Evaluation of the Nasopharyngeal Microbiota in Beef Cattle Transported to a Feedlot, With a Focus on Lactic Acid-Producing Bacteria

Abstract

The nasopharyngeal (NP) microbiota is important in defining respiratory health in feedlot cattle, with certain NP commensals potentially protecting against bovine respiratory disease (BRD) pathogens. In the present study, we evaluated longitudinal changes in the NP microbiota with a focus on lactic acid-producing bacteria (LAB) and their linkage with BRD-associated bacteria in steers (n = 13) that were first transported to an auction market, and then to a feedlot. Deep nasopharyngeal swabs were collected at the farm before transportation to the auction market (day 0), at feedlot placement (day 2), and 5 (day 7) and 12 (day 14) days after feedlot placement. Swabs were processed for the assessment of the NP microbiota using 16S rRNA gene sequencing, and for the detection of Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni by culturing. Possible associations among the top 15 most relatively abundant bacterial genera were predicted using a stepwise-selected generalized linear mixed model. Correlations between LAB and BRD-associated Pasteurellaceae families were also assessed. In addition, antimicrobial activity of selected LAB isolates against M. haemolytica was evaluated in vitro. A noticeable shift was observed in the NP microbial community structure, and in the relative abundance of LAB families as a result of auction market exposure, transport and feedlot placement. Varying degrees of positive or negative associations between the 15 most relatively abundant genera were observed. Many of the LAB families were inversely correlated with the BRD-associated Pasteurellaceae family as the cattle were transported to the auction market and then to the feedlot. Nearly all steers were culture-negative for M. haemolytica and H. somni, and P. multocida became less prevalent after feedlot placement. Isolates from the Lactobacillaceae, Streptococcaceae, and Enterococcaceae families inhibited the growth of M. haemolytica. The results of this study indicated that the NP microbiota became more diverse with an increase in microbial richness following transport to an auction market and feedlot. This study provides evidence of potential cooperation and exclusion taking place in the respiratory microbial community of cattle which may be useful for developing microbial-based strategies to mitigate BRD.

Keywords: antimicrobial activity; auction market; bovine respiratory disease; feedlot cattle; lactic acid-producing bacteria; nasopharyngeal microbiota; respiratory pathogens.

Figure 1

Principal coordinates analysis (PCoA) plot of the Bray-Curtis dissimilarities of the nasopharyngeal microbiota by sampling day for (A) PC1 vs. PC2 and (B) PC2 vs. PC3. (C) PCoA plot of the Jaccard distances of the nasopharyngeal microbiota of cattle (n = 13) by sampling day. The percentage of variation explained by each principal coordinate is indicated on the axes.

Figure 2

(A) Relative abundance of total lactic acid-producing bacteria (LAB) (defined as order Lactobacillales); (B) Proportion of LAB familes within the order of Lactobacillales across time points; (C) Box and whisker plots of the percent relative abundance of 6 families observed within LAB in the nasopharyngeal microbiota of cattle (n = 13) by sampling time. Colored dots indicate outliers. Different lowercase letters within each plot indicate significantly different means (P < 0.05).

Figure 3

Box and whisker plots of the 15 most abundant genera in the nasopharyngeal microbiota of cattle (n = 13) by sampling time. Colored dots indicate outliers. The box in the box plots indicates the interquartile range (IQR) (middle 50% of the data), the middle line represents the median value, and the whiskers represents 1.5 times the IQR. Different lowercase letters indicate significantly different means (P < 0.05).

Figure 4

Box and whisker plots of the (A) number of OTUs and (B) Shannon diversity index of the nasopharyngeal microbiota of cattle (n = 13) by sampling time. The box in the box plots indicates the interquartile range (IQR) (middle 50% of the data), the middle line represents the median value, and the whiskers represents 1.5 times the IQR. Different lowercase letters indicate significantly different means (P < 0.05).

Figure 5

Growth inhibitory effects of lactic acid bacteria (LAB) strains isolated from the nasopharynx of healthy feedlot cattle against a bovine respiratory pathogen Mannheimia haemolytica serotype 1 strain, as determined by the agar slab method. (A) mean inhibitory zones from triplicate tests. (B) An example of the agar slabs showing inhibition zones on a lawn of M. haemolytica.