An MLSA-based online scheme for the rapid identification of Stenotrophomonas isolates

An online scheme to assign Stenotrophomonas isolates to genomic groups was developed using the multilocus sequence analysis (MLSA), which is based on the DNA sequencing of selected fragments of the housekeeping genes ATP synthase alpha subunit (atpA), the recombination repair protein (recA), the RNA polymerase alpha subunit (rpoA) and the excision repair beta subunit (uvrB). This MLSA-based scheme was validated using eight of the 10 Stenotrophomonas species that have been previously described. The environmental and nosocomial Stenotrophomonas strains were characterised using MLSA, 16S rRNA sequencing and DNA-DNA hybridisation (DDH) analyses. Strains of the same species were found to have greater than 95% concatenated sequence similarity and specific strains formed cohesive readily recognisable phylogenetic groups. Therefore, MLSA appeared to be an effective alternative methodology to amplified fragment length polymorphism fingerprint and DDH techniques. Strains of Stenotrophomonas can be readily assigned through the open database resource that was developed in the current study (www.steno.lncc.br/)

Aeromicrobium choanae sp. nov., an actinobacterium isolated from the choana of a garden warbler

A Gram-stain-positive, non-spore-forming actinobacterium, strain 9H-4(T), isolated from the choana of a garden warbler (Sylvia borin) was studied to examine its taxonomic position. On the basis of 16S rRNA gene sequence analysis it was shown that strain 9H-4(T) belongs to the genus Aeromicrobium with Aeromicrobium flavum TYLN1(T) (98.7% similarity) and Aeromicrobium tamlense SSW1-57(T) (98.4 %) as the nearest neighbours and forms a separate branch in a neighbour-joining phylogenetic tree based on 16S rRNA gene sequences. DNA-DNA hybridizations confirmed its novel species identity based on 39 and 46% DNA-DNA relatedness with A. flavum DSM 19355(T) and A. tamlense DSM 19087(T), respectively. The predominant menaquinone of strain 9H-4(T) was MK-9(H-4). The peptidoglycan contained LL-diaminopimelic acid as the diagnostic diamino acid. The major fatty acids (C-18 : 1 omega 9c, 10-methyl C-18 : 0, C-16 : 0, C-18 : 0, C-16 : 0 2-OH) were consistent with the fatty acid patterns reported for members of the genus Aeromicrobium. The DNA G+C content of strain 9H-4(T) was 70.8 mol%. The distinct genotypic, chemotaxonomic, physiological and biochemical characteristics support the classification of strain 9H-4(T) as a representative of a novel species of the genus Aeromicrobium, for which the name Aeromicrobium choanae sp. nov. is proposed. The type strain is 9H-4(T) (=ZIM B1021(T)=LMG 29165(T)=CCM 8650(T))