title: Dereplication by automated ribotyping of a competitive exclusion culture bacterial isolate library.
abstract: Concerns over the development of antibiotic-resistant bacteria within the food animal industry have intensified the search for natural approaches to the prevention and treatment of bacterial diseases. Competitive exclusion cultures are the foundation of a disease-management strategy based on the use of benign bacterial strains to prevent the establishment of pathogenic bacteria within a specific host. Differentiation of phenotypically ambiguous isolates is a critical step in establishing a manageable library of bacteria for use in the development of defined competitive exclusion cultures. We used automated ribotyping techniques to dereplicate a large collection of phenotypically ambiguous isolates from a continuous-flow competitive exclusion culture. A total of 157 isolates were screened following an EcoRI restriction enzyme digestion. The 157 isolates were resolved into 23 ribogroups, which represents an 85% reduction in the number of isolates in the bacterial isolate library. Seventy-six percent of the isolates fit into one of five ribogroups. This work demonstrated that automated ribotyping is an effective and efficient tool for dereplication of diverse bacterial isolate libraries.
authors.affiliation: U.S. Department of Agriculture, Agricultural Research Service, Southern Plains Agricultural Research Center, Food and Feed Safety Research Unit, 2881 F&B Road, College Station, Texas 77845, USA. sheffield@ffsru.tamu.edu
authors.forename: Cynthia
authors.initials: C
authors.lastname: Sheffield
authors.forename: Kate
authors.initials: K
authors.lastname: Andrews
authors.forename: Roger
authors.initials: R
authors.lastname: Harvey
authors.forename: Tawni
authors.initials: T
authors.lastname: Crippen
authors.forename: David
authors.initials: D
authors.lastname: Nisbet
mesh_terms: D000898:Antibiosis; D001331:Automation; D001419:Bacteria / Q000145:classification*; D015169:Colony Count, Microbial; D010802:Phylogeny; D015183:Restriction Mapping; D021521:Ribotyping / Q000379:methods*; D012680:Sensitivity and Specificity