Effects of respiratory virus vaccination and bovine respiratory disease on the respiratory microbiome of feedlot cattle

Abstract

IntroductionThe objectives of this study were to evaluate the impacts of two modified-live virus (MLV) vaccination protocols and respiratory disease (BRD) occurrence on the microbial community composition of the nasopharynx in feedlot cattle.MethodsThe treatment groups included in this randomized controlled trial included: 1) no viral respiratory vaccination (CON), 2) intranasal, trivalent, MLV respiratory vaccine in addition to a parenteral BVDV type I and II vaccine (INT), and 3) parenteral, pentavalent, MLV respiratory vaccination against the same agents (INJ). Calves (n = 525) arrived in 5 truckload blocks and were stratified by body weight, sex, and presence of a pre-existing identification ear-tag. A total of 600 nasal swab samples were selected for DNA extraction and subsequent 16S rRNA gene sequencing to characterize the microbiome of the upper respiratory tract. Nasal swabs collected on d 28 from healthy cattle were used to evaluate the impact of vaccination on upper respiratory tract (URT) microbial communities.ResultsFirmicutes were less abundant in INT calves (n = 114; P < 0.05) and this difference was attributed to decreased relative abundance (RA) of Mycoplasma spp. (P = 0.04). Mannheimia and Pasteurella had lower RA in INT (P < 0.05). The microbiome in healthy animals on d 28 had increased Proteobacteria (largely Moraxella spp.) and decreased Firmicutes (comprised almost exclusively of Mycoplasma spp.) compared to animals that were treated for or died from BRD (P < 0.05). Cattle that died had a greater RA of Mycoplasma spp. in their respiratory microbiome on d 0 (P < 0.02). Richness was similar on d 0 and 28, but diversity increased for all animals on d 28 (P>0.05).

Tulathromycin metaphylaxis increases nasopharyngeal isolation of multidrug resistant Mannheimia haemolytica in stocker heifers

“…Historically, MH has been the bacterial species most commonly isolated from the lungs of beef cattle that have died from respiratory disease and continues to be found frequently in cattle with respiratory disease ( 4 , 57 ). However, ongoing studies of the upper respiratory tract microbiome suggest that other bacterial taxa are differentially abundant in cattle that go on to develop clinical BRD ( 26 , 58 ). Care should be taken before concluding that AMR found in MH are predictive of AMR in other BRD associated microbes, or that these findings would be reflected in other beef cattle management situations.…”

Effectiveness of stabilization methods for the immediate and short-term preservation of bovine fecal and upper respiratory tract genomic DNA

“…Significant systematic differences or biases in microbiome data that are associated with different sample preservation methods have been clearly demonstrated in studies of human feces [ 36 ], even though changes in community composition are often smaller than differences between sample types or among study subjects [ 35 ]. Regardless, small systematic differences in non-dominant taxa can have far reaching consequences for animal and ecosystem health [ 5 ]. Therefore, there is a need to expand our understanding of how stabilization methods shift microbial community composition in the absence of variation associated with differing sample types or study subjects (i.e., biological variation) to isolate the effect of different stabilization methods.…”

“…Host-associated microbial communities play crucial roles in human health and the health of all animals [1][2][3][4][5][6][7]. Studies commonly target microbial communities of the gastrointestinal tract (GIT) where a large proportion of host-associated microbes reside, and GIT microbial communities have been implicated in a wide variety of health issues [8][9][10][11][12][13][14][15][16][17][18].…”

“…To this end, fecal samples are frequently collected and analyzed as a proxy for lower intestine microbial communities. Analogous to the past decade's boom of microbiome research in people (i.e., Human Microbiome Project, American Gut Project), research investigating the role that microbial communities play in the health of livestock and agricultural environments has surged in recent years [5,[19][20][21][22][23][24]. This is encouraged by a shifting dogma in animal sciences and veterinary medicine from culture-based microbiology studies of the past to culture-independent methods investigating features of interest (i.e., antimicrobial resistance, virulence, etc.)…”

“…The bovine GIT microbiome has been linked to several diseases that are important both clinically and financially, and is associated with growth, production, and efficiency of cattle [19,20,25]. The composition of microbial communities in the respiratory tract of cattle has increasingly been implicated in pneumonia or bovine respiratory disease (BRD), which is the most common disease requiring antimicrobial drug treatment among beef cattle in North America [5,21,[26][27][28]. Researchers commonly collect fecal samples to characterize GIT communities and use swabs to collect upper respiratory tract secretion samples.…”