Skip to main content
ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Food Safety and Enteric Pathogens Research » Research » Publications at this Location » Publication #388568

Research Project: Intestinal Microbial Ecology and Non-Antibiotic Strategies to Limit Shiga Toxin-Producing Escherichia coli (STEC) and Antimicrobial Resistance Transmission in Food Animals

Location: Food Safety and Enteric Pathogens Research

Title: Characterization of Two Novel Butyrate-Producing Species Isolated From Swine Feces

item WATKINS, HANNAH - Iowa State University
item Trachsel, Julian
item Loving, Crystal
item Anderson, Christopher

Submitted to: World Microbe Forum
Publication Type: Abstract Only
Publication Acceptance Date: 6/24/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: The ability to identify putative members of the porcine gut microbiome and their metabolites has potential applications that extend to maintained animal health. Representative species that produce the short-chain fatty acid butyrate, in particular, are valuable points of study given the compound’s important role in promoting colonic homeostasis and conveying increased resistance to enteric pathogens. Two anaerobic butyrate-producing species previously cultured from the feces of a sow and post-weaning piglet were designated Roseburia sp. 499 and 831b based on phylogenetic analysis of conserved genes and fragmented genomes. Here, we describe ongoing work to expand upon the evolutionary relationship and physiology of these isolates. The addition of long-read Oxford Nanopore sequences resulted in complete, circular genomes for 499 (3.38 Mbp; 38.2% GC) and 831b (3.13 Mbp; 40.7% GC), with evidence of a large 243 kbp circular plasmid in 831b. Phylogenetic analysis with the Genome Taxonomy Database (GTDB) confirmed position of 831b in the genus Roseburia, while 499 was classified to the genus 14-2 of Lachnospiraceae. Both isolates represent new species, with low average nucleotide identity (<80%) and alignment fraction to other members of their respective genera. The substrate utilization and carbon metabolism of 499 diverged from other species classified as 14-2 in GTDB, including the presence of pyruvate formate-lyase activating enzyme, citrate (Re)-synthase, certain glycoside hydrolases, polysaccharide lyases targeting pectin (PL9), and unique carbohydrate-binding modules for starch molecules. The metabolic profile of 831b displayed an array of carbohydrate-active enzymes shared across Roseburia. Both isolate genomes lacked butyrate kinase genes and were experimentally confirmed to use butyryl coenzyme A:acetate CoA transferase gene products in the terminal step of butyrate synthesis. Further, the two genomes suggest the potential for spore formation. Moving forward, we will detail the ecology and validate genomic predictions for substrate utilization and carbon metabolism in these two butyrate-producers.