scholarly journals Mining Genomes of Three Marine Sponge-Associated Actinobacterial Isolates for Secondary Metabolism

2015 ◽  
Vol 3 (5) ◽  
Author(s):  
Hannes Horn ◽  
Ute Hentschel ◽  
Usama Ramadan Abdelmohsen
Keyword(s):  
Secondary Metabolism ◽  
Marine Sponge ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Genome Sequences

Here, we report the draft genome sequences of three actinobacterial isolates, Micromonospora sp. RV43, Rubrobacter sp. RV113, and Nocardiopsis sp. RV163 that had previously been isolated from Mediterranean sponges. The draft genomes were analyzed for the presence of gene clusters indicative of secondary metabolism using antiSMASH 3.0 and NapDos pipelines. Our findings demonstrated the chemical richness of sponge-associated actinomycetes and the efficacy of genome mining in exploring the genomic potential of sponge-derived actinomycetes.

scholarly journals Draft Genome Sequences of Fungus Aspergillus calidoustus

2016 ◽  
Vol 4 (2) ◽  
Author(s):  
Fabian Horn ◽  
Jörg Linde ◽  
Derek J. Mattern ◽  
Grit Walther ◽  
Reinhard Guthke ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Genome Sequence ◽  
Functional Annotation ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Draft Genome Sequence ◽  
Genome Sequences

Here, we report the draft genome sequence of Aspergillus calidoustus (strain SF006504) . The functional annotation of A. calidoustus predicts a relatively large number of secondary metabolite gene clusters. The presented genome sequence builds the basis for further genome mining.

scholarly journals Analysis of Draft Genome Resources of Thirty-Three Canadian Strains of Pseudomonas syringae pv. tomato isolated between 1992 and 2008 Reveals achromobactin virulence cluster that is absent in the reference strain DC3000

2021 ◽  
Author(s):  
James Tambong ◽  
Renlin Xu ◽  
Diane Cuppels ◽  
Julie T Chapados ◽  
suzanne Gerdis ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Draft Genome ◽  
Genome Mining ◽  
Gene Clusters ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequences ◽  
Protein Coding ◽  
Genome Data ◽  
Bacterial Speck Disease

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck disease of field and greenhouse tomato plants. Only one Canadian whole genome sequence of this economically important pathogen is publicly available in NCBI GenBank. Here, we report 33 whole genome sequences of Canadian strains of P. syringae pv. tomato isolated in Ontario, Canada, between 1992 and 2008. The genome sequences exhibited average nucleotide identity values of 98.64-98.72 % with P. syringae pv. tomato ICMP 2844PT and DC3000, validating the taxonomic standing of these Canadian strains. The genome sizes ranged from 6.20-6.39 Mbp with G+C content of 58.6% and comprised 5,889-6,166 protein-coding sequences (CDSs). The strains had pan- and core-genomes of 6808 and 4,993 gene clusters, respectively. Genome mining of the strains for virulence factors identified typical adherence genes, proteins related to antiphagocytosis, secretion system apparatuses and effectors. Also, partial or complete achromobactin biosynthetic cluster and iron transport genes were identified in all the Canadian strains but absent in P. syringae pv. tomato DC3000 or ICMP 2844 (pathotype). These new whole genome data of Canadian strains of P. syringae pv. tomato could be useful resources in understanding the evolution of this pathogen.

scholarly journals Draft Genome Sequences of Six Vibrio Strains Isolated from the Atlantic Intertidal Marine Sponge Ophlitaspongia papilla

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Anoop Alex ◽  
Vijayakumari Pratheepa ◽  
Joana Martins ◽  
Agostinho Antunes
Keyword(s):  
Comparative Genomics ◽  
Marine Sponge ◽  
Molecular Mechanisms ◽  
Draft Genome ◽  
Genome Mining ◽  
Genome Sequences ◽  
Content Type ◽  
Bioactive Potential ◽  
Microbial Symbioses

ABSTRACT We report here the genome sequences of six Vibrio strains isolated from an Atlantic intertidal marine sponge, Ophlitaspongia papilla. Genome mining and comparative genomics will assist in deciphering the bioactive potential of the symbiotic microbes and molecular mechanisms of sponge-microbial symbioses.

scholarly journals Isolation and Identification of Actinomycetes Strains from Switzerland and their Biotechnological Potential

2020 ◽  
Vol 74 (5) ◽  
pp. 382-390 ◽  
Author(s):  
Fabienne Arn ◽  
David Frasson ◽  
Ivana Kroslakova ◽  
Fabio Rezzonico ◽  
Joël F. Pothier ◽  
...  
Keyword(s):  
Draft Genome ◽  
Genome Mining ◽  
Bioactive Compound ◽  
Gene Clusters ◽  
Natural Compounds ◽  
Rrna Gene ◽  
Cultivation Conditions ◽  
Screening Assay ◽  
Isolation And Identification ◽  
Bioinformatics Analyses

Actinomycetes strains isolated from different habitats in Switzerland were investigated for production of antibacterial and antitumoral compounds. Based on partial 16S rRNA gene sequences, the isolated strains were identified to genus level. Streptomyces as the largest genus of Actinobacteriawas isolated the most frequently. A screening assay using the OmniLog instrument was established to facilitate the detection of active compounds from actinomycetes. Extracts prepared from the cultivated strains able to inhibit Staphylococcus aureusand Escherichia coliwere further analysed by HPLC and MALDI-TOF MS to identify the produced antibiotics. In this study, the bioactive compound echinomycin was identified from two isolated Streptomycesstrains. Natural compounds similar to TPU-0037-C, azalomycin F4a 2-ethylpentyl ester, a derivative of bafilomycin A1, milbemycin-α8 and dihydropicromycin were detected from different isolated Streptomyces strains. Milbemycin-α8 showed cytotoxic activity against HT-29 colon cancer cells. The rare actinomycete,Micromonospora sp. Stup16_C148 produced a compound that matches with the antibiotic bottromycin A2. The draft genome sequence from Actinokineospora strain B136.1 was determined using Illumina and nanopore-based technologies. The isolated strain was not able to produce antibacterial compounds under standard cultivation conditions. The antiSMASH bioinformatics analyses of the genome from strain B136.1 identified biosynthetic gene clusters with identity values between 4% to 90% to known gene clusters encoding antibiotics. The combinations of cultivation conditions, screening assays, analytical methods and genome mining are important tools to characterize strains of actinomycetes for the identification of their potential to produce natural compounds with antimicrobial activity.

scholarly journals Draft Genome Assembly of the Entomopathogenic Bacterium Photorhabdus luminescens subsp. sonorensis Caborca

2019 ◽  
Vol 8 (36) ◽  
Author(s):  
Duy An Duong ◽  
Patricia Espinosa-Artiles ◽  
Rousel A. Orozco ◽  
István Molnár ◽  
S. Patricia Stock
Keyword(s):  
Secondary Metabolism ◽  
Genome Assembly ◽  
Draft Genome ◽  
Gene Clusters ◽  
Insect Species ◽  
Photorhabdus Luminescens ◽  
Putative Gene ◽  
Content Type ◽  
Draft Genome Assembly ◽  
Wide Range

Photorhabdus luminescens subsp. sonorensis strain Caborca is an entomopathogenic bacterium with a dual lifestyle, namely, as a mutualist of the Heterorhabditis sonorensis nematode and a pathogen to a wide range of insect species. The genome assembly, in 231 contigs, is 5.2 Mbp long and includes 25 putative gene clusters for secondary metabolism.

scholarly journals Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses

2019 ◽  
Vol 7 (12) ◽  
pp. 635
Author(s):  
Anoop Alex ◽  
Agostinho Antunes
Keyword(s):  
Comparative Genomics ◽  
Marine Sponge ◽  
Draft Genome ◽  
Carbon Sources ◽  
Gene Clusters ◽  
Marine Sponges ◽  
Symbiotic Association ◽  
Limited Information ◽  
Secretion Systems ◽  
Genomic Signatures

The most recently described bacterial members of the genus Endozoicomonas have been found in association with a wide variety of marine invertebrates. Despite their ubiquity in the host holobiont, limited information is available on the molecular genomic signatures of the symbiotic association of Endozoicomonas with marine sponges. Here, we generated a draft genome of Endozoicomonas sp. OPT23 isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative genomics analyses. Genome-specific analysis and metabolic pathway comparison of the members of the genus Endozoicomonas revealed the presence of gene clusters encoding for unique metabolic features, such as the utilization of carbon sources through lactate, L-rhamnose metabolism, and a phenylacetic acid degradation pathway in Endozoicomonas sp. OPT23. Moreover, the genome harbors genes encoding for eukaryotic-like proteins, such as ankyrin repeats, tetratricopeptide repeats, and Sel1 repeats, which likely facilitate sponge-bacterium attachment. The genome also encodes major secretion systems and homologs of effector molecules that seem to enable the sponge-associated bacterium to interact with the sponge and deliver the virulence factors for successful colonization. In conclusion, the genome analysis of Endozoicomonas sp. OPT23 revealed the presence of adaptive genomic signatures that might favor their symbiotic lifestyle within the sponge host.

scholarly journals Diverse and Abundant Secondary Metabolism Biosynthetic Gene Clusters in the Genomes of Marine Sponge Derived Streptomyces spp. Isolates

Marine Drugs ◽  
2018 ◽  
Vol 16 (2) ◽  
pp. 67 ◽  
Author(s):  
Stephen Jackson ◽  
Lisa Crossman ◽  
Eduardo Almeida ◽  
Lekha Margassery ◽  
Jonathan Kennedy ◽  
...  
Keyword(s):  
Secondary Metabolism ◽  
Marine Sponge ◽  
Gene Clusters ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Streptomyces Spp

scholarly journals Draft Genome Sequences of the Three Massilia Strains AB1, ST3, and ZL223

2021 ◽  
Vol 10 (30) ◽  
Author(s):  
Ariel A. Bradley ◽  
Zoephia Laughlin ◽  
Saralexis Torres ◽  
Loralyn M. Cozy
Keyword(s):  
Draft Genome ◽  
Genomic Data ◽  
Gene Clusters ◽  
Nucleotide Identity ◽  
Average Nucleotide Identity ◽  
Biosynthetic Gene ◽  
Genome Sequences ◽  
Biosynthetic Gene Clusters ◽  
Antibiotic Discovery

To increase the genomic data available for antibiotic discovery, three independently isolated antibiotic-producing Massilia strains were sequenced. No more than 84% average nucleotide identity was shared with publicly available Massilia genomes, and a low similarity of predicted biosynthetic gene clusters to known clusters was found.

scholarly journals Draft Genome Sequences of a Bacillus subtilis Strain, a Bacillus velezensis Strain, a Paenibacillus Strain, and an Acinetobacter baumannii Strain, All Isolated from the Phyllosphere of Lactuca sativa or Solanum lycopersicum

2021 ◽  
Vol 10 (4) ◽  
Author(s):  
Claudia Y. Muñoz ◽  
Anne de Jong ◽  
Oscar P. Kuipers
Keyword(s):  
Bacillus Subtilis ◽  
Acinetobacter Baumannii ◽  
Solanum Lycopersicum ◽  
Lactuca Sativa ◽  
Draft Genome ◽  
Gene Clusters ◽  
Subtilis Strain ◽  
Bacillus Velezensis ◽  
Genome Sequences ◽  
Microbe Interactions

ABSTRACT Four strains isolated from tomato and lettuce phyllosphere were sequenced in order to investigate the presence of novel antimicrobial gene clusters and to get a better understanding of plant microbe interactions. These strains comprise two Bacillus strains, one Paenibacillus strain, and one Acinetobacter strain.

scholarly journals Draft Genome Sequences of Six Bacillus Strains and One Brevibacillus Strain Isolated from the Rhizosphere of Perennial Ryegrass (Lolium perenne)

2019 ◽  
Vol 8 (4) ◽  
Author(s):  
Zhibo Li ◽  
Chunxu Song ◽  
Anne de Jong ◽  
Oscar P. Kuipers
Keyword(s):  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Plant Pathogens ◽  
Draft Genome ◽  
Gene Clusters ◽  
Antagonistic Activity ◽  
Genome Sequences ◽  
Modes Of Action ◽  
Bacillus Strains

Seven strains of endospore-forming bacteria with antagonistic activity against a series of plant pathogens were sequenced in order to investigate their antimicrobial gene clusters and antimicrobial modes of action. The selected strains include six Bacillus strains and one Brevibacillus strain.

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