scholarly journals Biotechnological and Ecological Potential of Micromonospora provocatoris sp. nov., a Gifted Strain Isolated from the Challenger Deep of the Mariana Trench

Marine Drugs ◽  
2021 ◽  
Vol 19 (5) ◽  
pp. 243
Author(s):  
Wael M. Abdel-Mageed ◽  
Lamya H. Al-Wahaibi ◽  
Burhan Lehri ◽  
Muneera S. M. Al-Saleem ◽  
Michael Goodfellow ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Gene Clusters ◽  
2D Nmr ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Mariana Trench ◽  
Chemical Structures ◽  
Desferrioxamine B ◽  
Challenger Deep

A Micromonospora strain, isolate MT25T, was recovered from a sediment collected from the Challenger Deep of the Mariana Trench using a selective isolation procedure. The isolate produced two major metabolites, n-acetylglutaminyl glutamine amide and desferrioxamine B, the chemical structures of which were determined using 1D and 2D-NMR, including 1H-15N HSQC and 1H-15N HMBC 2D-NMR, as well as high resolution MS. A whole genome sequence of the strain showed the presence of ten natural product-biosynthetic gene clusters, including one responsible for the biosynthesis of desferrioxamine B. Whilst 16S rRNA gene sequence analyses showed that the isolate was most closely related to the type strain of Micromonospora chalcea, a whole genome sequence analysis revealed it to be most closely related to Micromonospora tulbaghiae 45142T. The two strains were distinguished using a combination of genomic and phenotypic features. Based on these data, it is proposed that strain MT25T (NCIMB 15245T, TISTR 2834T) be classified as Micromonospora provocatoris sp. nov. Analysis of the genome sequence of strain MT25T (genome size 6.1 Mbp) revealed genes predicted to responsible for its adaptation to extreme environmental conditions that prevail in deep-sea sediments.

scholarly journals Whole Genome Sequence of Dermacoccus abyssi MT1.1 Isolated from the Challenger Deep of the Mariana Trench Reveals Phenazine Biosynthesis Locus and Environmental Adaptation Factors

Marine Drugs ◽  
2020 ◽  
Vol 18 (3) ◽  
pp. 131 ◽  
Author(s):  
Wael M. Abdel-Mageed ◽  
Bertalan Juhasz ◽  
Burhan Lehri ◽  
Ali S. Alqahtani ◽  
Imen Nouioui ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Biological Activities ◽  
Radical Scavenging ◽  
Gene Clusters ◽  
2D Nmr ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Isolation And Identification ◽  
Mariana Trench ◽  
Stress Related Genes

Dermacoccus abyssi strain MT1.1T is a piezotolerant actinobacterium that was isolated from Mariana Trench sediment collected at a depth of 10898 m. The organism was found to produce ten dermacozines (A‒J) that belonged to a new phenazine family and which displayed various biological activities such as radical scavenging and cytotoxicity. Here, we report on the isolation and identification of a new dermacozine compound, dermacozine M, the chemical structure of which was determined using 1D and 2D-NMR, and high resolution MS. A whole genome sequence of the strain contained six secondary metabolite-biosynthetic gene clusters (BGCs), including one responsible for the biosynthesis of a family of phenazine compounds. A pathway leading to the biosynthesis of dermacozines is proposed. Bioinformatic analyses of key stress-related genes provide an insight into how the organism adapted to the environmental conditions that prevail in the deep-sea.

scholarly journals Draft Whole Genome Sequence Analyses on Pseudomonas syringae pv. actinidiae Hypersensitive Response Negative Strains Detected from Kiwifruit Bleeding Sap Samples

2018 ◽  
Vol 108 (5) ◽  
pp. 552-560 ◽  
Author(s):  
Enrico Biondi ◽  
Alan Zamorano ◽  
Ernesto Vega ◽  
Stefano Ardizzi ◽  
Davide Sitta ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Genome Sequence ◽  
Hypersensitive Response ◽  
Time Window ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Optimal Time ◽  
Whole Genome ◽  
Isolation And Identification ◽  
The Difference

Kiwifruit bleeding sap samples, collected in Italian and Chilean orchards from symptomatic and asymptomatic plants, were evaluated for the presence of Pseudomonas syringae pv. actinidiae, the causal agent of bacterial canker. The saps were sampled during the spring in both hemispheres, before the bud sprouting, during the optimal time window for the collection of an adequate volume of sample for the early detection of the pathogen, preliminarily by molecular assays, and then through its direct isolation and identification. The results of molecular analyses showed more effectiveness in the P. syringae pv. actinidiae detection when compared with those of microbiological analyses through the pathogen isolation on the nutritive and semiselective media selected. The bleeding sap analyses allowed the isolation and identification of two hypersensitive response (HR) negative and hypovirulent P. syringae pv. actinidiae strains from different regions in Italy. Moreover, multilocus sequence analysis (MLSA) and whole genome sequence (WGS) were carried out on selected Italian and Chilean P. syringae pv. actinidiae virulent strains to verify the presence of genetic variability compared with the HR negative strains and to compare the variability of selected gene clusters between strains isolated in both countries. All the strains showed the lack of argK and coronatine gene clusters as reported for the biovar 3 P. syringae pv. actinidiae strains. Despite the biologic differences obtained in the tobacco bioassays and in pathogenicity assays, the MLSA and WGS analyses did not show significant differences between the WGS of the HR negative and HR positive strains; the difference, on the other hand, between PAC_ICE sequences of Italian and Chilean P. syringae pv. actinidiae strains was confirmed. The inability of the hypovirulent strains IPV-BO 8893 and IPV-BO 9286 to provoke HR in tobacco and the low virulence shown in this host could not be associated with mutations or recombinations in T3SS island.

scholarly journals Genome sequence analyses show that Neisseria oralis is the same species as ‘ Neisseria mucosa var. heidelbergensis’

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3920-3926 ◽  
Author(s):  
Julia S. Bennett ◽  
Keith A. Jolley ◽  
Martin C. J. Maiden
Keyword(s):  
Genome Sequence ◽  
Type Species ◽  
Whole Genome Sequence ◽  
23S Rrna ◽  
Rrna Gene ◽  
Whole Genome ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Neisseria Mucosa

Phylogenies generated from whole genome sequence (WGS) data provide definitive means of bacterial isolate characterization for typing and taxonomy. The species status of strains recently defined with conventional taxonomic approaches as representing Neisseria oralis was examined by the analysis of sequences derived from WGS data, specifically: (i) 53 Neisseria ribosomal protein subunit (rps) genes (ribosomal multi-locus sequence typing, rMLST); and (ii) 246 Neisseria core genes (core genome MLST, cgMLST). These data were compared with phylogenies derived from 16S and 23S rRNA gene sequences, demonstrating that the N. oralis strains were monophyletic with strains described previously as representing ‘ Neisseria mucosa var. heidelbergensis’ and that this group was of equivalent taxonomic status to other well-described species of the genus Neisseria . Phylogenetic analyses also indicated that Neisseria sicca and Neisseria macacae should be considered the same species as Neisseria mucosa and that Neisseria flavescens should be considered the same species as Neisseria subflava . Analyses using rMLST showed that some strains currently defined as belonging to the genus Neisseria were more closely related to species belonging to other genera within the family; however, whole genome analysis of a more comprehensive selection of strains from within the family Neisseriaceae would be necessary to confirm this. We suggest that strains previously identified as representing ‘ N. mucosa var. heidelbergensis’ and deposited in culture collections should be renamed N. oralis . Finally, one of the strains of N. oralis was able to ferment lactose, due to the presence of β-galactosidase and lactose permease genes, a characteristic previously thought to be unique to Neisseria lactamica , which therefore cannot be thought of as diagnostic for this species; however, the rMLST and cgMLST analyses confirm that N. oralis is most closely related to N. mucosa .

scholarly journals Whole genome sequence of Peribacillus sp. MUM 13 derived from mangrove forest in Malaysia

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Jodi Woan-Fei Law ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Mangrove Forest ◽  
Screening Program ◽  
Gene Clusters ◽  
Bioinformatic Analysis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Chemical Structures ◽  
Pathogenic Microbes ◽  
Unique Chemical

Acting like mini-factories, microorganisms are a valuable source of naturalbioactive compounds of unique chemical structures. Peribacillus sp. MUM 13 was recoveredfrom the mangrove forest in Malaysia during a screening program for bioactive microbes.Whole genome analysis revealed that the genome size of MUM 13 as 4,649,225 bp (with G+ C content of 40.8 %). Bioinformatic analysis predicted the presence of lassopeptidebiosynthetic gene clusters within the genome of MUM 13, which indicates the bioactivepotential of the strain and calls for further experiments to explore the strain characteristics,particularly in combatting against pathogenic microbes.

scholarly journals Isolation, Identification, and Complete Genome Assembly of an Endophytic Bacillus velezensis YB-130, Potential Biocontrol Agent Against Fusarium graminearum

2020 ◽  
Vol 11 ◽  
Author(s):  
Wen Xu ◽  
Liyong Zhang ◽  
Paul H. Goodwin ◽  
Mingcong Xia ◽  
Jie Zhang ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Biological Control Agent ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Yield Reduction ◽  
Rrna Gene ◽  
Whole Genome ◽  
Bacillus Velezensis ◽  
Fungal Plant Pathogens ◽  
Dual Cultures

Wheat scab caused by F. graminearum is a highly destructive disease that leads to yield reduction and mycotoxin contamination of grains. In this study, an endophytic bacterium of strain YB-130 was isolated from surface sterilized wheat spikes with scab symptoms and identified as Bacillus velezensis by whole genome annotation, 16S rRNA gene and average nucleotide identities analysis. The whole-genome sequence of strain YB-130 was obtained by PacBio sequencing. 88 putative Carbohydrate-Active Enzymes and 12 gene clusters encoding for secondary metabolites were identified in the YB-130 genome, including one gene cluster for the synthesis of lanthipeptide only found in strain YB-130 genome. In dual cultures, strain YB-130 significantly inhibited the growth of F. graminearum PH-1 and other eight fungal plant pathogens, indicating a broad antifungal activity. Furthermore, strain YB-130 was able to significantly inhibit spore morphology and hyphal development of F. graminearum PH-1. Strain YB-130 also reduced deoxynivalenol production by F. graminearum PH-1 in dual cultures, possibly due to its ability to suppress the expression of tri5, tri3, and tri8 that are required for deoxynivalenol production in F. graminearum. Overall, B. velezensis YB-130 is a promising biological control agent of both F. graminearum infection and mycotoxin production.

scholarly journals Whole genome sequence of Streptomyces colonosanans strain MUSC 93JT isolated from mangrove forest in Malaysia

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Jodi Woan-Fei Law ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Kok-Gan Chan
Keyword(s):  
Bioactive Compounds ◽  
Genome Sequence ◽  
Antioxidant Activities ◽  
Human Cancer ◽  
Wide Spectrum ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Selective Toxicity ◽  
Human Cancer Cell Lines

Under the family Actinobacteria, streptomycetes are ubiquitous in nature, producing a wide spectrum of bioactive compounds including antibacterial, antioxidant, anticancer and immunomodulatory properties. During a screening programme in Malaysia, Streptomyces colonosanans MUSC 93JT was isolated as a novel Streptomyces sp. from the mangrove soil in Sarawak. The strain exhibited potent antioxidant activities and cytotoxic activity against several human cancer cell lines. Due to these data, the strain was subjected to whole genome sequencing to uncover its genomic potential and further improve the understanding of the strain. The genome of MUSC 93JT consists of 7,015,076 bp (G + C content of 69.90%), carrying a total of 5,859 protein coding genes. Analysis using a bioinformatics tool, antiSMASH predicted a total of four biosynthetic gene clusters which displayed similarity of more than 70% to known gene clusters and one of which was associated with the production of a natural protectant, ectoine. Displaying selective toxicity that kills only cancer cells, ectoine has showed its potential to be developed as therapeutic agents for humans. Altogether, the current project clearly highlights the importance of under-explored environment like mangrove in natural product discovery. The availability of whole genome sequence MUSC 93JT warrants subsequent in-depth investigation and optimization for the production of bioactive compounds which can be exploited for the health and wellbeing of mankind.

scholarly journals Photobacterium galatheae sp. nov., a bioactive bacterium isolated from a mussel in the Solomon Sea

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4503-4507 ◽  
Author(s):  
Henrique Machado ◽  
Sonia Giubergia ◽  
Ramona Valentina Mateiu ◽  
Lone Gram
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Genome Sequence ◽  
Sequence Data ◽  
Novel Species ◽  
Solomon Islands ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome ◽  
Gene Similarity

A novel, Gram-negative marine bacterium, S2753T, was isolated from a mussel of the Solomon Sea, Solomon Islands. Analysis of the 16S rRNA gene sequence and whole genome sequence data placed strain S2753T in the genus Photobacterium with the closest relative being Photobacterium halotolerans DSM 18316T (97.7 % 16S rRNA gene similarity). Strain S2753T was able to grow from 15 to 40 °C and in NaCl concentrations of 0.5 to 9 % (w/v). The predominant fatty acids were 16 : 1ω7c/16 : 1ω6c (27.9 %), 16 : 0 (22.1 %) and 18 : 1ω7c/8 : 1ω6c (21.4 %). The genomic DNA G+C mol content was 49.5 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic differences, strain S2753T is considered to represent a novel species of the genus Photobacterium. Furthermore, whole genome sequence analysis comparing S2753T and type-strains of closely related species of the genus Photobacterium also demonstrated that the strain is genomically distinct enough to be considered a novel species. The name Photobacterium galatheae is proposed and the type-strain is S2753T( = LMG 28894T = DSM 100496T).

scholarly journals Enhancing PCR Capacity To Detect ‘Candidatus Liberibacter asiaticus’ Utilizing Whole Genome Sequence Information

Plant Disease ◽  
2020 ◽  
Vol 104 (2) ◽  
pp. 527-532 ◽  
Author(s):  
Minli Bao ◽  
Zheng Zheng ◽  
Xiaoan Sun ◽  
Jianchi Chen ◽  
Xiaoling Deng
Keyword(s):  
Genome Sequence ◽  
Biological Information ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Sequence Information ◽  
Whole Genome ◽  
Candidatus Liberibacter Asiaticus ◽  
Genomic Locus ◽  
Candidatus Liberibacter ◽  
Liberibacter Asiaticus

‘Candidatus Liberibacter asiaticus’ (CLas) is an unculturable α-proteobacterium associated with citrus Huanglongbing (HLB; yellow shoot disease). PCR procedures that accurately confirm or exclude CLas infection in citrus tissue/Asian citrus psyllid (ACP) samples are critical for HLB management. When CLas was described in 1994, a 23-bp signature oligonucleotide sequence (OI1) in the 16S rRNA gene (rrs, three genomic copies) was identified based on Sanger sequencing. OI1 contains single nucleotide polymorphisms (SNPs) distinguishing CLas from non-CLas species. The SNPs were used to design the primer HLBas, a key primer for a commonly used TaqMan PCR system (HLBas-PCR) for CLas detection. Recent developments in next-generation sequencing technology have led to the identification of 15 CLas whole genome sequence strains (WGSs). Analyses of CLas WGSs have generated a significant amount of biological information that could help to improve CLas detection. Utilizing the WGS information, this study re-evaluated the sequence integrity of OI1/HLBas and identified and/or confirmed a missing nucleotide G in the two primers. Replacement primers for OI1 and HLBas are proposed. At low cycle threshold (Ct) values (e.g., <30), HLBas-PCR remained reliable in CLas determination. At high Ct values (e.g., >30), HLBas-PCR alone was unreliable in differentiating whether samples contain low CLas titers or whether CLas is not present. The availability of ribonucleotide reductase (RNR)-PCR derived from the five-copy nrdB gene helped to resolve this problem. To further enhance low CLas titer detection, a 4CP-PCR system, based on a four-copy genomic locus, was developed. Evaluation of 107 HLB samples (94 citrus and 13 ACP) showed that 4CP-PCR was more sensitive than HLBas-PCR and shared similar sensitivity with RNR-PCR.

scholarly journals Tatumella saanichensis sp. nov., isolated from a cystic fibrosis patient

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1959-1966 ◽  
Author(s):  
Dobryan M. Tracz ◽  
Matthew W. Gilmour ◽  
Philip Mabon ◽  
Daniel R. Beniac ◽  
Linda Hoang ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Cystic Fibrosis ◽  
Sequence Analysis ◽  
Cystic Fibrosis Patient ◽  
Clinical Isolate ◽  
Genome Sequence ◽  
Clinical Investigation ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Whole Genome

Polyphasic taxonomic analysis was performed on a clinical isolate (NML 06-3099T) from a cystic fibrosis patient, including whole-genome sequencing, proteomics, phenotypic testing, electron microscopy, chemotaxonomy and a clinical investigation. Comparative whole-genome sequence analysis and multilocus sequence analysis (MLSA) between Tatumella ptyseos ATCC 33301T and clinical isolate NML 06-3099T suggested that the clinical isolate was closely related to, but distinct from, the species T. ptyseos. By 16S rRNA gene sequencing, the clinical isolate shared 98.7 % sequence identity with T. ptyseos ATCC 33301T. A concatenate of six MLSA loci (totalling 4500 bp) revealed < 93.9 % identity between T. ptyseos ATCC 33301T, other members of the genus and the clinical isolate. A whole-genome sequence comparison between NML 06-3099T and ATCC 33301T determined that the average nucleotide identity was 76.24 %. The overall DNA G+C content of NML 06-3099T was 51.27 %, consistent with members of the genus Tatumella. By matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS analysis, NML 06-3099T had a genus-level match, but not a species-level match, to T. ptyseos. By shotgun proteomics, T. ptyseos ATCC 33301T and NML 06-3099T were found to have unique proteomes. The two strains had similar morphologies and multiple fimbriae, as observed by transmission electron microscopy, but were distinguishable by phenotypic testing. Cellular fatty acids found were typical for members of the Enterobacteriaceae. NML 06-3099T was susceptible to commonly used antibiotics. Based on these data, NML 06-3099T represents a novel species in the genus Tatumella, for which the name Tatumella saanichensis sp. nov. is proposed (type strain NML 06-3099T = CCUG 55408T = DSM 19846T).

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