Search

Three Gram-reaction-positive bacterial strains, designated KSW-18T, KSW2-22, and KSW4-11T, were isolated from seawater, and two dried seaweed samples collected at Gwakji Beach in Jeju, Republic of Korea, respectively, and their taxonomic positions were examined by a polyphasic approach. The 16S rRNA gene phylogeny showed that strain KSW4-11T was tightly associated with Microbacterium oleivorans NBRC 103075T, while strains KSW-18T and KSW2-22 formed a distinctive subline at the base of a clade including the above two strains. The three isolates showed high sequence similarity with one another (99.7–99.9%; 1–4 nt differences) and Microbacterium oleivorans (99.8–99.9%; 1–3 nt differences). The chemotaxonomic features were typical for the genus Microbacterium; Lysine as the diagnostic diamino acid and N-glycolylated muramic acid of the peptidoglycans, the predominant menaquinones of MK-11, MK-10 and MK-12, the major fatty acids of anteiso-C15:0 and anteiso-C17:0, and the major polar lipids including diphosphatidylglycerol, phosphatidylglycerol, and two or three unidentified glycolipids. In core genome-based phylogenetic tree, strains KSW-18T and KSW2-22 were closely associated with Microbacterium oleivorans NBRC 103075T, while strain KSW4-11T formed a distinctive subline at the base of a clade including the above three strains, in contrast to the 16S rRNA gene tree. Strains KSW-18T and KSW2-22 shared an OrthoANIu of 98.6% and a digital DNA–DNA hybridization of 87.6% with each other, representing that they were strains of a species, while the OrthoANIu and digital DNA–DNA hybridization values between strains KSW-18T and KSW4-11T, and between both of these isolates and all members of the genus Microbacterium were ≤86.5% and ≤30.7%, respectively. The analyses of overall genomic relatedness indices and phenotypic distinctness support that the three isolates represent two new species of the genus Microbacterium. Based on the results obtained here, Microbacterium aquilitoris sp. nov. (type strain KSW-18T = KCTC 49623T = NBRC 115222T) and Microbacterium gwkjiense sp. nov. (type strain KSW4-11T = KACC 23321T = DSM 116380T) are proposed. [ABSTRACT FROM AUTHOR]

Bone is a kind of meat processing by-product with high nutritional value but low in calorie, which is a typical food in China and parts of East Asian countries. Microbial fermentation by lactic acid bacteria showed remarkable advantages to increase the absorption of nutrients from bone cement by human body. Streptococcus thermophilus CICC 20372 is proven to be a good starter for bone cement fermentation. No genes encoding virulence traits or virulence factors were found in the genome of S. thermophilus CICC 20372 by a thorough genomic analysis. Its notable absence of antibiotic resistance further solidifies the safety. Furthermore, the genomic analysis identified four types of gene clusters responsible for the synthesis of antimicrobial metabolites. A comparative metabolomic analysis was performed by cultivating the strain in bone cement at 37 °C for 72 h, with the culture in de Man, Rogosa, and Sharpe (MRS) medium as control. Metabolome analysis results highlighted the upregulation of pathways involved in 2-oxocarboxylic acid metabolism, ATP-binding cassette (ABC) transporters, amino acid synthesis, and nucleotide metabolism during bone cement fermentation. S. thermophilus CICC 20372 produces several metabolites with health-promoting function during bone cement fermentation, including indole-3-lactic acid, which is demonstrated ameliorative effects on intestinal inflammation, tumor growth, and gut dysbiosis. In addition, lots of nucleotide and organic acids were accumulated at higher levels, which enriched the fermented bone cement with a variety of nutrients. Collectively, these features endow S. thermophilus CICC 20372 a great potential strain for bone food processing. [ABSTRACT FROM AUTHOR]

Genus Niallia has recently been separated taxonomic group from the Bacillus based on conserved signature indels in the genome. Unlike bioremediation, its role in plant biomass hydrolysis has not garnered considerable attention. The present study investigates the genomic potential of a novel Niallia sp. CRN 25 for applications in lignocellulose hydrolysis, significant enzyme production, and bioremediation. The CRN 25 strain exhibits xylosidase, cellobiosidase, α-arabinosidase, and α-D-galactosidase activity as 0.03 U/ml whereas β-D-glucosidase and glucuronidase as 0.06 U/ml and 0.01 U/ml, respectively. Further genome sequencing reveals nine copies of GH43 gene coding for hemicellulose-specific xylanase enzyme attached to the CBM 6 domain for increased processivity. The presence of β-glucosidase and β-galactosidase indicates the possible application of CRN 25 in facilitating the valorization of plant biomass into value-added products. Apart from this, genes of FMN-dependent NADH-azoreductase, cytochrome P450, and nitrate reductase, playing a crucial role in bioremediation processes, were annotated. Biosynthetic gene clusters (BGCs), responsible for synthesizing specialized metabolites of terpenes and lasso peptides, were also found in the genome. Conclusively genomic sketch of Niallia sp. CRN 25 reveals versatile metabolic potential for diverse environmental applications. [ABSTRACT FROM AUTHOR]

Known for its species abundance and evolutionary status complexity, family Roseobacteraceae is an important subject of many studies on the discovery, identification, taxonomic status, and ecological properties of marine bacteria. This study compared and analyzed the phylogenetic, genomic, biochemical, and chemo taxonomical properties of seven species from three genera (Psychromarinibacter, Lutimaribacter, and Maritimibacter) of the family Roseobacteraceae. Moreover, a novel strain, named C21-152T was isolated from solar saltern sediment in Weihai, China. The values of 16S rRNA gene sequence similarity, the average nucleotide identity (ANI), the average amino acid identity (AAI), and the digital DNA–DNA hybridization (dDDH) between genomes of the novel strain and Psychromarinibacter halotolerans MCCC 1K03203T were 97.19, 78.49, 73.45, and 21.90%, respectively. Genome sequencing of strain C21-152T revealed a complete Sox enzyme system related to thiosulfate oxidization as well as a complete pathway for the final conversion of hydroxyproline to α-ketoglutarate. In addition, strain C21-152T was resistant to many antibiotics and had the ability to survive below 13% salinity. This strain had versatile survival strategies in saline environments including salt-in, compatible solute production and compatible solute transport. Some of its physiological features enriched and complemented the knowledge of the characteristics of the genus Psychromarinibacter. Optimum growth of strain C21-152T occurred at 37 ℃, with 5–6% (w/v) NaCl and at pH 7.5. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain C21-152T should represent a novel specie of the genus Psychromarinibacter, for which the name Psychromarinibacter sediminicola sp. nov. is proposed. The type strain is C21-152T (= MCCC 1H00808T = KCTC 92746T = SDUM1063002T). [ABSTRACT FROM AUTHOR]

Keratinibaculum paraultunense strain KD-1 T (= JCM 18769 T = DSM 26752 T) is a strictly anaerobic rod-shaped bacterium. Under optimal conditions, feather keratin can be completely degraded by strain KD-1 within 24 h. Genomic sequencing showed that the genome was a single circular chromosome consisting of 2,307,997 base pairs (bp), with an average G + C content of 29.8% and no plasmids. A total of 2308 genes were annotated, accounting for 88.87% of the genomic sequence, and 1495 genes were functionally annotated. Among these, genes Kpa0144, Kpa0540, and Kpa0541 encoding the thioredoxin family members were identified, and may encode the potential disulfide reductases, with redox activity for protein disulfide bonds. Two potential keratinase-encoding genes, Kpa1675 and Kpa2139, were also identified, and corresponded to the ability of strain KD-1 to hydrolyze keratin. Strain KD-1 encoded genes involved in the heterotrophic metabolic pathways of 14 amino acids and various carbohydrates. The metabolic pathways for amino acid and carbohydrate metabolism were mapped in strain KD-1 based on KEGG annotations. The complete genome of strain KD-1 provided fundamental data for the further investigation of its physiology and genetics. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the genomic features of novel Kenyan virulent phage isolates infecting carbapenemase-producing Klebsiella pneumoniae and to determine the safety of their lysates using mice model in a preclinical study. The genomics showed that the Klebsiella phages vB_KpM_CPRSA and vB_KpM_CPRSB belonged to the genus Slopekvirus with a similarity index of less than 92% compared to the most closest relative species. Their genomes did not contain antimicrobial resistance and toxin genes. Then endotoxin levels in the Klebsiella phage lysates were statistically significant (p value ˃ 0.05). The serum activities of aspartate aminotransferase, alanine aminotransferase and urea in the group of balb/c mice injected with bacteriophage lysates through the intravenous route were higher compared to that of the intranasal route. Unexpectedly, there was mild congestion of the central veins of kidneys and liver without damage to renal tubules and hepatocytes and a lack of physical discomfort and pain in the mice. Our study isolated and characterised Klebsiella phages against carbapenem-resistant K. pneumoniae, which are promising therapeutic agents for the treatment of respiratory tract infections using the topical mode of administration as the preferred route of bacteriophage delivery. [ABSTRACT FROM AUTHOR]

A genome led phylophasic study was designed to determine the taxonomic status of a strain, DSM 45956, recovered from a Saharan desert soil. A wealth of taxonomic data, including average nucleotide identity and DNA:DNA hybridization (DDH) values, showed that the isolate and the type strains of Actinopolyspora lacussalsi and Actinopolyspora righensis belong to the same species. Consequently, it is proposed that A. righensis is a heterotypic synonym of A. lacussalsi. Similarly, DDH values and associated phenotypic data show that A. lacussalsi contains two subspecies, A. lacussalsi subsp. lacussalsi and A. lacussalsi subsp. righensis which includes isolate DSM 45956. [ABSTRACT FROM AUTHOR]

A novel aerobic bacterium, strain PS-22 of the genus Moraxella, was isolated from the skin of freshwater pufferfish (Tetraodon cutcutia). Cells were Gram stain negative, aerobic, non-motile, and coccoid. Optimum growth occurred at 28–30 °C and pH 6.5–7.5. The major cellular fatty acids were C18:1 ω9c, C10:0, C16:0, and C12:0 anteiso. The predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipid, amino lipid, and seven unknown lipids. The genome size is 2.68 Mbp, and the DNA G + C content was 43.3%. A gene ontology study revealed that the major fraction of genes were associated with biological processes (46.81%), followed by molecular function (34.27%) and cellular components (18.8%). Comparisons of 16S rRNA gene sequences revealed 99.11–90% sequence similarity with the closely related type strains of the genus Moraxella. The average nucleotide identity (ANI) and average amino acid identity (AAI) of strain PS-22 with reference type strains of the genus Moraxella were below 95–96%, and the corresponding in silico DNA–DNA hybridization (DDH) values were below 70%. A phylogenetic tree based on genome-wide core genes and 16S rRNA gene sequences revealed that strain PS-22 clustered with Moraxella osloensis CCUG350T in both the phylogenetic trees. Genotypic and phenotypic characteristics of strain PS-22 represent a novel species for which Moraxella tetraodonis sp. nov. is proposed. The type strain is PS-22T (= TBRC 15232T = NBRC 115236T). [ABSTRACT FROM AUTHOR]

Black quarter (BQ) is an infectious disease affecting cattle and small ruminants worldwide caused by Gram-positive anaerobic bacterium Clostridium chauvoei. In this study, a draft genome sequence of C. chauvoei NIVEDIBQ1 strain isolated from clinical case of black quarter was analyzed. Sequence analysis indicated that genome had 2653 predicted coding DNA sequences, harbored numerous genes, mobile genetic elements for pathogenesis, and virulence factors. Computational analysis revealed that strain contained 30 virulence-associated genes. An intact genomic region highly similar to the Clostridium phage was present in the genome. Presence of CRISPR systems and the transposon components likely contribute to the genome plasticity. Strain encode diverse spectrum of degradative carbohydrate-active enzymes (CAZymes). Comparative SNP analysis revealed that the genomes of the C. chauvoei strains analyzed were highly conserved. Phylogenetic analysis of strains and available genome (n = 21) based on whole-genome multi-locus sequence typing (wgMLST) and core orthologous genes showed the clustering of strains into two different clusters suggesting geographical links. [ABSTRACT FROM AUTHOR]

A Gram-stain-negative, cocci-to-oval-shaped bacterial strain, designated XZZS9T, was isolated from the rhizosphere soil of Pinus sylvestris var. mongolica and characterized taxonomically using a polyphasic approach. Growth occurred at 20–35 °C (optimum, 28 °C), pH 6.0–11.0 (optimum, pH 7.0), and in 0–1% NaCl (optimum, 0%). Phylogenetic analysis based on 16S rRNA gene sequencing indicated that strain XZZS9T was related to members of the genus Roseococcus, with the highest sequence identity to Roseococcus microcysteis NIBR12T (96.9%). The major cellular fatty acids (> 5% of the total) were C18:1ω7c and C19:0 cyclo ω8c. The major isoprenoid quinone was Q-9 and the polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, an unidentified glycophospholipid, and an unidentified phospholipid. Genome sequencing revealed that had a genome size of 4.79 Mbp with a G + C content of 69.5%. Comparative genomic analyses clearly separated strain XZZS9T from the known species of the genus Roseococcus based on average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values below the thresholds for species delineation. Genome annotations did not find pufL and pufM genes in strain XZZS9T, suggesting a possible lack of photosynthetic reaction. Based on genotypic and phenotypic characteristics, strain XZZS9T represents a novel species of the genus Roseococcus, for which we propose the name Roseococcus pinisoli sp. nov. The type strain is XZZS9T (= KCTC 82435T = JCM 34402T = GDMCC 1.2158T). [ABSTRACT FROM AUTHOR]

A Gram stain-positive, rod-shaped, and subterminal endospore-forming bacterium, designated strain YIM B01967T, was isolated from a forest soil sample collected in Ailaoshan National Nature Reserve, Yuxi City, Xinpin county, Yunnan province, China. Strain YIM B01967T showed the highest 16S rRNA gene sequence similarity with Viridibacillus arvi (99.1%) and Viridibacillus arenosi (98.9%). Based on the phylogenetic and 16S rRNA gene sequence results, strain YIM B01967T was affiliated to the genus Viridibacillus. The growth of YIM B01967T was observed at 15–35 °C (optimum, 28 °C), pH 7.0–9.0 (optimum, pH 7.5) and in the presence of 0–2% (w/v) NaCl (optimum in 2% NaCl). The cell wall sugars include ribose, glucose, arabinose, galactose, and mannose. The quinone system consisted of the major compound MK-8 and moderate amounts of MK-7. The major fatty acids (> 10%) included iso-C15:0, anteiso-C15:0, C16:1ω10c. The major polar lipids profile included DPG, PME. The cell wall peptidoglycan was most likely of the type A4α with an l-Lys-d-Asp interpeptide bridge. The genomic DNA G + C content of strain YIM B01967T was 36.3 mol%. The ANI and digital DNA–DNA hybridization (dDDH) values between strain YIM B01967T and Viridibacillus arvi DSM 16317 T, Viridibacillus arenosi DSM 16319 T were 61.0% and 32.1%, 60.0% and 33.1% based on the draft genome sequence. The results support the conclusion that strain YIM B01967T represents a novel species of the genus Viridibacillus, for which the name Viridibacillus soli sp. nov., is proposed. The type strain is YIM B01967T (= KCTC 43249 T = CGMCC 1.18436 T). [ABSTRACT FROM AUTHOR]

A Gram-reaction-negative, strictly aerobic, betaproteobacterial strain, designated SAP-35T, was isolated from sap extracted from Acer pictum in Mt. Halla in Jeju, Republic of Korea, and its taxonomic status was examined by a polyphasic approach. Cells of the organism were non-sporulating, motile rods and grew at 4–30 °C, pH 6–7 and in the absence of NaCl. 16S rRNA gene- and whole genome-based phylogenetic analyses showed that strain SAP-35T belonged to the family Oxalobacteraceae and was closely related to Rugamonas rivuli (98.9% 16S rRNA gene sequence similarity) and Rugamonas aquatica (98.4%). The phylogenomic clustering and average amino acid identity values supported that strain SAP-35T belonged to the genus Duganella and two Rugamonas species should be transferred to the genus Duganella. The major isoprenoid quinone of the isolate was Q-8. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The predominant fatty acids were summed feature 3, C16:0 and C17:0 cyclo. The G + C content of genome was 64.9%. The average nucleotide identity and dDDH values between strain SAP-35T and the members of the genera Rugamonas and Duganella were < 85.1% and < 49%, respectively. Based on the combined data presented here, strain SAP-35T (= KCTC 72227T = NBRC 113903T) represents a novel species of the genus Duganella, for which the name Duganella aceris sp. nov. is proposed. Also, Rugamonas aquatica Lu et al. (Int J Syst Evol Microbiol 70: 3328–3334, 2020) and Rugamonas aquatica Lu et al. 2020 are reclassified as Duganella aquatica comb. nov., with the emended description of the genus Rugamonas. [ABSTRACT FROM AUTHOR]

This work describes the characterization and genome annotation of Salmonella phage vB_SalM_8-19 (referred to as 8-19) isolated from sewage samples collected in a pig farm in Jilin, China. This phage was capable of infecting 60% Salmonella strains in our lab stock. The genome of phage 8-19 is composed of linear double-stranded DNA that is 52,648 bp in length with a G + C content of 46.02%; containing 74 ORFs and no tRNA genes. In October 2019, phylogenetic analyses indicated that phage 8-19 might belong to a novel cluster among the other similar phages which have not been specifically classified within some new genus in family Myoviridae. Recently, the International Committee on Taxonomy of Viruses (ICTV) defined phage 8-19 and its related phages as genus Rosemountvirus, family Myoviridae. This new genus, known as Rosemountvirus, is rarely reported in the literature. [ABSTRACT FROM AUTHOR]

A bacterial strain designated NYYP31T was isolated from the leaves of an annual halophytes, Suaeda corniculata Bunge, collected from the southern edge of the Gurbantunggut desert, north-west China. Strain NYYP31T was Gram-staining negative, strictly aerobic, rod-shaped, non-motile, and non-spore-forming. Growth was observed at 4–42 °C, at pH 5.0–10.0, in the presence of up to 8% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences and coding sequences of 92 protein clusters showed that strain NYYP31T should be assigned to the genus Sphingobacterium. 16S rRNA gene sequence similarity analysis showed that strain NYYP31T was most closely related to the type strain of Sphingobacterium daejeonense (97.9%) and Sphingobacterium lactis (97.7%). The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15:0, iso-C17:0 3-OH and summed feature 3 (C16:1ω7c and/or C16:1ω6c). The polar lipids were phosphatidylethanolamine, two unidentified phospholipids, three unidentified lipids, three unidentified amino phospholipids, and two unidentified glycolipids. The genomic DNA G + C content was 36.4 mol%. The average nucleotide identity (ANI) values for strain NYYP31T to the type strains of S. daejeonense and S. lactis were 77.9 and 74.1%, respectively, which were below the cut-off level (95–96%) for species delineation. Based on the above results, strain NYYP31T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium endophyticum sp. nov. is proposed. The type strain is NYYP31T (= CGMCC 1.16979T = NBRC 114258T). [ABSTRACT FROM AUTHOR]

In this study, the genome of a new strain of lytic Staphylococcus aureus Herelleviridae, vBSM-A1, was characterized and annotated. The phage was isolated from sewage samples collected in Xinjiang Province, China. The genome of vBSM-A1 was found to comprise a linear double-stranded DNA of 140,654 bp length, with a G + C content of 30.33%. A total of 215 ORFs were detected in the phage DNA, 74 of which were functionally assigned. The 3D structure model of endolysin LysK (ORF 143) was created using Phyre2. [ABSTRACT FROM AUTHOR]

A Gram-staining positive, motile, rod-shaped and subterminal endospore-forming bacterium, designated strain SYSU K30005T, was isolated from a soil sample collected from a karst cave in Libo county, Guizhou province, south-western China. Strain SYSU K30005T showed the highest 16S rRNA gene sequence similarity with Lysinibacillus fusiformis (98.6%) and Lysinibacillus sphaericus (98.2%). In phylogenetic tree, strain SYSU K30005T clade with the members of the genus Lysinibacillus. Based on the phylogenetic and 16S gene sequence result, strain SYSU K30005T was affiliated to the genus Lysinibacillus. The growth of SYSU K30005T was observed at 15–37 °C (optimum, 28 °C), pH 6.0–9.0 (optimum, pH 7.0) and in the presence of 0–4% (w/v) NaCl (optimum in 3.5% NaCl). Cell wall peptidoglycan type was A4α (Lys–Asp). The cell-wall sugars of SYSU K30005T were ribose, galactose and mannose and MK-7 was the only quinone. The fatty acids (> 5% of total fatty acids) were iso-C15:0, anteiso-C15:0, iso-C16:0 and iso-C17:0. The polar lipids profile included diphosphatidylglycerol, phosphatideylglycerol, phosphatidylethanolamine and an unidentified phospholipid. The genomic DNA G + C content was 37.2 mol%. The average nucleotide identity values between SYSU K30005T and its closest relatives were below the cut-off level (95–96%) for species delineation. The results support the conclusion that strain SYSU K30005T represents a novel species of the genus Lysinibacillus, for which we proposed the name Lysinibacillus cavernae sp. nov. The type strain is SYSU K30005T (= KCTC 43130T = CGMCC 1.17492T). [ABSTRACT FROM AUTHOR]

Bone is a kind of meat processing by-product with high nutritional value but low in calorie, which is a typical food in China and parts of East Asian countries. Microbial fermentation by lactic acid bacteria showed remarkable advantages to increase the absorption of nutrients from bone cement by human body. Streptococcus thermophilus CICC 20372 is proven to be a good starter for bone cement fermentation. No genes encoding virulence traits or virulence factors were found in the genome of S. thermophilus CICC 20372 by a thorough genomic analysis. Its notable absence of antibiotic resistance further solidifies the safety. Furthermore, the genomic analysis identified four types of gene clusters responsible for the synthesis of antimicrobial metabolites. A comparative metabolomic analysis was performed by cultivating the strain in bone cement at 37 °C for 72 h, with the culture in de Man, Rogosa, and Sharpe (MRS) medium as control. Metabolome analysis results highlighted the upregulation of pathways involved in 2-oxocarboxylic acid metabolism, ATP-binding cassette (ABC) transporters, amino acid synthesis, and nucleotide metabolism during bone cement fermentation. S. thermophilus CICC 20372 produces several metabolites with health-promoting function during bone cement fermentation, including indole-3-lactic acid, which is demonstrated ameliorative effects on intestinal inflammation, tumor growth, and gut dysbiosis. In addition, lots of nucleotide and organic acids were accumulated at higher levels, which enriched the fermented bone cement with a variety of nutrients. Collectively, these features endow S. thermophilus CICC 20372 a great potential strain for bone food processing., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Genus Niallia has recently been separated taxonomic group from the Bacillus based on conserved signature indels in the genome. Unlike bioremediation, its role in plant biomass hydrolysis has not garnered considerable attention. The present study investigates the genomic potential of a novel Niallia sp. CRN 25 for applications in lignocellulose hydrolysis, significant enzyme production, and bioremediation. The CRN 25 strain exhibits xylosidase, cellobiosidase, α-arabinosidase, and α-D-galactosidase activity as 0.03 U/ml whereas β-D-glucosidase and glucuronidase as 0.06 U/ml and 0.01 U/ml, respectively. Further genome sequencing reveals nine copies of GH43 gene coding for hemicellulose-specific xylanase enzyme attached to the CBM 6 domain for increased processivity. The presence of β-glucosidase and β-galactosidase indicates the possible application of CRN 25 in facilitating the valorization of plant biomass into value-added products. Apart from this, genes of FMN-dependent NADH-azoreductase, cytochrome P450, and nitrate reductase, playing a crucial role in bioremediation processes, were annotated. Biosynthetic gene clusters (BGCs), responsible for synthesizing specialized metabolites of terpenes and lasso peptides, were also found in the genome. Conclusively genomic sketch of Niallia sp. CRN 25 reveals versatile metabolic potential for diverse environmental applications., (© 2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Strain 6021052837T was isolated from the blood culture of a hemodialysis patient on Chocolat PolyViteX medium at 37 °C after 2 days of incubation. Colonies could not be identified by our systematic MALDI-TOF Mass Spectrometry screening. The16S rRNA gene sequencing showed that the strain had 96% sequence identity with Cohnella formosensis (Genbank accession number JN806384), the phylogenetic closely related type strain of a species with standing in nomenclature, which putatively classifies it as a new species. The colonies cultivated on Columbia agar with 5% sheep blood medium at 37 °C after 24 h of incubation, are white pigmented, their size varied from 1.5 to 2 mm in diameter. Strain 6021052837T is an aerobic, Gram-negative, motile, spore forming rod, which cannot grow microaerophilically or under anaerobic conditions. The major fatty acids are branched saturated fatty acids: 14-methyl-pentadecanoic acid (34%) and 12-methyl-tetradecanoic acid (31%). The 6.328 Mb long genome, composed of 25 contigs, has a G+C content of 57.24%. Out of the 5710 predicted genes, 5646 were protein-coding genes and 64 were RNAs. A total of 3239 genes (57.37%) were assigned as putative function (by COGs) and 288 genes were identified as ORFans (5.1%). Average genomic identity of orthologous gene sequences (AGIOS) of strain 6021052837T against genomes of the type strains of related species ranged between 58.26 and 79.63%, respectively. According to our taxonogenomics results, we propose the creation of Cohnella massiliensis sp. nov. that contains the type strain 6021052837T (= CSUR P2659, =DSM103435). [ABSTRACT FROM AUTHOR]

Vibrio alginolyticus is a common marine bacterium implicated in disease outbreaks in marine farmed fish and invertebrates. Due to the inappropriate use of antibiotics in aquaculture, alternative therapies have been proposed. One of the most promising options is the use of lytic bacteriophages to control pathogenic bacteria. This work describes the isolation and characterization of a lytic phage (VEN) against a V. alginolyticus strain (V2) isolated from a disease outbreak in common dentex (Dentex dentex) cultured at the Hellenic Centre for Marine Research (HCMR) in Crete, Greece. The bacteriophage is morphologically similar to phages from Podoviridae family and remained stable for 1 year at 4 °C and over 1 h when kept at 50 °C. VEN was able to lyse the host bacteria at several multiplicity of infection (MOI) (0.1-100) in liquid cultures. However, it was unable to infect other V. alginolyticus strains. Its genome consists of 44,603 bp with a GC content of 43.5%, while sequence analysis revealed the presence of 54 potential ORFs with a T7-like genomic organization. Almost 65% of the predicted ORFs presented homology with proteins of the vibriophages Vc1 and phi-A318 infecting Vibrio cyclitrophicus and Vibrio alginolyticus, respectively. Phylogenetic analysis applying the amino acid sequence of the large terminase subunit confirmed the close relationship of these phages. Furthermore, the comparison of the RNA polymerase of these phages revealed that the motifs A, B and C related to the catalytic activity and the recognition loop related to promotor identification were also conserved. VEN has an obligate lytic life cycle demonstrated by experimental data and genomic analysis. These results suggest that VEN may provide a good candidate to control recurrent diseases caused by V. alginolyticus at HCMR. [ABSTRACT FROM AUTHOR]

A Gram stain-positive, rod-shaped, and subterminal endospore-forming bacterium, designated strain YIM B01967 T , was isolated from a forest soil sample collected in Ailaoshan National Nature Reserve, Yuxi City, Xinpin county, Yunnan province, China. Strain YIM B01967 T showed the highest 16S rRNA gene sequence similarity with Viridibacillus arvi (99.1%) and Viridibacillus arenosi (98.9%). Based on the phylogenetic and 16S rRNA gene sequence results, strain YIM B01967 T was affiliated to the genus Viridibacillus. The growth of YIM B01967 T was observed at 15-35 °C (optimum, 28 °C), pH 7.0-9.0 (optimum, pH 7.5) and in the presence of 0-2% (w/v) NaCl (optimum in 2% NaCl). The cell wall sugars include ribose, glucose, arabinose, galactose, and mannose. The quinone system consisted of the major compound MK-8 and moderate amounts of MK-7. The major fatty acids (> 10%) included iso-C 15:0 , anteiso-C 15:0 , C 16:1 ω10c. The major polar lipids profile included DPG, PME. The cell wall peptidoglycan was most likely of the type A4α with an L-Lys-D-Asp interpeptide bridge. The genomic DNA G + C content of strain YIM B01967 T was 36.3 mol%. The ANI and digital DNA-DNA hybridization (dDDH) values between strain YIM B01967 T and Viridibacillus arvi DSM 16317  T , Viridibacillus arenosi DSM 16319  T were 61.0% and 32.1%, 60.0% and 33.1% based on the draft genome sequence. The results support the conclusion that strain YIM B01967 T represents a novel species of the genus Viridibacillus, for which the name Viridibacillus soli sp. nov., is proposed. The type strain is YIM B01967 T (= KCTC 43249  T  = CGMCC 1.18436  T )., (© 2021. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The phylogenetic heterogeneity of anoxygenic phototrophic bacteria has been revealed by 16S rRNA sequence analysis, the results of which have led to extensive taxonomic rearrangements within previously defined taxa of phototrophs and stimulated interest in this group of organisms. Anoxygenic photosynthetic bacteria can be found within 4 of the 12 phylogenetic lineages, and in some cases are highly related to non-photosynthetic members of these groups. The largest number of phototrophs are found in the class Proteobacteria. Comparative phylogenetic analysis using 23S rDNA sequences generally supports the topology obtained from 16S rDNA sequences. The photosynthetic reaction centers are conserved in all photosynthetic bacteria, and are of two types. One is shared by the Proteobacteria and Chloroflexus aurantiacus and is similar to Photosystem II of cyanobacteria, while heliobacteria and Chlorobium and relatives possess a reaction center similar to the cyanobacterial Photosystem I. These similarities are supported by sequence analysis of core reaction center peptides, but contradict phylogenies reconstructed from rRNA sequence analysis. Genome analysis by means of physical mapping has been performed for only three species of anoxygenic phototrophs. Some conservation of operon structure and gene sequence has been found within the Proteobacteria, but does not extend to other phototrophs. [ABSTRACT FROM AUTHOR]