The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot

Abstract

Background: The nasopharyngeal (NP) microbiota plays an important role in bovine health, comprising a rich and diverse microbial community. The nasopharynx is also the niche for potentially pathogenic agents which are associated with bovine respiratory disease (BRD), a serious and costly illness in feedlot cattle. We used 14 beef heifers from a closed and disease-free herd to assess the dynamics of the NP microbiota of cattle that are transported to a feedlot. Cattle were sampled prior to transport to the feedlot (day 0) and at days 2, 7, and 14.

Results: The structure of the NP microbiota changed significantly over the course of the study, with the largest shift occurring between day 0 (prior to transport) and day 2 (P < 0.001). Phylogenetic diversity and richness increased following feedlot placement (day 2; P < 0.05). The genera Pasteurella, Bacillus, and Proteus were enriched at day 0, Streptococcus and Acinetobacter at day 2, Bifidobacterium at day 7, and Mycoplasma at day 14. The functional potential of the NP microbiota was assessed using PICRUSt, revealing that replication and repair, as well as translation pathways, were more relatively abundant in day 14 samples. These differences were driven mostly by Mycoplasma. Although eight cattle were culture-positive for the BRD-associated bacterium Pasteurella multocida at one or more sampling times, none were culture-positive for Mannheimia haemolytica or Histophilus somni.

Conclusions: This study investigated the effect that feedlot placement has on the NP microbiota of beef cattle over a 14-d period. Within two days of transport to the feedlot, the NP microbiota changed significantly, increasing in both phylogenetic diversity and richness. These results demonstrate that there is an abrupt shift in the NP microbiota of cattle after transportation to a feedlot. This may have importance for understanding why cattle are most susceptible to BRD after feedlot placement.

Keywords: 16S rRNA gene; Bovine respiratory disease; Cattle; Feedlot; Livestock; Microbiome; Nasopharyngeal microbiota.

Fig. 1

The 20 most relatively abundant archaeal and bacterial genera in the nasopharyngeal microbiota of cattle at days 0, 2, 7, and 14 of the study. For each sampling time n = 14 except day 0, where n = 13

Fig. 2

The relative abundance of bacterial genera associated with bovine respiratory disease in the nasopharyngeal microbiota of cattle. Cattle were sampled at a ranch (Day 0) prior to shipping to a feedlot and then 2, 7, and 14 days after feedlot placement. a Mannheimia, b Mycoplasma, c Pasteurella

Fig. 3

Genera enriched in the nasopharyngeal microbiota of cattle at specific sampling times, as determined using linear discriminant analysis effect size (LEfSe) analysis. Only genera with a linear discriminant analysis (LDA) score (log₁₀) of > 4.0 are displayed. Cattle were sampled at a ranch (Day 0) prior to shipping to a feedlot and then 2, 7, and 14 days after feedlot placement. For each sampling time n = 14 except day 0, where n = 13

Fig. 4

Alpha-diversity (within-sample) analysis of the nasopharyngeal microbiota of cattle over time. Cattle were sampled at a ranch (Day 0) prior to shipping to a feedlot and then 2, 7, and 14 days after feedlot placement. a equitability (evenness), b richness, c phylogenetic diversity (PD whole tree), and d the Shannon index. The solid, horizontal black line denotes the mean

Fig. 5

Principal coordinate analysis of the nasopharyngeal microbiota of cattle. Plots of the unweighted UniFrac distances by sampling time are shown. Cattle were sampled at a ranch (Day 0) prior to shipping to a feedlot and then 2, 7, and 14 days after feedlot placement. The percent variation explained by the principal coordinates is indicated on the axes

Fig. 6

Functional predictions for the nasopharyngeal (NP) microbiota of cattle, as calculated using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt). a Number of KEGG orthologies (KOs) per NP sample. b Principal coordinate analysis plot of Bray-Curtis distances for KOs in each NP sample by sampling time. Cattle were sampled at a ranch (Day 0) prior to shipping to a feedlot and then 2, 7, and 14 days after feedlot placement