Leucobacter soli sp. nov., from soil amended with humic acid

Staphylococcus brunensis sp. nov. isolated from human clinical specimens with a staphylococcal cassette chromosome-related genomic island outside of the rlmH gene bearing the ccrDE recombinase gene complex

Novel species of coagulase-negative staphylococci, which could serve as reservoirs of virulence and antimicrobial resistance factors for opportunistic pathogens from the genus Staphylococcus, are recognized in human and animal specimens due to advances in diagnostic techniques. Here, we used whole-genome sequencing, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize five coagulase-negative strains from the Staphylococcus haemolyticus phylogenetic clade obtained from human ear swabs, wounds, and bile. Based on the results of polyphasic taxonomy, we propose the species Staphylococcus brunensis sp. nov. (type strain NRL/St 16/872T = CCM 9024T = LMG 31872T = DSM 111349T). The genomic analysis revealed numerous variable genomic elements, including staphylococcal cassette chromosome (SCC), prophages, plasmids, and a unique 18.8 kb-long genomic island SbCIccrDE integrated into the ribosomal protein L7 serine acetyltransferase gene rimL. SbCIccrDE has a cassette chromosome recombinase (ccr) gene complex with a typical structure found in SCCs. Based on nucleotide and amino acid identity to other known ccr genes and the distinct integration site that differs from the canonical methyltransferase gene rlmH exploited by SCCs, we classified the ccr genes as novel variants, ccrDE. The comparative genomic analysis of SbCIccrDE with related islands shows that they can accumulate virulence and antimicrobial resistance factors creating novel resistance elements, which reflects the evolution of SCC. The spread of these resistance islands into established pathogens such as Staphylococcus aureus would pose a great threat to the healthcare system. IMPORTANCE The coagulase-negative staphylococci are important opportunistic human pathogens, which cause bloodstream and foreign body infections, mainly in immunocompromised patients. The mobile elements, primarily the staphylococcal cassette chromosome mec, which confers resistance to methicillin, are the key to the successful dissemination of staphylococci into healthcare and community settings. Here, we present a novel species of the Staphylococcus genus isolated from human clinical material. The detailed analysis of its genome revealed a previously undescribed genomic island, which is closely related to the staphylococcal cassette chromosome and has the potential to accumulate and spread virulence and resistance determinants. The island harbors a set of conserved genes required for its mobilization, which we recognized as novel cassette chromosome recombinase genes ccrDE. Similar islands were revealed not only in the genomes of coagulase-negative staphylococci but also in S. aureus. The comparative genomic study contributes substantially to the understanding of the evolution and pathogenesis of staphylococci.

Leucobacter allii sp. nov. and Leucobacter rhizosphaerae sp. nov., isolated from rhizospheres of onion and garlic, respectively

Three bacterial strains, H21R-40^T and H21R-36 from garlic (Allium sativum) and H25R-14^T from onion (Allium cepa), were isolated from plant rhizospheres sampled in the Republic of Korea. Results of 16S rRNA gene sequence analysis revealed the highest sequence similarity of strain H21R-40^T to Leucobacter celer subsp. astrifaciens CBX151^T (97.3 %) and Leucobacter triazinivorans JW-1^T (97.2 %), and strain H25R-14^T to Leucobacter insecticola HDW9B^T (98.8 %) and Leucobacter humi Re6^T (98.4 %), while the sequence similarity between strains H21R-40^T and H21R-36 was 99.8 %. According to the phylogenomic tree, strains H21R-40^T with H21R-36 formed an independent clade separable from other Leucobacter species within the genus Leucobacter and strain H25R-14^T clustered with Leucobacter insecticola HDW9B^T, Leucobacter coleopterorum HDW9A^T and Leucobacter viscericola HDW9C^T. Strains H21R-40^T and H21R-36 had orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values (98.1 % and 86.9 %, respectively) higher than the threshold ranges for species delineation (95-96 % and 70 %, respectively). The OrthoANI and dDDH values between two strains (H21R-40^T and H25R-14^T) and the type strains of species of the genus Leucobacter were lower than 81 and 24 %, respectively. The peptidoglycan type of three strains was type B1. The major menaquinones and major polar lipids of the strains were MK-11 and MK-10, and diphosphatidylglycerol, phatidylglycerol and an unidentified glycolipid, respectively. The major fatty acids (more than 10 % of the total fatty acids) of strains H21R-40^T and H21R-36 were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0, and those of strain H25R-14^T were anteiso-C_15 : 0 and iso-C_16 : 0. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that the strains represent two novel species of the genus Leucobacter, named Leucobacter allii sp. nov. (H21R-40^T and H21R-36) and Leucobacter rhizosphaerae sp. nov. (H25R-14^T). The respective type strains are H21R-40^T (=DSM 114348^T=JCM 35241^T=KACC 21839^T=NBRC 115481^T) and H25R-14^T (=DSM 114346^T=JCM 35239^T=KACC 21837^T=NBRC 115479^T).

Paenibacillus arenilitoris sp. nov., isolated from seashore sand and genome mining revealed the biosynthesis potential as antibiotic producer

Strain IB182493^T, a marine, aerobic, Gram-stain-negative and motile bacterium, was isolated from seashore sand of South China Sea. Cells grew optimally at 25-30 °C, pH 7.0-8.0 and with 2-4% NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Paenibacillus, and was most closely related to Paenibacillus harenae DSM 16969 ^T (similarity 96.6%) and Paenibacillus alkaliterrae DSM 17040 ^T (similarity 96.1%). The chemotaxonomic characteristics of strain IB182493^T included MK-7 as the predominant isoprenoid quinone, anteiso-C_15:0 and iso-C_16:0 as the major cellular fatty acids and meso-diaminopimelic acid as the diagnostic diaminoacid in cell wall peptidoglycan. The polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified phospholipids. The DNA G + C content of strain IB182493^T was 56.2 %. The values of whole genome average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between the isolate and the closely related type strains were less than 84.7% and 23.6%, respectively. On the basis of phenotypic and chemotaxonomic properties, phylogenetic distinctiveness and genomic data, we named the strain as Paenibacillus arenilitoris sp. nov. and proposed that strain IB182493^T (= MCCC 1K04626^T = JCM 34215 ^T) in the genus Paenibacillus represents a novel species.

Staphylococcus ratti sp. nov. Isolated from a Lab Rat

Staphylococci from the Staphylococcus intermedius-Staphylococcus hyicus species group include numerous animal pathogens and are an important reservoir of virulence and antimicrobial resistance determinants. Due to their pathogenic potential, they are possible causative agents of zoonoses in humans; therefore, it is important to address the properties of these strains. Here we used a polyphasic taxonomic approach to characterize the coagulase-negative staphylococcal strain NRL/St 03/464^T, isolated from the nostrils of a healthy laboratory rat during a microbiological screening of laboratory animals. The 16S rRNA sequence, MALDI-TOF mass spectrometry and positive urea hydrolysis and beta-glucuronidase tests clearly distinguished it from closely related Staphylococcus spp. All analyses have consistently shown that the closest relative is Staphylococcus chromogenes; however, values of digital DNA-DNA hybridization <35.3% and an average nucleotide identity <81.4% confirmed that the analyzed strain is a distinct Staphylococcus species. Whole-genome sequencing and expert annotation of the genome revealed the presence of novel variable genetic elements, including two plasmids named pSR9025A and pSR9025B, prophages, genomic islands and a composite transposon that may confer selective advantages to other bacteria and enhance their survival. Based on phenotypic, phylogenetic and genomic data obtained in this study, the strain NRL/St 03/464^T (= CCM 9025^T = LMG 31873^T = DSM 111348^T) represents a novel species with the suggested name Staphylococcus ratti sp. nov.