Linking Microbial Community Structure and Function to Characterize Antibiotic Resistant Bacteria and Antibiotic Resistant Genes From Cattle Feces.

There is widespread interest in monitoring the development of antibiotic resistant bacteria and antibiotic resistance genes in agriculturally impacted environments, however little is known about the relationships between bacterial community structure, and antibiotic resistance gene profiles.   Cattle manure serves as the vehicle by which intestinal bacteria carrying antibiotic resistance genes are transferred to the environment.  Thus, the first step in tracking the transmission of antibiotic resistant bacteria and antibiotic resistance genes is to understand these parameters in the fecal source material.

Whole community DNA sequencing was used to characterize the antibiotic resistant genes in feedlot cattle feces, and identify the bacteria likely carrying these genes.  Additionally, public metagenomic databases were mined to compare community structure and antibiotic resistant gene profiles from other environments.  Results indicate that in feedlot cattle feces, the detected fluoroquinolone resistance genes likely belong to 59 bacteria genera.  The majority (50%) are carried by members of the Bacteroides genus, followed by Clostridium (15%).  At the level of class, the predominant bacteria carrying fluoroquinolone resistance genes in cattle feces are Bacteroidetes, Clostridia, and Bacilli in a 9:3:1 ratio, compared to 1:2:1 in cattle rumen, and 1:6:3 in Antarctic marine derived lake. 

Whole community DNA sequencing using high-throughput techniques provides information on both taxonomic and functional genes from a sample.  While the current “second-generation” pyrosequencing tools are not readily accessible to most researchers at this time, new sequencing platforms have recently been introduced that have the potential to make sequencing-based approaches more accessible by reducing the cost of a sequencing run to under $800. New tools are publicly available that link functional gene assignments to taxonomic information, allowing insight into which bacteria are potentially carrying the genes of interest.  We used these tools to identify which bacteria were carrying antibiotic resistance genes in cattle feces.