-term subacute rumen acidosis; microbiota; rumen epithelium