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Auto Tag: Genome mining

July 7, 2019  |  

Genome sequences of Shewanella baltica and Shewanella morhuae strains isolated from the gastrointestinal tract of freshwater fish.

We present here the genome sequences of Shewanella baltica strain CW2 and Shewanella morhuae strain CW7, isolated from the gastrointestinal tract of Salvelinus namaycush (lean lake trout) and Coregonus clupeaformis (whitefish), respectively. These genome sequences provide insights into the niche adaptation of these specific species in freshwater systems. Copyright © 2018 Castillo et al.

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July 7, 2019  |  

Complete genome sequence of Streptomyces sp. strain BSE7F, a Bali mangrove sediment actinobacterium with antimicrobial activities.

The strain Streptomyces sp. BSE7F, a novel Streptomyces strain isolated from Indonesian mangrove sediment, displays antimicrobial activities against Gram-positive bacteria, Gram-negative bacteria, and yeast. Bioinformatic analysis of the genome sequence revealed the occurrence of 22 biosynthetic gene clusters disclosing the secondary metabolite capacity of strain BSE7F. Copyright © 2018 Handayani et al.

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July 7, 2019  |  

Complete genome sequence of Clostridium kluyveri JZZ applied in Chinese strong-flavor liquor production.

Chinese strong-flavor liquor (CSFL), accounting for more than 70% of both Chinese liquor production and sales, was produced by complex fermentation with pit mud. Clostridium kluyveri, an important species coexisted with other microorganisms in fermentation pit mud (FPM), could produce caproic acid, which was subsequently converted to the key CSFL flavor substance ethyl caproate. In this study, we present the first complete genome sequence of C. kluyveri isolated from FPM. Clostridium kluyveri JZZ contains one circular chromosome and one circular plasmid with length of 4,454,353 and 58,581 bp, respectively. 4158 protein-coding genes were predicted and 2792 genes could be assigned with COG categories. It possesses the pathway predicted for biosynthesis of caproic acid with ethanol. Compared to other two C. kluyveri genomes, JZZ consists of longer chromosome with multiple gene rearrangements, and contains more genes involved in defense mechanisms, as well as DNA replication, recombination, and repair. Meanwhile, JZZ contains fewer genes involved in secondary metabolites biosynthesis, transport, and catabolism, including genes encoding Polyketide Synthases/Non-ribosomal Peptide Synthetases. Additionally, JZZ possesses 960 unique genes with relatively aggregating in defense mechanisms and transcription. Our study will be available for further research about C. kluyveri isolated from FPM, and will also facilitate the genetic engineering to increase biofuel production and improve fragrance flavor of CSFL.

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July 7, 2019  |  

Complete genome sequence of Agrobacterium pusense VsBac-Y9, a bacterial symbiont of the dark septate endophytic fungus Veronaeopsis simplex Y34 with potential for improving fungal colonization in roots.

A Rhizobium-related bacterium (Rhizobium sp. VsBac-Y9) is a symbiont living with the dark septate endophytic (DSE) fungus Veronaeopsis simplex Y34. Co-inoculation of Rhizobium sp. VsBac-Y9 with V. simplex Y34 improves the fungal colonization of tomato roots, resulting in a significant increase in aboveground biomass. This study sequenced the complete genome of this V. simplex-helper bacterium using the PacBio and Illumina MiSeq platforms. Hybrid assembly using SPAdes outputted a circular chromosome, a linear chromid, and a circular plasmid for a total genome 5,321,211 bp in size with a G?+?C content of 59.2%. Analysis of concatenated housekeeping genes (atpD-dnaK-groEL-lepA-recA-rpoB-thrE) and calculation of average nucleotide identity, showed that VsBac-Y9 was affiliated with the species Agrobacterium pusense (syn. Rhizobium pusense). Genome analysis revealed that A. pusense VsBac-Y9 contains a series of genes responsible for the host interactions with both fungus and plant. Such genomic information will provide new insights into developing co-inoculants of endophytic fungus and its symbiotic bacterium in future agricultural innovation. Copyright © 2018 Elsevier B.V. All rights reserved.

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July 7, 2019  |  

Complete genome of Micromonospora sp. strain B006 reveals biosynthetic potential of a Lake Michigan Actinomycete.

Actinomycete bacteria isolated from freshwater environments are an unexplored source of natural products. Here we report the complete genome of the Great Lakes-derived Micromonospora sp. strain B006, revealing its potential for natural product biosynthesis. The 7-megabase pair chromosome of strain B006 was sequenced using Illumina and Oxford Nanopore technologies followed by Sanger sequencing to close remaining gaps. All identified biosynthetic gene clusters (BGCs) were manually curated. Five known BGCs were identified encoding desferrioxamine, alkyl- O-dihydrogeranylmethoxyhydroquinone, a spore pigment, sioxanthin, and diazepinomicin, which is currently in phase II clinical trials to treat Phelan-McDermid syndrome and co-morbid epilepsy. We report here that strain B006 is indeed a producer of diazepinomicin and at yields higher than previously reported. Moreover, 11 of the 16 identified BGCs are orphan, eight of which were transcriptionally active under the culture condition tested. Orphan BGCs include an enediyne polyketide synthase and an uncharacteristically large, 36-module polyketide synthase-nonribosomal peptide synthetase BGC. We developed a genetics system for Micromonospora sp. B006 that will contribute to deorphaning BGCs in the future. This study is one of the few attempts to report the biosynthetic capacity of a freshwater-derived actinomycete and highlights this resource as a potential reservoir for new natural products.

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July 7, 2019  |  

Near- complete genome sequences of Streptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines.

Streptomyces sp. strains AC1-42T and AC1-42W, isolated from bat guano from Cabalyorisa Cave, Mabini, Pangasinan, Philippines, are active against Bacillus subtilis subsp. subtilis KCTC 3135T. The near-complete genome sequences reported here represent a possible source of ribosomally synthesized, posttranslationally mod- ified peptides, such as lantipeptides, bacteriocins, linaridin, and a lasso peptide.

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July 7, 2019  |  

Draft genome sequence of the xanthocidin-producing strain Streptomyces sp. AcE210, isolated from a root nodule of Alnus glutinosa (L.).

Streptomyces sp. strain AcE210 exhibited antibacterial activity toward Gram-positive microorganisms and turned out to be a rare producer of the special- ized metabolite xanthocidin. The 10.6-Mb draft genome sequence gives insight into the complete specialized metabolite production capacity and builds the basis to find and locate the biosynthetic gene cluster of xanthocidin.

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July 7, 2019  |  

Genome analysis of Vallitalea guaymasensis strain L81 isolated from a deep-sea hydrothermal vent system.

Abyssivirga alkaniphila strain L81T, recently isolated from a black smoker biofilm at the Loki’s Castle hydrothermal vent field, was previously described as a mesophilic, obligately anaerobic heterotroph able to ferment carbohydrates, peptides, and aliphatic hydrocarbons. The strain was classified as a new genus within the family Lachnospiraceae. Herein, its genome is analyzed and A. alkaniphila is reassigned to the genus Vallitalea as a new strain of V. guaymasensis, designated V. guaymasensis strain L81. The 6.4 Mbp genome contained 5651 protein encoding genes, whereof 4043 were given a functional prediction. Pathways for fermentation of mono-saccharides, di-saccharides, peptides, and amino acids were identified whereas a complete pathway for the fermentation of n-alkanes was not found. Growth on carbohydrates and proteinous compounds supported methane production in co-cultures with Methanoplanus limicola. Multiple confurcating hydrogen-producing hydrogenases, a putative bifurcating electron-transferring flavoprotein—butyryl-CoA dehydrogenase complex, and a Rnf-complex form a basis for the observed hydrogen-production and a putative reverse electron-transport in V. guaymasensis strain L81. Combined with the observation that n-alkanes did not support growth in co-cultures with M. limicola, it seemed more plausible that the previously observed degradation patterns of crude-oil in strain L81 are explained by unspecific activation and may represent a detoxification mechanism, representing an interesting ecological function. Genes encoding a capacity for polyketide synthesis, prophages, and resistance to antibiotics shows interactions with the co-occurring microorganisms. This study enlightens the function of the fermentative microorganisms from hydrothermal vents systems and adds valuable information on the bioprospecting potential emerging in deep-sea hydrothermal systems.

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July 7, 2019  |  

Complete genome sequence of Arcticibacterium luteifluviistationis SM1504 T, a cytophagaceae bacterium isolated from Arctic surface seawater

Arcticibacterium luteifluviistationis SM1504Twas isolated from Arctic surface seawater and classified as a novel genus of the phylum Bacteroides. To date, no Arcticibacterium genomes have been reported, their genomic compositions and metabolic features are still unknown. Here, we reported the complete genome sequence of A. luteifluviistationis SM1504T, which comprises 5,379,839bp with an average GC content of 37.20%. Genes related to various stress (such as radiation, osmosis and antibiotics) resistance and gene clusters coding for carotenoid and flexirubin biosynthesis were detected in the genome. Moreover, the genome contained a 245-kb genomic island and a 15-kb incomplete prophage region. A great percentage of proteins belonging to carbohydrate metabolism especially in regard to polysaccharides utilization were found. These related genes and metabolic characteristics revealed genetic basis for adapting to the diverse extreme Arctic environments. The genome sequence of A. luteifluviistationis SM1504Talso implied that the genus Arcticibacterium may act as a vital organic carbon matter decomposer in the Arctic seawater ecosystem.

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July 7, 2019  |  

Complete genome sequence of the polymyxin E (colistin)-producing Paenibacillus sp. strain B-LR.

Paenibacillus bacteria are recovered from varied niches, including human lung, rhizosphere, marine sediments, and hemolymph. Paenibacilli can have plant growth-promoting activities and be antibiotic producers. They can produce exopolysaccharides and enzymes of industrial interest. Illumina and PacBio reads were used to produce a complete genome sequence of the colistin producer Paenibacillus sp. strain B-LR.

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July 7, 2019  |  

Velez bacillusL-1The pear Botrytis cinerea and Penicillium bacteria of suppression role evaluation and all Genome Analysis

[Objective] Clear Velez bacillus(Bacillus S rDNA Sequence) L-1The pear Botrytis cinerea and Penicillium bacteria of suppression role clear Bacteria L-1Sterile fermentation broth antagonistic activity of stability and may be of Antagonistic mechanism. [Methods] by in vitro determination, living determination and pathogenic bacteria mycelium morphology observation evaluation StrainL-1The pear Botrytis cinerea and Penicillium bacteria of antagonistic activity. To pear Botrytis cinerea bacteria for try pathogenic bacteria use Oxford Cup method determination StrainL-1Sterile fermentation broth antagonistic activity of stability. UsePacbio rsiiThree generations sequencing technology determinationL-1Of all gene sequence will all gene sequence and gene protein sequence databaseBLASTComparison Analysis prediction StrainL-1May be of secondary metabolism product and potential of role mechanism. [Results] The StrainL-1The pear Botrytis cinerea and Penicillium bacteria of living inhibition rate respectively92.88%And77.47%Can caused by pathogenic bacteria mycelium enlargement, deformity. StrainL-1In10% NaClOf culture medium in can still normal growth its sterile fermentation broth high temperature resistant, acid, alkali, UV irradiation and protease degradation on pathogenic bacteria has stability of antagonistic activity. All gene sequence analysis results showed that strainL-1Yes112A Gene Involved in the many kinds of carbon source of metabolism can use many kinds of carbon source the growth; containing involved in spermidine, trehalose and strain stress resistance related compounds synthesis of gene; secondary metabolism prediction results display:L-1Containing SynthesisSurfactin,Fengycin,Bacillibactin,Bacillaene,Macolactin,Difficidin,BacilysinAnd many kinds of peptide chitosan and polyketide sugar resistance compounds of gene cluster and can degradation pathogenic bacteria cell wallß-1,3-Glucanase and chitinase related of gene; in addition StrainL-1Containing generation acetoin and can induced Plant Resistance of gene. [Conclusion] StrainL-1Can effective antagonistic many kinds of pear of after disease resistance strong antagonistic activity stability prediction StrainL-1Can by producing many kinds of antagonistic activity compounds and cell wall hydrolysis enzymes and induced Plant Resistance implementation disease prevention effect has very big of application potential.

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