Metagenomic evidence of the prevalence and distribution patterns of antimicrobial resistance genes in dairy agroecosystems

<p>Antimicrobial resistance (AR) is a global problem with serious implications for public health. AR genes are frequently detected on animal farms but little is known about their origin and distribution patterns. We hypothesized that AR genes can transfer from animal feces to the environment via manure and to this end we characterized and compared the resistomes (collections of AR genes) of animal feces, manure, and soil samples collected from five dairy farms using a metagenomics approach. Resistomes constituted only up to 1% of the total gene content, but were variable by sector and also farm.  Broadly, the identified AR genes were associated with18 antibiotic resistances classes across all samples; however, the most abundant genes were those encoding for multi-drug resistance (MDR) efflux systems (44.75%), followed by resistance to vancomycin (12.48%), tetracycline (10.52%), bacitracin (10.43%), beta-lactam resistance (7.12%) and MLS efflux pump (6.86%) antimicrobials. The AR gene profiles were variable between farms; farm 09 was categorized as a high risk farm as a greater proportion of AR genes were common to at least three sectors, suggesting possible transfer of organism(s)/horizontal transfer of AR genes. Taxonomic characterization of AR genes revealed that a majority of AR genes were associated with the phylum Proteobacteria. Nonetheless, there were several members of Bacteroidetes, particularly Bacteroides genus and several lineages from Firmicutes that carried similar AR genes in different sectors, suggesting a strong potential for horizontal transfer of AR genes between unrelated bacterial hosts in different sectors of the farms. Further studies are required to affirm the horizontal gene transfer mechanisms between microbiomes of different sectors in animal agroecosystems.</p> <p> </p

Comparison of 454 and PGM platforms

<p>Files containing all raw sequences and mapping files from 454 and PGM platforms</p

Comparison of rumen microbial communities in dairy herds of different production

In the US, there is a substantial difference in annual milk production between dairy herds.  We hypothesized that the rumen microbial composition will be different between higher and lower yielding dairy herds and that each dairy herd will have a distinct microbial  fingerprint.  This study included 85 Holstein dairy cows from two farms: Farm12 (M305;, 12,324 kg; n=47; primiparous cows: 24, multiparous cows: 23) and Farm9 (M305;, 9,693 kg; n=38; primiparous cows: 19, multiparous cows: 19).  Bacterial diversity from rumen samples was characterized using 16S rRNA gene sequencing using Ion Torrent (PGM)Ion Torrent platform.   Differences in microbial communities between farms were greater  (p<0.001) (adonisAdonis:; R2=0.16;, p<0.001) than within farm.  Five bacterial lineages namely Prevotella (48-51 %), Bacteroidales (10-12 %), Unclassified bacteria (5-8 %), Succinivibrionaceae (1.4-6.6 %) and Prevotellaceae (3.8-4.7 %) were observed to differentiate the community clustering patterns between the two farms. A notable finding is the greater (p<0.05) contribution of Succinivibrionaceae in Farm12 compared to Farm9. Furthermore, in Farm12, this bacterial populations was higher (p<0.05)  in the high yielding cows compared to low yielding cows in both parity groups. Prevotella, S24-7 and Succinivibrionaceae were found to be positively correlated with fat corrected milk and feed efficiency, and a majority of Firmicutes genera were found to be positively correlated with milk fat ( %) and protein ( %). It was concluded that characterizing ruminal microbiota across elite herds is required to identify specialist rumen microbes across herds varying in milk production.      <br><br

Differences in the equine fecal microbiome using different sampling times and sites

<div>To investigate the effect of different sampling techniques (rectum vs. stall floor ), locations (center vs. surface of the fecal ball) and time of sample collection post-defecation on the equine fecal microbiome.</div><div><br></div