Upper respiratory tract microbiota of dairy calves experimentally challenged with BRSV

Bovine respiratory disease (BRD) is a leading cause of morbidity and mortality in cattle of all ages. The bovine respiratory microbiome plays a critical role in respiratory health. Despite current research, a lack of data exists surrounding the impact of viral infection on the bovine nasal microbiota. A key BRD virus, Bovine Respiratory Syncytial Virus (BRSV) is an enveloped, single stranded RNA virus of the order Mononegavirales, amongst the most significant viral agents in BRD cases in Ireland. The objective of this study was to characterise the nasal microbiota of dairy calves following experimental challenge with BRSV. Holstein-Friesian bull calves (mean age (SD) 120.7 days (14.15); mean weight (SD) 154.7 (13.6kg)) were administered either BRSV inoculate (103.5 TCID50/ml × 15 ml) (n=12) or were mock challenged with sterile phosphate buffered saline (n=6). Nasal swab samples were collected prior to euthanasia on day (d) 7 post-challenge. Microbial DNA was extracted from nasal swabs using the Powerlyzer PowerSoil extraction kit. Sequencing libraries were prepared using the Nanopore 16S barcoding kit (SQK-16S024) and amplicons purified using AmPureXP beads. Libraries were pooled and sequenced on a MinION flow cell (9.4 chemistry) using the Mk1C Device. Raw FASTQ files were uploaded to the EPI2ME platform and analysis performed using the Fastq 16S workflow (v2022.01.07). The top genera identified in BRSV challenged animals were Pasteurella, Moraxella and Mannheimia spp. with Pasteurella multocida, Moraxella nonliquefaciens and Mannheimia varigena identified as the most common species. Moraxella, Pasteurella and Mannheimia spp. were the most common genera identified in controls on d7, while Moraxella nonliquefaciens, Pasteurella multocida and Mannheimia varigena were the most common species identified. In conclusion, differences were identified in the top genera between BRSV infected and non-infected calves, suggesting that BRSV infection causes a dysbiosis of the nasal microbiome. Understanding the respiratory microbiota dynamics during disease development provides valuable insight into BRD pathogenesis.