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1.1 Background:Bovine respiratory disease (BRD) is caused by interactions among host, environment, and pathogens. The current standard for antemortem pathogen identification in cattle with BRD is deep-guarded nasopharyngeal swabbing, which is challenging, costly, and waste generating. The objective was to compare the ability to recover Mannheimia haemolytica and compare microbial community structure using 29.5 inch (74.9 cm) deep-guarded nasopharyngeal swabs, 16 inch (40.6 cm) unguarded proctology swabs, or 6 inch (15.2 cm) unguarded nasal swabs when characterized using culture, real time-qPCR, and 16S rRNA gene sequencing. Samples for aerobic culture, qPCR, and 16S rRNA gene sequencing were collected from the upper respiratory tract of high-risk cattle 2 weeks after feedlot arrival. 1.2 ResultsThere was high concordance of culture and qPCR results for all swab types (results for 77% and 81% of samples animals completely across all 3 swab types for culture and qPCR respectively). Microbial communities were highly similar among samples collected with different swabs types, and differences identified relative to treatment for BRD were also similar. Positive qPCR results for M. haemolytica were highly concordant (81% agreed completely), but samples collected by deep-guarded swabbing had higher Ct values (Kruskal-Wallis analysis of variance on ranks, P < 0.05; Dunn-test for pairwise comparison with Benjamini-Hochberg correction, P < 0.05) and lower frequency of positive compared to nasal and proctology swabs (McNemar’s Chi-square test, P M. haemolytica by culture, 16S rRNA microbiome, and qPCR.