title: Deciphering upper respiratory tract microbiota complexity in healthy calves and calves that develop respiratory disease using shotgun metagenomics.
abstract: Bovine respiratory disease (BRD) is a multifactorial disorder responsible for severe economic losses in dairy and feedlot herds. Advances in next-generation sequencing mean that microbial communities in clinical samples, including non-culturable bacteria, can be characterized. Our aim was to evaluate the microbiota of the upper respiratory tract of healthy calves and calves with BRD using whole-genome sequencing (shotgun metagenomics). We performed deep nasopharyngeal swabs on 16 Holstein heifer calves (10 healthy and 6 diagnosed with BRD during the study) at 14 and 28 d of life in 1 dairy herd near Ithaca, New York. Total DNA was extracted, and whole-genome sequencing was performed using the MiSeq Illumina platform (Illumina Inc., San Diego, CA). Samples included 5 predominant phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Tenericutes. At the genus level, we observed differences between groups for Pseudomonas spp. At the species level, Mannheimia haemolytica was the most abundant bacterium detected. We detected significant differences between groups of calves in the relative abundance of Pseudomonas fluorescens. Pasteurella multocida was among the 20 most abundant species, and Moraxella catarrhalis, commonly associated with pneumonia in humans, was detected in all groups. Analysis of resistance to antibiotics and compounds profiling revealed differences in cobalt-zinc-cadmium resistance. Further research to elucidate the role of Moraxella catarrhalis in BRD is warranted. Genes that were resistant to cobalt-zinc-cadmium, observed mostly in calves with BRD, might be associated with difficulties in antibiotic treatment.
authors.affiliation: Department of Medical Clinic, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil 05508-270.
authors.forename: Natália C
authors.initials: NC
authors.lastname: Gaeta
authors.affiliation: Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, NY.
authors.forename: Svetlana F
authors.initials: SF
authors.lastname: Lima
authors.affiliation: Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, NY.
authors.forename: Andre G
authors.initials: AG
authors.lastname: Teixeira
authors.affiliation: Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, NY.
authors.forename: Erika K
authors.initials: EK
authors.lastname: Ganda
authors.affiliation: Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, NY; Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Neston CH64 7TE, United Kingdom.
authors.forename: Georgios
authors.initials: G
authors.lastname: Oikonomou
authors.affiliation: Department of Medical Clinic, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil 05508-270.
authors.forename: Lilian
authors.initials: L
authors.lastname: Gregory
authors.affiliation: Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca 14853, NY. Electronic address: rcb28@cornell.edu.
authors.forename: Rodrigo C
authors.initials: RC
authors.lastname: Bicalho
mesh_terms: D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000382:microbiology; D005260:Female; D016978:Mannheimia haemolytica; D056186:Metagenomics; D064307:Microbiota; D016979:Pasteurella multocida; D012137:Respiratory System / Q000382:microbiology*
keywords: bovine respiratory disease; calf; whole-genome sequencing