Pseudomonas Tumuqiensis Sp. Nov., Isolated From Greenhouse Soil

A Gram-stain-negative, aerobic, rod-shaped and motile bacterium, named LAMW06T, was isolated from greenhouse soil in Beijing, China. In the 16S rRNA gene sequence comparison, strain LAMW06T had the highest similarity with Pseudomonas cuatrocienegasensis 1NT was 97.4%. Phylogenetic analysis base on the 16S rRNA and three housekeeping gene sequences (gyrB, rpoB and rpoD) indicated that LAMW06T represented a member of the genus Pseudomonas. The genome sequence size of the isolate was 5.5 Mb, with the DNA G+C content of 63.5 mol%. The average nucleotide identity and DNA–DNA hybridization values between strain LAMW06T and closely related members of Pseudomonas borbori R-20821T, Pseudomonas taeanensis MS-3T and Pseudomonas cuatrocienegasensis 1NT were 90.9%, 82.4%, 81.5 % and 43.0%, 25.9%, 24.6 % respectively. The major fatty acids contained summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), C18:1 ω7c and C16:0. The primary respiratory quinone was ubiquinone-9. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, six aminophospholipids, six phospholipids, one aminolipid and one glycolipid. According to the genotypic, phylogenetic and chemotaxonomic data, strain LAMW06T represents a novel species within the genus Pseudomonas, for which the name Pseudomonas tumuqiensis sp. nov. is proposed. The type strain is LAMW06T (=GDMCC 1.2003T =KCTC 72829T).

Haloterrigena Gelatinilytica sp. nov., A New Extremely Halophilic Archaeon Isolated From Salt-Lake

Two extremely halophilic strains, designated SYSU A558-1T and SYSU A121-1, were isolated from a saline sediment sample collected from Aiding salt lake, China. Cells of strains SYSU A558-1T and SYSU A121-1 were Gram-stain-negative, coccoid, and non-motile. The isolates were aerobic and grew at NaCl concentration of 10-30% (optimum, 20-22%), at 20-55ºC (optimum, 37-42ºC) and at pH 6.5-8.5 (optimum, 7.0-8.0). Cells lysed in distilled water. Major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, disulphated diglycosyl diether-1 and one unidentified glycolipid. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that the two strains SYSU A558-1T and SYSU A121-1 were closely related to the membranes of the genus Haloterrigena. Phylogenetic trees based on strains SYSU A558-1T and SYSU A121-1 16S rRNA gene sequence, rpoB' gene sequence and concatenation of 87 protein markers demonstrated a robust clade with Haloterrigena turkmenica, Haloterrigena salifodinae and Haloterrigena salina. The genomic DNA G+C contents of strains SYSU A558-1T and SYSU A121-1 were 65.8 and 65.0%, respectively. Phenotypic, chemotaxonomic characteristics and phylogenetic properties suggested that the two strains SYSU A558-1T and SYSU A121-1 represent a novel species of the genus Haloterrigena, for which the name Haloterrigena gelatinilytica sp. nov. is proposed. The type strain is SYSU A558-1T (= KCTC 4259T = CGMCC 1.15953T).

Phylogeny of different Helicobacter pylori strains could not be explained by 16S rRNA gene due to high similarity in gene sequence across strains

Understanding the evolutionary relatedness of different strains of a species helped identify strain-specific differences that may be useful for disease diagnosis and treatment. Typically, such strain level typing would be augmented by molecular assays such as DNA sequencing, and phylogenetic tree analysis. This work utilizes public data on the 16S rRNA gene sequence of different strains of Helicobacter pylori to help plot the phylogenetic tree that describes the evolutionary trajectories of the different strains. Results from multiple sequence alignment reveals high level of conservation in 16S rRNA gene sequence across strains. This then translates into a phylogenetic tree structure that suggests very close evolutionary relationships of the different strains except for one outlier strain. Even in the case of the outlier strain, its evolutionary distance from other brethren was also not large. Overall, the results obtained in this study indicates that 16S rRNA gene may not capture strain-level phylogeny between different strains of the same species, and point to efforts in elucidating this phylogenetic effect in other genes of the species. Such genes may be involved in virulence during pathogenesis in humans, and may thus be subjected to higher evolutionary pressure and natural selection.

Identification and Chemotype Profiling of Fusarium Head Blight Disease in Triticale

This study aimed to assess the disease incidence and distribution of toxigenic in Korean triticale. The pathogen of triticale that cause Fusarium head blight were isolated from five different triticale cultivars that cultivated in Suwon Korea at 2021 year. The 72 candidate were classified as a Fusarium asiaticum by morphology analysis and by ITS1, TEF-1α gene sequence analysis. And the results of pathogenicity with 72 isolates on seedling triticale, 71 isolates were showed disease symptom. Also, seven out of 71 Fusarium isolates were inoculated on the wheat, to test the pathogenicity on the different host. The results showed more low pathogenicity on the wheat than triticale. The results of analysis of toxin type with 72 isolates, 64.6% isolates were produced nivalenol type toxin and other 4.6% and 30.8% isolates were produce 3-acetyldeoxynivalenol and 15-acetyldeoxynivalenol, respectively. To select fungicide for control, the 72 Fusarium isolates were cultivated on the media that containing four kinds fungicide. The captan, hexaconazole, and difenoconazole·propiconazole treated Fusarium isolates were not showed resistance response against each fungicide. However, six isolates out of 72 isolates, showed resistance response to fludioxonil. This study is first report that F. asiaticum causes Fusarium head blight disease of triticale in Korea.

Jeotgalibacillus Auranticolor sp. nov., Isolated from Freshwater Collected from Baiyangdian Lake Lake, China

A novel Gram-positive, strictly aerobic, rod-shaped, orange-pigmented bacterial strain, designated R-1-5s-1T, was isolated from Baiyangdian Lake, China. Strain R-1-5s-1T grew at 15-37℃ (optimum 37℃) and pH 7-11 (optimum pH 8) in Luria-Bertani medium. Based on 16S rRNA gene sequence analysis, strain R-1-5s-1T was assigned to the genus Jeotgalibacillus and showed the closest relationships with Jeotgalibacillus salarius ASL-1T (97.69%), Jeotgalibacillus alkaliphilus JC303T (97.29%), Jeotgalibacillus marinus DSM 1297T (97.15%), Jeotgalibacillus campisalis SF-57T (97.01%), and Jeotgalibacillus spp. (≤ 97%). The predominant polar lipids were phosphatidylglycerol and diphosphatidylglycerol; the major cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0, and anteiso-C17:0; and the major respiratory quinones were MK-7 and MK-8. The peptidoglycan type of the cell wall was A1a linked via L-lysine as the diamino acid. The G+C content was 43.6%, and the draft genome size of strain R-1-5s-1T was 3.4 Mbp. Between strain R-1-5s-1T and the related strain J. salarius ASL-1T, the ANI and dDDH relatedness values were 78.9% and 20.8%, respectively. Phylogenetic, chemotaxonomic, and genotypic analyses revealed that strain R-1-5s-1T is a novel species in the genus Jeotgalibacillus, for which the name Jeotgalibacillus auranticolor sp. nov. is proposed. The type strain is R-1-5s-1T (=CGMCC 1.13567T=KCTC 43038T).

Azospirillum Actinidiae sp. nov., a Nitrogen-Fixing Bacterium Isolated From The Roots of Kiwifruit Plants

A novel diazotrophic bacterium, designated CCTCC AB 2021101T, was isolated from fresh roots of kiwifruit. Cells of strain CCTCC AB 2021101T were Gram-negative, aerobic and rod-shaped, with motility provided by peritrichous flagella. The 16S rRNA analysis showed that strain CCTCC AB 2021101T belongs to the genus Azospirillum and is closely related to Azospirillum melinis (98.32%), Azospirillum oryzae (97.73%), Azospirillum lipoferum (96.98%), Azospirillum humicireducens (96.49%) and Azospirillum largimobile (96.01%) and lower sequence similarity (<96.0 %) to all other species of the genus Azospirillum. Strain CCTCC AB 2021101T was able to grow well at 35–40℃ and pH 6.0–7.0, and tolerated up to 3.0 % (w/v) NaCl. The major saturated fatty acids are C14:0, C16:0 and C18:0. C18:1 ω7c and C16:0 3-OH were the major unsaturated and hydroxylated fatty acid. The G+C content was 67.8 mol%. Strain CCTCC AB 2021101T gave positive amplification for dinitrogen reductase (nifH gene). Highest nifH gene sequence similarities were obtained with Azospirillum brasilense AWB14T(95.9%), Azospirillum zeae Gr24T(95.56%), Azospirillum picis DSM 19922T(96.79%), Azospirillum lipoferum B22T(94.88%) and Azospirillum oryzae COC8T(94.88%). The activity of the nitrogenase of the strain was further confirmed by acetylene-reduction assay, which was recorded as 81 nmol ethylene h-1. Based on these data, strain CCTCC AB 2021101T is considered to represent a novel endophytic diazotrophs species in the genus Azospirillum, for which the name Azospirillum actinidiae sp. nov. is proposed. The type strain is CCTCC AB 2021101T.

Gene Sequence Clustering Based on the Profile Hidden Markov Model with Differential Identifiability

In the era of big data, next-generation sequencing produces a large amount of genomic data. With these genetic sequence data, research in biology fields will be further advanced. However, the growth of data scale often leads to privacy issues. Even if the data is not open, it is still possible for an attacker to steal private information by a member inference attack. In this paper, we proposed a private profile hidden Markov model (PHMM) with differential identifiability for gene sequence clustering. By adding random noise into the model, the probability of identifying individuals in the database is limited. The gene sequences could be unsupervised clustered without labels according to the output scores of private PHMM. The variation of the divergence distance in the experimental results shows that the addition of noise makes the profile hidden Markov model distort to a certain extent, and the maximum divergence distance can reach 15.47 when the amount of data is small. Also, the cosine similarity comparison of the clustering model before and after adding noise shows that as the privacy parameters changes, the clustering model distorts at a low or high level, which makes it defend the member inference attack.

Enterococcus innesii sp. nov., isolated from the wax moth Galleria mellonella

Four bacterial strains were isolated from two different colony sources of the wax moth Galleria mellonella. They were characterized by a polyphasic approach including 16S rRNA gene sequence analysis, core-genome analysis, average nucleotide identity (ANI) analysis, digital DNA–DNA hybridization (dDDH), determination of G+C content, screening of antibiotic resistance genes, and various phenotypic analyses. Initial analysis of 16S rRNA gene sequence identities indicated that strain GAL7T was potentially very closely related to Enterococcus casseliflavus and Enterococcus gallinarum , having 99.5–99.9 % sequence similarity. However, further analysis of whole genome sequences revealed a genome size of 3.69 Mb, DNA G+C content of 42.35 mol%, and low dDDH and ANI values between the genomes of strain GAL7T and closest phylogenetic relative E. casseliflavus NBRC 100478T of 59.0 and 94.5 %, respectively, indicating identification of a putative new Enterococcus species. In addition, all novel strains encoded the atypical vancomycin-resistance gene vanC-4. Results of phylogenomic, physiological and phenotypic characterization confirmed that strain GAL7T represented a novel species within the genus Enterococcus , for which the name Enterococcus innesii sp. nov. is proposed. The type strain is GAL7T (=DSM 112306T=NCTC 14608T).

Electrochemical DNA biosensor based on platinum-gold bimetal decorated graphene modified electrode for the detection of Vibrio Parahaemolyticus specific tlh gene sequence

Background: By using bimetal nanocomposite modified electrode, the electrochemical DNA biosensor showed the advantages of high sensitivity, low cost, rapid response and convenient operation, which was applied for disease diagnosis, food safety, and biological monitoring. Objective: A nanocomposite consisting of platinum (Pt)-gold (Au) bimetal and two-dimensional graphene (GR) was synthesized by hydrothermal method, which was modified on the surface of carbon ionic liquid electrode and further used for the immobilization of probe ssDNA related to Vibrio Parahaemolyticus tlh gene to construct an electrochemical DNA sensor. Method: Potassium ferricyanide was selected as electrochemical indicator, cyclic voltammetry was used to study the electrochemical behaviours of different modified electrodes and differential pulse voltammetry was employed to test the analytical performance of this biosensor for the detection of target gene sequence. Results: This electrochemical DNA biosensor could detect the Vibrio Parahaemolyticus tlh gene sequence as the linear concentration in the range from 1.0×10-13 mol L-1 to 1.0×10-6 mol L-1 with the detection limit as 2.91×10-14 mol L-1 (3σ). Conclusion: This proposed electrochemical DNA biosensor could be used to identify the special gene sequence with good selectivity, low detection limit and wide detection range.

Alkalibacter mobilis sp. nov., an anaerobic bacterium isolated from a coastal lake

A novel anaerobic chemoorganotrophic, facultatively alkaliphilic bacterium (strain M17 DMBT) was isolated from a coastal lake (Golubitsckoe, Taman Peninsula, Russia). Cells were motile rods, 1.6–2.1 µm long and 0.45 µm in diameter. The temperature range for growth was 14–42 °C, with an optimum at 30 °C. The pH range for growth was pH 5.5–10.0, with an optimum at pH 8.0–8.5. Growth of strain M17 DMBT was observed at NaCl concentrations of 1–12 % (w/v) with optimum growth at 1.5–2.0 %. Strain M17 MBTutilized glucose, fructose, sucrose, ribose, mannose, raffinose, arabinose, dextrin, yeast extract, peptone, carbon monoxide, vanillic acid and 3,4-dimethoxybenzoic acid. The end products from glucose fermentation were acetate and ethanol. The DNA G+C content of strain M17 DMBT was 39.1 mol%. The closest phylogenetic relative of strain M17 DMBT was Alkalibacter saccharofermentans with 97.8 % 16S rRNA gene sequence similarity. The OrthoANI value between M17 DMBT and A. saccharofermentans was 70.4 %. Based on the phenotypic, genotypic and phylogenetic characteristics of the isolate, strain M17 DMBT is considered to represent a novel species of the genus Alkalibacter for which the name Alkalibacter mobilis sp. nov. is proposed. The type strain of Alkalibacter mobilis is M17 DMBT (=KCTC 15920T=VKM B-3408T).