Our first observation was that a majority of clinical strains were in fact not trueP. agglomeransas defined by Gavini et al. [1] based on SB-715992 taxonomic discrepencies revealed by sequence analysis of the 16S rDNA andgyrBgenes. All biocontrol strains in the collection were found to be correctly identified asP. agglomerans. The reason for this discrepancy is ascribed to the fact that bacteria selected for their biological

SAR302503 purchase control properties are typically better characterized, including DNA sequencing, in comparison to those obtained in clinical diagnostics where rapid identification for implementation of therapeutic treatment is the primary concern and relies on less precise biochemical identification methods (e.g., API20E and Vitek-2 from bioMerieux or Phoenix from BD Diagnostic Systems). Biochemical methods have previously been shown to misidentifyP. agglomeransandEnterobacterspp. [43,46–49], which our results confirm. Additionally, many archival strains were deposited in culture collections more than 30 years ago when the genusPantoeawas not yet taxonomically established and biochemical identification was less accurate. TheEnterobacter/Pantoeagenus has undergone numerous taxonomical rearrangements [1,41,48,50–53] (Figure8) and our

results indicate that many strains previously identified asE. agglomeransorE. herbicolahave been improperly transferred into the compositeP. agglomeransspecies [1]. Although previous studies based on DNA-DNA hybridization alerted Natural Product Library purchase that theE. agglomerans-E. herbicolacomplex is composed from several unrelated species [52,54,55] (Figure8), these names continue to be utilized as subjective synonyms. In this study, we analyzed the current subdivisions ofP. agglomeransbased on DNA-DNA hybridization and used sequence analysis to establish valid identity of representative strains for eachE. agglomeransbiotype as defined by Brenner et al. [41], and biotype XILeclercia

adecarboxylata[52]. We could not confirm the identity of strain LMG 5343 asP. agglomerans, indicating that biotype V should not be included inP. agglomeransas previously hypothesized by Beji et al. [53]. Our BLAST analysis of strains belonging to other biotypes that have not yet been assigned to a particular species showed the highest similarity of these strains to undefinedEnterobacterorErwiniaspp. second Sequences belonging toP. agglomeransisolates and a wide-range of other bacteria described as unknown or uncultured bacterium frequently were scattered as top hits in the BLAST-search (see Additional file 2 -Table S2). These sequences were not closely related to any of the individual type strains of thePantoeaspecies. This indicates the risk that a high number ofEnterobacterandErwiniastrains present in the databases are misidentified asPantoea. The problematic classification of strains belonging to the classicalE. agglomeransbasonym is further demonstrated by the observation of incorrect culture collection designations.