Halorubrum salipaludis sp. nov., isolated from the saline-alkaline soil.

A novel extremely halophilic archaeon, designated WN019T, was isolated from the natural saline-alkali wetland soil of Binhai new district, Tianjin, China. Cells of WN019T were aerobic, motile, and pleomorphic rod-shaped, 0.5-0.8 µm in width and 2.0-2.5 µm in length, and the growth occurred optimally at 33-37 °C, pH 7.5-8.0, and in the presence of 15.0-20.0% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequence comparison showed that the isolate belonged to the genus Halorubrum and exhibited moderate sequence similarity of 97.8% to Halorubrum saccharovorum JCM 8865T. The major respiratory quinones of strain WN019T were MK-8 and MK-8 (H2), and the major polar lipids were glycolipid (GL), phospholipid (PL), phosphatidylglycerol-sulphate (PGS), phosphatidylglycerol (PG) and phosphatidylglycerol-phosphate-methyl ester (Me-PGP). The DNA G + C content of the strain was 67.4 mol%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) value based on whole genome sequences of strain WN019T and Halorubrum saccharovorum JCM 8865T were 87.5% and 35.4%, respectively. Phenotypic, chemotaxonomic, phylogenetic, and genomic analyses suggested that strain WN019T represents a novel species of the genus Halorubrum, for which the name Halorubrum salipaludis sp. nov. is proposed. The type strain is WN019T (= KCTC 4269T = ACCC 19977T).

Halomonas humidisoli Sp. Nov., Isolated From Saline-Alkaline Soil.

A Gram staining-negative, halophilic, aerobic, non-motile bacteria, designated strain WN018T, were isolated from the natural saline-alkali wetland soil of Binhai new district, Tianjin, China (38°46'N, 117°13'E). Cells of strain WN018T were short rod-shaped, 0.3-0.4 µm wide and 0.5-1.9 µm long, and growth occurred optimally at 30-33 °C, pH 7.5-8.0, and in the presence of 4-8% (w/v) NaCl. Based on 16S rRNA gene sequence analysis, the isolates could be affiliated to the genus Halomonas, exhibiting highest sequence similarity of 97.50% to Halomonas venusta DSM 4743T. The DNA G+C content of the strain was 63.8%. The distinct phylogenetic position and phenotypic traits distinguished the novel isolate from its nearest neighbors. The major respiratory quinone of strain WN018T was Q-9 (91.0%) and Q-8 (9.0%), and the dominant fatty acids were C16:0, C14:0, C10:0, C12:0 3-OH. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), three phospholipids (PL), aminolipid (AL), and two unidentified lipids (L). The average nucleotide identity (ANI) based on whole-genome sequences of strain WN018T and Halomonas hydrothermalis DSM 15725T was 93.02%, and the dDDH value between these two strains was determined to be 49.7%. Therefore, we propose a novel species in the genus Halomonas to accommodate the novel isolate: Halomonas humidisoli sp. nov. (type strain WN018T = ACCC 19975T = KCTC 52854T).

Halovibrio salipaludis sp. nov., Isolated from Saline-Alkaline Soil.

A Gram-staining-negative, halophilic, aerobic, oval-shaped or vibrio-shaped, motile by a polar flagellum strain, designated YL5-2T, was isolated from natural saline-alkaline wetland soil of Binhai new district, Tianjin, China. Strain YL5-2T grew optimally at 35 °C, pH 7.5-8.0, and in the presence of 10-25% (w/v) NaCl on MA medium. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolate belonged to the genus Halovibrio and exhibited high sequence similarity of 97.7% to Halovibrio variabilis DSM 3050T. The sole respiratory ubiquinone of strain YL5-2T is Q-9, and the dominant fatty acids were C18:1ω9c, C16:0, C19:0 cycloω8c, and Summed Feature 8. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), and lipid (L). The DNA G+C content of the strain was 62.1 mol%. The average nucleotide identity (ANI) based on whole genome sequences of strain YL5-2T and Halovibrio variabilis DSM 3050T was 93.85%, and the dDDH value between these two strains was determined to be 52.0%. Phenotypic, chemotaxonomic, phylogenetic, and genomic analyses suggested that strain YL5-2T represent a novel species of the genus Halovibrio, for which the name Halovibrio salipaludis sp. nov. is proposed. The type strain is YL5-2T (=KCTC 52852T=ACCC 19971T).

Aliifodinibius salipaludis sp. nov., Isolated from Saline-Alkaline Soil.

A Gram-staining-negative, oblong or rod-shaped, non-flagellated and facultatively anaerobic bacterium, designated WN023T, was isolated from natural saline-alkali wetland soil of Binhai new district, Tianjin, China. The colonies of strain WN023T on marine agar 2216 (MA) have a brown, circular, wet pigmentation, and its cells are approximately 1-1.5 µm × 2.0-2.5 µm in size. Growth occurred at 15-45 °C, but optimally at 33-37 °C, in the presence of 5.0-25.0% (w/v) NaCl, but optimally at 10.0-15.0% (w/v) NaCl, and at a pH 6.5-11.0, but optimally at 7.5-8.0. Phylogenetic analysis of the 16S rRNA gene indicates that strain WN023T is a member of the genus Aliifodinibius within the family Balneolaceae, and the 16S rRNA gene sequence similarity of strain WN023T with its close relative Aliifodinibius halophilus KCTC 42497T, Aliifodinibius salicampi KACC 19060T, Aliifodinibius roseus KCTC 23442T, Aliifodinibius sediminis ACCC 10714T, and Fodinibius salinus ACCC 10716T was 97.3%, 94.5%, 93.9%, 93.71%, and 92.7%, respectively. Strain WN023T contained menaquinone-7 (MK-7) as the predominant menaquinone, and iso C15:0, Sum in feature 3 (C16:1ω6c and/or C16:1ω7c), and iso C17:1ω9c as the major fatty acids. The major polar lipids were glycolipid (GL), aminolipid (AL), phospholipid (PL), phosphatidylcholine (PC), phosphatidylethanolamine (PE), diphosphatidylglycerol (DPG), and lipid (L). The size of the draft genome as presented here was 3,583,276 bp in size, and the G+C content is 42.2 mol%. These combined physiological, biochemical, phylogenetic, and genotypic data supported placement of strain WN023T in the genus Aliifodinibius and indicated that it was distinct from all other members in the genus Aliifodinibius. This was also confirmed by the low DNA-DNA hybridization values (38.4%) between strain WN023T and the most closely related recognized Aliifodinibius species-A. halophilus KCTC 42497T. Therefore, we propose a novel species in the genus Aliifodinibius to accommodate the novel isolate: Aliifodinibius salipaludis sp. nov. (type strain WN023T = KCTC 52855T = ACCC 19978T).

Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species.

BACKGROUND: Akkermansia muciniphila is an important bacterium that resides on the mucus layer of the intestinal tract. Akkermansia muciniphila has a high abundance in human feces and plays an important role in human health. OBJECTIVE: In this article, 23 whole genome sequences of the Akkermansia genus were comparatively studied. METHODS: Phylogenetic trees were constructed with three methods: All amino acid sequences of each strain were used to construct the first phylogenetic tree using the web server of Composition Vector Tree Version 3. The matrix of Genome-to-Genome Distances which were obtained from GGDC 2.0 was used to construct the second phylogenetic tree using FastME. The concatenated single-copy core gene-based phylogenetic tree was generated through MEGA. The single-copy genes were obtained using OrthoMCL. Population structure was assessed by STRUCTURE 2.3.4 using the SNPs in core genes. PROKKA and Roary were used to do pan-genome analyses. The biosynthetic gene clusters were predicted using antiSMASH 4.0. IalandViewer 4 was used to detect the genomic islands. RESULTS: The results of comparative genomic analysis revealed that: (1) The 23 Akkermansia strains formed 4 clades in phylogenetic trees. The A. muciniphila strains isolated from different geographic regions and ecological niches, formed a closely related clade. (2) The 23 Akkermansia strains were divided into 4 species based on digital DNA-DNA hybridization (dDDH) values. (3) Pan-genome of A. muciniphila is in an open state and increases with addition of new sequenced genomes. (4) SNPs were not evenly distributed throughout the A. muciniphila genomes. The genes in regions with high SNP density are related to metabolism and cell wall/membrane envelope biogenesis. (5) The thermostable outer-membrane protein, Amuc_1100, was conserved in the Akkermansia genus, except for Akkermansia glycaniphila PytT. CONCLUSION: Overall, applying comparative genomic and pan-genomic analyses, we classified and illuminated the phylogenetic relationship of the 23 Akkermansia strains. Insights of the evolutionary, population structure, gene clusters and genome islands of Akkermansia provided more information about the possible physiological and probiotic mechanisms of the Akkermansia strains, and gave some instructions for the in-depth researches about the use of Akkermansia as a gut probiotic in the future.

Complete Genome Sequencing of Bacillus velezensis WRN014, and Comparison with Genome Sequences of other Bacillus velezensis Strains.

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

Melatonin protects H9c2 cells against ischemia/reperfusion­induced apoptosis and oxidative stress via activation of the Nrf2 signaling pathway.

Melatonin can protect against cardiac ischemia/reperfusion (I/R) injury in models in vitro and in vivo by regulating oxidative stress and apoptosis; however, the precise molecular mechanisms involved remain unclear. Nuclear factor erythroid 2­related factor 2 (Nrf2) is a transcription factor, which has been associated with the regulation of oxidative stress by translocating to the nucleus. Therefore, the present study investigated whether activation of the Nrf2 signaling pathway may be responsible for the protective effects of melatonin on I/R­injured cardiomyocytes. In the present study, H9c2 cells were subjected to simulated I/R (SIR) injury and pretreated with melatonin and/or Nrf2 small interfering RNA (siRNA). Cell viability was detected via Cell Counting kit­8 assay, apoptosis was examined by caspase­3 cleavage and activity analysis; oxidative stress levels were determined by specific activity analysis assays. In the present study, it was observed that SIR induced significant increases in apoptosis and oxidative stress, and enhanced Nrf2 expression within H9c2 cells. Pretreatment with melatonin partially reversed these alterations and promoted Nrf2 nuclear translocation. Transfection with Nrf2 siRNA inhibited the protective effects of melatonin on SIR­induced H9c2 cells. These results indicated that melatonin may protect H9c2 cells against I/R injury by reducing apoptosis and oxidative stress; this effect may be mediated via activation of the Nrf2 signaling pathway. Collectively, the results of the present study may suggest melatonin as a potential therapeutic agent against cardiac I/R injury.