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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Environmental Microbial & Food Safety Laboratory » Research » Publications at this Location » Publication #314963

Title: Metagenomic analysis of the bovine hindgut from Salmonella Kentucky and Cerro-shedding dairy cows

item Haley, Bradd
item PETTENGILL, JAMES - Food And Drug Administration(FDA)
item GORHAM, SASHA - Food And Drug Administration(FDA)
item OTTESEN, ADREA - Food And Drug Administration(FDA)
item Karns, Jeffrey
item Van Kessel, Jo Ann

Submitted to: American Society for Microbiology
Publication Type: Abstract Only
Publication Acceptance Date: 3/5/2015
Publication Date: 5/31/2015
Citation: Haley, B.J., Pettengill, J., Gorham, S., Ottesen, A., Karns, J.S., Van Kessel, J.S. 2015. Metagenomic analysis of the bovine hindgut from Salmonella Kentucky and Cerro-shedding dairy cows. Meeting Abstract. American Society for Microbiology, New Orleans, LA, May 30-June 2, 2015.

Interpretive Summary: .

Technical Abstract: In the United States Salmonella enterica subsp. enterica serovars Kentucky and Cerro are frequently isolated from dairy cows that appear asymptomatic. Although they are not major contributors to the salmonellosis burden, these serovars have been implicated in human clinical cases in recent years. To investigate the diversity of the bovine hindgut as well as associations between Salmonella status and bacterial diversity, the 16S rRNA metagenomes of fecal samples from cows on a single dairy farm were sequenced. Fecal grab samples were collected from 20 dairy cows on five different sampling dates. Samples were enriched for S. enterica in tetrathionate broth. Enrichments that were identified as Salmonella-positive using real time PCR were struck on XLT4 agar. Conventional PCR targeting the invA gene was conducted on suspected Salmonella colonies. For metagenomic analysis, genomic DNA was extracted from each fecal sample followed by two rounds of conventional PCR with 16S rRNA specific primers and Nextera DNA indices, respectively. Paired-end sequencing of 16S rRNA amplicons was performed on the Illumina MiSeq platform using 500 cycle V2 cartridges. Sequencing reads were analyzed with QIIME v. 1.8.0. A high level of variability was observed between samples, demonstrating that the microbial profiles of bovine hindguts are diverse. To determine whether Salmonella status, sampling year, or sampling group explained a significant amount of the variation in microbial diversity, we performed a constrained ordination analyses (distance based RDA; rb-RDA) on the unifrac distance matrix produced with QIIME. Results indicated that there was a significant difference in the microbial diversity associated with sampling year but not for sampling group or Salmonella status. Members of the order Clostridiales were the primary taxonomic group whose abundance differed between years.