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Two new strains JP48 T and JP55 affiliated with the acidobacterial class Terriglobia have been isolated from fen soil sampled in the Fichtelgebirge Mountains near Bayreuth, Germany. Both strains were Gram-stain-negative, non-motile, non-spore-forming rods that divide by binary fission, segregate exopolysaccharide-like material and form capsules. Strains JP48 T and JP55 grew at 4-36 °C (optimum at 27 °C), pH 3.6-7.3 (optimum at pH 4.6-5.5) and with NaCl concentrations of 0-3% (optimum at 1.0%; w/v). Strains JP48 T and JP55 grew aerobically on a wide range of organic substrates including mono- and oligosaccharides, amino acids and short-chained fatty acids. MK-8 was identified as the major respiratory quinone. The major fatty acids for strains JP48 T and JP55 were iso -C 15 : 0 , C 16 : 1  ω7c, C 16 : 0 and iso -diabolic acid. Phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, lysophophatidylethanolamine, phosphatidylcholine, unidentified glyco- and glycophospholipids, and unidentified high mass lipid species were the major polar membrane lipids. The G+C content of strains JP48 T and JP55 was 57.4 and 57.2 mol%, respectively. The genomes of strains JP48 T and JP55 contained nine potential secondary metabolite regions encoding for the compound classes NRPS(-like), T3PKS, terpene, or lanthipeptide class IV. Phylogenetic reconstruction and 16S rRNA gene sequence similarities of 98.3 and 96.9% identified Edaphobacter dinghuensis DHF9 T and Edaphobacter lichenicola DSM 104462 T as the most closely related type strains to strains JP48 T and JP55. Based on their phenotype, phylogeny and chemotaxonomy, we propose the novel species Edaphobacter paludis sp. nov. (type strain JP48 T =DSM 109919 T =CECT 30269 T ; additional strain JP55=DSM 109920=CECT 30268) within the class Terriglobia of the phylum Acidobacteriota .

Strains USC-21046 T and USC-21048 T were isolated from foaming coastal marine waters on the Sunshine Coast, Queensland, Australia. Both strains displayed growth and morphological characteristics typical for members belonging to the genus Nocardia . The major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine, and the major fatty acids were C 16 : 0 , C 18 : 1  ω9 c , C 18 : 0 and C 18 : 0 10-methyl. The mycolic acids of strains USC-21046 T and USC-21048 T consisted of chain lengths between 50-64 and 56-68, respectively. Moreover, both of those strains contained meso -diaminopimelic acid and ribose, arabinose, glucose and galactose as whole cell sugars. Based on the phylogenomic results, both strains belonged to the genus Nocardia with strain USC-21046 T showing an 80.4 % genome similarity to N. vinacea NBRC 16497 T and N. pseudovaccinii NBRC 100343 T , whereas USC-21048 T strain showed an 83.6 % genome similarity to N. aobensis NBRC 100429 T . Both strains were delineated from their closely related relatives based on physiological (e.g. growth on sole carbon source) and chemotaxonomic (e.g. cellular fatty composition) differences. The digital DNA-DNA hybridization (dDDH) values between USC-21046 T and USC-21048 T and their closely related relatives were below the dDDH threshold value of ≤70 % used for the taxonomic classification of novel species status. The genome length of strains USC-21046 T and USC-21048 T were 6 878 863 and 7 066 978 bp, with G+C contents of 65.2 and 67.8 mol%, respectively. For the novel isolates, we propose the names Nocardia australiensis sp. nov. with the type strain USC-21046 T (=DSM 111727 T =NCCB 100867 T ) and Nocardia spumae sp. nov. with the type strain USC-21048 T (=DSM 111726 T =NCCB 100868 T ).

A new Vibrio strain, K08M4 T , was isolated from the broad-nosed pipefish Syngnathus typhle in the Kiel Fjord. Infection experiments revealed that K08M4 T was highly virulent for juvenile pipefish. Cells of strain K08M4 T were Gram-stain-negative, curved rod-shaped and motile by means of a single polar flagellum. The strain grew aerobically at 9-40° C, at pH 4-10.5 and it tolerated up to 12 % (w/v) NaCl. The most prevalent (>10 %) cellular fatty acids of K08M4 T were C 16 : 1 ω 7 c and C 16 : 0 . Whole-genome comparisons revealed that K08M4 T represents a separate evolutionary lineage that is distinct from other Vibrio species and falls within the Splendidus clade. The genome is 4,886,292 bp in size, consists of two circular chromosomes (3,298,328 and 1, 587,964 bp) and comprises 4,178 protein-coding genes and 175 RNA genes. In this study, we describe the phenotypic features of the new isolate and present the annotation and analysis of its complete genome sequence. Based on these data, the new isolate represents a new species for which we propose the name Vibrio syngnathi sp. nov. The type strain is K08M4 T (=DSM 109818 T =CECT 30086 T ).

A novel Gram-negative, aerobic, motile, rod-shaped, beige-pigmented bacterium, strain ARW1-2F2 T , was isolated from a seawater sample collected from Roscoff, France. Strain ARW1-2F2 T was catalase-negative and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA sequences revealed that strain ARW1-2F2 T was closely related to Arcobacter lekithochrous LFT 1.7 T and Arcobacter caeni RW17-10 T (95.8 and 95.5 % gene sequence similarity, respectively). The genome of strain ARW1-2F2 T was sequenced and had a G+C content of 28.7%. Two different measures of genome similarity, average nucleotide identity based on blast and digital DNA-DNA hybridization, indicated that strain ARW1-2F2 T represents a new Arcobacter species. The predominant fatty acids were C 16 : 1 ω7 c /C 16 : 1 ω6 c and C 18 : 1 ω7 c /C 18 : 1 ω6 c . The results of a polyphasic analysis supported the description of strain ARW1-2F2 T as representing a novel species of the genus Arcobacter , for which the name Arcobacter roscoffensis sp. nov. is proposed with the type strain ARW1-2F2 T (DSM 29169 T =KCTC 52423 T ).

A novel sulphur-reducing bacterium was isolated from a pyrite-forming enrichment culture inoculated with sewage sludge from a wastewater treatment plant. Based on phylogenetic data, strain J.5.4.2-T.3.5.2 T could be affiliated with the phylum Synergistota . Among type strains of species with validly published names, the highest 16S rRNA gene sequence identity value was found with Aminiphilus circumscriptus ILE-2 T (89.2 %). Cells of the new isolate were Gram-negative, non-spore-forming, straight to slightly curved rods with tapered ends. Motility was conferred by lateral flagella. True branching of cells was frequently observed. The strain had a strictly anaerobic, asaccharolytic, fermentative metabolism with peptides and amino acids as preferred substrates. Sulphur was required as an external electron acceptor during fermentative growth and was reduced to sulphide, whereas it was dispensable during syntrophic growth with a Methanospirillum species. Major fermentation products were acetate and propionate. The cellular fatty acid composition was dominated by unsaturated and branched fatty acids, especially iso-C 15 : 0 . Its major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and distinct unidentified polar lipids. Respiratory lipoquinones were not detected. Based on the obtained data we propose the novel species and genus Aminithiophilus ramosus , represented by the type strain J.5.4.2-T.3.5.2 T (=DSM 107166 T =NBRC 114655 T ) and the novel family Aminithiophilaceae fam. nov. to accommodate the genus Aminithiophilus . In addition, we suggest reclassifying certain members of the Synergistaceae into new families to comply with current standards for the classification of higher taxa. Based on phylogenomic data, the novel families Acetomicrobiacea e fam. nov., Aminiphilaceae fam. nov., Aminobacteriaceae fam. nov., Dethiosulfovibrionaceae fam. nov. and Thermovirgaceae fam. nov. are proposed.

The intriguing recent discovery of Campylobacter coli strains, especially of clade 1, that (i) possess mosaic C. coli / C. jejuni alleles, (ii) demonstrate mixed multilocus sequence types (MLSTs) and (iii) have undergone genome-wide introgression has led to the speculation that these two species may be involved in an accelerated rate of horizontal gene transfer that is progressively leading to the merging of both species in a process coined 'despeciation'. In an MLST-based neighbour-joining tree of a number of C. coli and C. jejuni isolates of different clades, three prominent Campylobacter isolates formed a seemingly separate cluster besides the previously described C. coli and C. jejuni clades. In the light of the suspected, ongoing genetic introgression between the C. coli and C. jejuni species, this cluster of Campylobacter isolates is proposed to present one of the hybrid clonal complexes in the despeciation process of the genus. Specific DNA methylation as well as restriction modification systems are known to be involved in selective uptake of external DNA and their role in such genetic introgression remains to be further investigated. In this study, the phylogeny and DNA methylation of these putative C. coli / C. jejuni hybrid strains were explored, their genomic mosaic structure caused by C. jejuni introgression was demonstrated and basic phenotypic assays were used to characterize these isolates. The genomes of the three hybrid Campylobacter strains were sequenced using PacBio SMRT sequencing, followed by methylome analysis by Restriction-Modification Finder and genome analysis by Parsnp, Smash++ and blast. Additionally, the strains were phenotypically characterized with respect to growth behaviour, motility, eukaryotic cell invasion and adhesion, autoagglutination, biofilm formation, and water survival ability. Our analyses show that the three hybrid Campylobacter strains are clade 1 C . coli strains, which have acquired between 8.1 and 9.1 % of their genome from C. jejuni . The C. jejuni genomic segments acquired are distributed over the entire genome and do not form a coherent cluster. Most of the genes originating from C. jejuni are involved in chemotaxis and motility, membrane transport, cell signalling, or the resistance to toxic compounds such as bile acids. Interspecies gene transfer from C. jejuni has contributed 8.1-9.1% to the genome of three C. coli isolates and initiated the despeciation between C. jejuni and C. coli . Based on their functional annotation, the genes originating from C. jejuni enable the adaptation of the three strains to an intra-intestinal habitat. The transfer of a fused type II restriction-modification system that recognizes the CAYNNNNNCTC/GAGNNNNNRTG motif seems to be the key for the recombination of the C. jejuni genetic material with C. coli genomes.

A haloalkaliphilic hydrolytic actinobacterium, strain ACPA22 T , was enriched and isolated in pure culture from saline alkaline soil (soda solonchak) in northeastern Mongolia. The isolate was facultatively alkaliphilic, growing at pH 6.5-10.5 (optimum at 7.3-9.0) and highly salt-tolerant, tolerating up to 3 M total Na + as carbonates. The hydrolytic nature of ACPA22 T was confirmed by two different growth-dependent methods and by the presence of multiple glycosidase-encoding genes in the genome. The 16S rRNA gene-based phylogenetic analysis demonstrated that strain ACPA22 T formed a deep-branching lineage within the family Glycomycetaceae, with the highest sequence similarity value to Glycomyces buryatensis 18 T (92.1 %) and Salininema proteolyticum Miq-4 T (91.8 %). The average amino acid identity values (56.1-61.5 %) between ACPA22 T and other Glycomycetaceae members with available genomes did not exceed the threshold reported for different genera. The cell wall of ACPA22 T contained meso -diaminopimelic acid, glycine, glutamic acid and alanine in a molar ratio, characteristic of the peptidoglycan type A1γ'. The whole-cell sugars included mannose, galactose, arabinose, ribose and xylose. The major menaquinones were MK-10(Н 4 ) and MK-11(Н 4 ). The identified polar lipids were represented by phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. In addition, the strain had a few unidentified characteristic polar lipids, including an amine-containing phospholipid with chromatographic mobility similar to that of phosphatidylinositol. The polar lipid fatty acids were dominated by anteiso-C 17 : 0 and iso-C 16 : 0 . The genome included a chromosome of 3.94 Mbp (G+C content 61.5 mol%) encoding 3285 proteins and two plasmids of 59.8 and 14.8 kBp. Based on the data obtained in this study, a new genus and species, Natronoglycomyces albus gen. nov., sp. nov, is proposed with the type strain ACPA22 T (=DSM 106290 T =VKM Ac-2771 T ).

Clostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce a publicly accessible database within EnteroBase (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that comparable levels of resolution and precision are attained by EnteroBase cgMLST and single-nucleotide polymorphism analysis. EnteroBase currently contains 18 254 quality-controlled C. difficile genomes, which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. This hierarchical clustering is used to identify and name populations of C. difficile at all epidemiological levels, from recent transmission chains through to epidemic and endemic strains. Moreover, it puts newly collected isolates into phylogenetic and epidemiological context by identifying related strains among all previously published genome data. For example, HC2 clusters (i.e. chains of genomes with pairwise distances of up to two cgMLST alleles) were statistically associated with specific hospitals ( P <10 -4 ) or single wards ( P =0.01) within hospitals, indicating they represented local transmission clusters. We also detected several HC2 clusters spanning more than one hospital that by retrospective epidemiological analysis were confirmed to be associated with inter-hospital patient transfers. In contrast, clustering at level HC150 correlated with k -mer-based classification and was largely compatible with PCR ribotyping, thus enabling comparisons to earlier surveillance data. EnteroBase enables contextual interpretation of a growing collection of assembled, quality-controlled C. difficile genome sequences and their associated metadata. Hierarchical clustering rapidly identifies database entries that are related at multiple levels of genetic distance, facilitating communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile .

Two strains of the family Rhodospirillaceae were isolated from the rhizosphere of the medicinal plant Hypericum perforatum . Cells of both strains were Gram-stain-negative, motile by means of a single polar flagellum, non-spore-forming, non-capsulated, short rods that divided by binary fission. Colonies were small and white. Strains R5913 T and R5959 T were oxidase-positive, mesophilic, neutrophilic and grew optimally without NaCl. Both grew under aerobic and microaerophilic conditions and on a limited range of substrates with best results on yeast extract. Major fatty acids were C 19 : 0 cyclo ω 8 c and C 16 : 0 ; in addition, C 18 : 1 ω7 c was also found as a predominant fatty acid in strain R5913 T . The major respiratory quinone was ubiquinone 10 (Q-10). The DNA G+C contents of strains R5913 T and R5959 T were 66.0 and 67.4 mol%, respectively. 16S rRNA gene sequence comparison revealed that the closest relatives (<92 % similarity) of the strains are Oceanibaculum pacificum MCCC 1A02656 T , Dongia mobilis CGMCC 1.7660 T , Dongia soli D78 T and Dongia rigui 04SU4-P T . The two novel strains shared 98.6 % sequence similarity and represent different species on the basis of low average nucleotide identity of their genomes (83.8 %). Based on the combined phenotypic, genomic and phylogenetic investigations, the two strains represent two novel species of a new genus in the family Rhodospirillaceae , for which the name Hypericibacter gen. nov. is proposed, comprising the type species Hypericibacter terrae sp. nov. (type strain R5913 T =DSM 109816 T =CECT 9472 T ) and Hypericibacter adhaerens sp. nov. (type strain R5959 T =DSM 109817 T =CECT 9620 T ).

A Gram-stain-positive, rod-shaped, aerobic, non-motile, white, opaque bacterial isolate, designated 924/12 T , was isolated from the nose of a laboratory mouse in Düsseldorf, Germany. The 16S rRNA gene sequence analyses indicated the phylogenetic position of the strain within the genus Leucobacter. Similarity levels over 97 % were recorded between the 16S rRNA gene sequence of strain 924/12 T and the type strains of the species Leucobacter chironomi DSM 19883 T (99.5 %), followed by Leucobacter celersubsp. astrifaciens CBX151 T (97.6 %), Leucobacter celersubsp. celer NAL101 T (97.5 %), 'Leucobacter kyeonggiensis' F3-P9 (97.5 %), Leucobacter zeae CC-MF41 T (97.3 %), Leucobacter chromiiresistens JG31 T (97.1 %), Leucobacter triazinivorans JW-1 T (97.1 %), Leucobacter corticis 2 C-7 T (97.0 %) and Leucobacter aridicolis CIP108388 T (97.0 %). DNA-DNA hybridization and whole genomic comparison, mandatory to taxonomically separate strain 924/12 T from the type strain of L. chironomi, revealed similarity values of 40.4 and 30.8 %, respectively, thus below the threshold of 70 % recommended differentiating between species. The cell-wall amino acids of the novel isolate were diaminobutyric acid, alanine, glycine, threonine and glutamic acid. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, glycolipid and one unknown lipid, whereas the predominant menaquinones were MK-11 and MK-10. The genomic DNA G+C content of strain 924/12 T was 70.6 mol%. Phylogenetic analyses based on the 16S rRNA gene sequences and the phenotypical differences between strain 924/12 T and the other closely related type strains of the genus Leucobacter indicated that strain 924/12 T represents a novel species within the genus Leucobacter, family Microbacteriaceae, for which the name Leucobacter muris sp. nov. is proposed. The type strain is 924/12 T (=DSM 101948 T =CCM 8761 T ).

Phenotypic change is a hallmark of bacterial adaptation during chronic infection. In the case of chronic Pseudomonas aeruginosa lung infection in patients with cystic fibrosis, well-characterized phenotypic variants include mucoid and small colony variants (SCVs). It has previously been shown that SCVs can be reproducibly isolated from the murine lung following the establishment of chronic infection with mucoid P. aeruginosa strain NH57388A. Using a combination of single-molecule real-time (PacBio) and Illumina sequencing we identify a large genomic inversion in the SCV through recombination between homologous regions of two rRNA operons and an associated truncation of one of the 16S rRNA genes and suggest this may be the genetic switch for conversion to the SCV phenotype. This phenotypic conversion is associated with large-scale transcriptional changes distributed throughout the genome. This global rewiring of the cellular transcriptomic output results in changes to normally differentially regulated genes that modulate resistance to oxidative stress, central metabolism and virulence. These changes are of clinical relevance because the appearance of SCVs during chronic infection is associated with declining lung function.

A Gram-stain-positive, rod-shaped, non-motile, spore-forming bacterium, strain EA-1 T , was isolated from hydrothermal sediment samples from the Azores (São Miguel, Portugal). 16S rRNA gene sequence analysis of the isolated bacterium revealed a phylogenetic affiliation with the genus Kyrpidia. The sequence similarity of the five 16S rRNA gene copies to its closest relative, Kyrpidia tusciae, ranged from 97.79 to 97.85 %. The in silico estimate of DNA-DNA hybridization was 56.0 %. The dominant fatty acids of the novel isolate were anteiso-C17 : 0 (49.9 %), iso-C17 : 0 (23.0 %) and iso-C16 : 0 (13.3 %), while the quinone detected was menaquinone MK-7. Analysis of polar lipids identified phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and additional unidentified compounds comprising two glycolipids, two phospholipids and two lipids. The presence of meso-diaminopimelic acid in the peptidoglycan and mannose, arabinose and ribose in the cell wall of strain EA-1 T were detected. The strain was able to grow heterotrophically as well as autotrophically with carbon dioxide as the sole carbon source and with hydrogen and oxygen as electron donor and acceptor, respectively. Based on its chemotaxonomic, physiological and genomic characteristics, the new strain is considered to represent a novel species within the genus Kyrpidia, for which the name Kyrpidiaspormannii sp. nov. is proposed. The type strain is strain EA-1 T (=DSM 106492 T =CCOS1194 T ).

Purpose: We resequenced the genome of Clostridium difficile 630Δerm (DSM 28645), a model strain commonly used for the generation of insertion mutants., Methodology: The genome sequence was obtained by a combination of single-molecule real-timeand Illumina sequencing technology., Results: Detailed manual curation and comparison to the previously published genomic sequence revealed sequence differences including inverted regions and the presence of plasmid pCD630. Manual curation of our previously deposited genome sequence of the parental strain 630 (DSM 27543) led to an improved genome sequence. In addition, the sequence of the transposon Tn5397 was completely identified. We manually revised the current manual annotation of the initial sequence of strain 630 and modified either gene names, gene product names or assigned EC numbers of 57 % of genes. The number of hypothetical and conserved hypothetical proteins was reduced by 152. This annotation was used as a template to annotate the most recent genome sequences of the strains 630Δerm and 630., Conclusion: Based on the genomic analysis, several new metabolic features of C. difficile are proposed and could be supported by literature and subsequent experiments.