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July 7, 2019

Complete genome sequence of Amycolatopsis orientalis CPCC200066, the producer of norvancomycin.

Amycolatopsis orientalis CPCC200066 is an actinomycete exploited commercially in China for the production of norvancomycin, an important glycopeptide antibiotic structurally close to the well-known vancomycin. The availability of the complete genome sequence of CPCC200066 would greatly strengthen our understanding of the regulation pattern of norvancomycin biosynthesis and ultimately improve its production, as well as potentiate discoveries of novel bioactive compounds. Here we report the complete genome sequence of A. orientalis CPCC200066, a circular chromosome consisting of 9,490,992bp. Forty putative secondary metabolite biosynthetic gene clusters, including norvancomycin, were predicted, covering 20.3% of the whole genome. To facilitate genetic manipulation of this strain, an efficient transformation system was established by constructing a novel integrative vector pIMBT1, which could be transferred into CPCC200066 by electroporation with high efficiency. FBT1 attB sites were also identified in other known Amycolatopsis genomes, indicating pIMBT1’s prospect to be a novel vector for genus Amycolatopsis. Copyright © 2017 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of the gamma-aminobutyric acid-producing strain Streptococcus thermophilus APC151.

Here is presented the whole-genome sequence of Streptococcus thermophilus APC151, isolated from a marine fish. This bacterium produces gamma-aminobutyric acid (GABA) in high yields and is biotechnologically suitable to produce naturally GABA-enriched biofunctional yogurt. Its complete genome comprises 2,097 genes and 1,839,134 nucleotides, with an average G+C content of 39.1%. Copyright © 2017 Linares et al.

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July 7, 2019

Complete genome sequence of Bordetella pertussis Pelita III, the production strain for an Indonesian whole-cell pertussis vaccine.

PT Bio Farma, the sole World Health Organization-approved Indonesian vaccine producer, manufactures a whole-cell whooping cough vaccine (wP) that, as part of a pentavalent diphtheria-tetanus-pertussis/hepatitis B/Haemophilus influenzae b (DTP/HB/Hib) vaccine, is used in Indonesia and many other countries. We report here the whole-genome sequence for Bordetella pertussis Pelita III, PT Bio Farma’s wP production strain. Copyright © 2017 Efendi et al.

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July 7, 2019

Complete genome sequence of Lysinibacillus sphaericus LMG 22257, a strain with ureolytic activity inducing calcium carbonate precipitation.

Microbiologically induced calcium carbonate precipitation shows the potential for use in bioremediation and construction consolidation, but the efficiency of this process must be improved. Lysinibacillus sphaericus LMG 22257 is a gram-positive ureolytic strain that has recently been applied for consolidating construction by mediating calcium carbonate precipitation. The complete genome sequence of L. sphaericus LMG 22257 is 3,436,578 base pairs with a GC content of 38.99%. The urea degradation pathway and genes related to extracellular polymeric substance biosynthesis were also identified. The strain can tolerate high alkalinity (pH up to 10) and high urea concentration (up to 3M). These findings provide insights into the microbiologically induced carbonate precipitation and extend the application of the metabolic potential of L. sphaericus LMG 22257 for bioremediation. Copyright © 2017 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of a versatile hydrocarbon degrader, Pseudomonas aeruginosa DN1 isolated from petroleum-contaminated soil.

Pseudomonas aeruginosa DN1 was isolated from a petroleum-contaminated soil from Changqing Oilfield with its capability to degrade high molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) and crude oil. Herein, the whole genome sequence analysis of P. aeruginosa strain DN1 was reported, consisting of a size of 6,641,902 bp chromosome assembled genome (67.09 mol% G + C content) and a 317,349 bp plasmid assembled genome (57.01 mol% G + C content). According to the genome information, strain DN1 encodes various genes related to degradation of aliphatic hydrocarbons and aromatic compounds. In addition, DN1 contains gene clusters for biosynthesis and regulation of biosurfactant rhamnolipids. These genes may serve as a basis of further elucidation of the genetic background of this promising strain, and provide insights into investigating the metabolic and regulatory mechanisms of hydrocarbon biodegradation.

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July 7, 2019

The evolutionary life cycle of the polysaccharide biosynthetic gene cluster based on the Sphingomonadaceae.

Although clustering of genes from the same metabolic pathway is a widespread phenomenon, the evolution of the polysaccharide biosynthetic gene cluster remains poorly understood. To determine the evolution of this pathway, we identified a scattered production pathway of the polysaccharide sanxan by Sphingomonas sanxanigenens NX02, and compared the distribution of genes between sphingan-producing and other Sphingomonadaceae strains. This allowed us to determine how the scattered sanxan pathway developed, and how the polysaccharide gene cluster evolved. Our findings suggested that the evolution of microbial polysaccharide biosynthesis gene clusters is a lengthy cyclic process comprising cluster 1???scatter???cluster 2. The sanxan biosynthetic pathway proved the existence of a dispersive process. We also report the complete genome sequence of NX02, in which we identified many unstable genetic elements and powerful secretion systems. Furthermore, nine enzymes for the formation of activated precursors, four glycosyltransferases, four acyltransferases, and four polymerization and export proteins were identified. These genes were scattered in the NX02 genome, and the positive regulator SpnA of sphingans synthesis could not regulate sanxan production. Finally, we concluded that the evolution of the sanxan pathway was independent. NX02 evolved naturally as a polysaccharide producing strain over a long-time evolution involving gene acquisitions and adaptive mutations.

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July 7, 2019

Genomic and phenotypic analyses of Pseudomonas psychrotolerans PRS08-11306 reveal a turnerbactin biosynthesis gene cluster that contributes to nitrogen fixation.

Plant-microbe interactions can provide agronomic benefits, such as enhancing nutrient uptake and providing fixed nitrogen. The Pseudomonas psychrotolerans strain PRS08-11306 was isolated from rice seeds and can enhance plant growth. Here, we analyzed the P. psychrotolerans genome, which is ~5Mb, with 4389 coding sequences, 77 tRNAs, and 7 rRNAs. Genome analysis identified a cluster of turnerbactin biosynthetic genes, which are responsible for the production of a catecholate siderophore and contribute to nitrogen fixation for the host. Analysis of the transcription factor mutant ?rpoS, which does not express this gene cluster, confirmed the relationship between the gene cluster and siderophore production. The nitrogen fixation characteristics of the cluster were confirmed in a plant growth-promoting experiment. The annotated full genome sequence of this strain sheds light on the role of P. psychrotolerans PRS08-11306 as a plant beneficial bacterium. Copyright © 2017. Published by Elsevier B.V.

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July 7, 2019

The complete chloroplast genome sequence of tung tree (Vernicia fordii): Organization and phylogenetic relationships with other angiosperms.

Tung tree (Vernicia fordii) is an economically important tree widely cultivated for industrial oil production in China. To better understand the molecular basis of tung tree chloroplasts, we sequenced and characterized its genome using PacBio RS II sequencing platforms. The chloroplast genome was sequenced with 161,528?bp in length, composed with one pair of inverted repeats (IRs) of 26,819?bp, which were separated by one small single copy (SSC; 18,758?bp) and one large single copy (LSC; 89,132?bp). The genome contains 114 genes, coding for 81 protein, four ribosomal RNAs and 29 transfer RNAs. An expansion with integration of an additional rps19 gene in the IR regions was identified. Compared to the chloroplast genome of Jatropha curcas, a species from the same family, the tung tree chloroplast genome is distinct with 85 single nucleotide polymorphisms (SNPs) and 82 indels. Phylogenetic analysis suggests that V. fordii is a sister species with J. curcas within the Eurosids I. The nucleotide sequence provides vital molecular information for understanding the biology of this important oil tree.

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July 7, 2019

Complete genome sequence of the aerobically denitrifying thermophilic bacterium Chelatococcus daeguensis TAD1

Chelatococcus daeguensis TAD1 is a themophilic bacterium isolated from a biotrickling filter used to treat NOx in Ruiming Power Plant, located in Guangzhou, China, which shows an excellent aerobic denitrification activity at high temperature. The complete genome sequence of this strain was reported in the present study. Genes related to the aerobic denitrification were identified through whole genome analysis. This work will facilitate the mechanism of aerobic denitrification and provide evidence for its potential application in the nitrogen removal.

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July 7, 2019

Biofilm formation potential of heat-resistant Escherichia coli dairy isolates and the complete genome of multidrug-resistant, heat-resistant strain FAM21845.

We tested the biofilm formation potential of 30 heat-resistant and 6 heat-sensitive Escherichia coli dairy isolates. Production of curli and cellulose, static biofilm formation on polystyrene (PS) and stainless steel surfaces, biofilm formation under dynamic conditions (Bioflux), and initial adhesion rates (IAR) were evaluated. Biofilm formation varied greatly between strains, media, and assays. Our results highlight the importance of the experimental setup in determining biofilm formation under conditions of interest, as correlation between different assays was often not a given. The heat-resistant, multidrug-resistant (MDR) strain FAM21845 showed the strongest biofilm formation on PS and the highest IAR and was the only strain that formed significant biofilms on stainless steel under conditions relevant to the dairy industry, and it was therefore fully sequenced. Its chromosome is 4.9 Mb long, and it harbors a total of five plasmids (147.2, 54.2, 5.8, 2.5, and 1.9 kb). The strain carries a broad range of genes relevant to antimicrobial resistance and biofilm formation, including some on its two large conjugative plasmids, as demonstrated in plate mating assays.IMPORTANCE In biofilms, cells are embedded in an extracellular matrix that protects them from stresses, such as UV radiation, osmotic shock, desiccation, antibiotics, and predation. Biofilm formation is a major bacterial persistence factor of great concern in the clinic and the food industry. Many tested strains formed strong biofilms, and especially strains such as the heat-resistant, MDR strain FAM21845 may pose a serious issue for food production. Strong biofilm formation combined with diverse resistances (some encoded on conjugative plasmids) may allow for increased persistence, coselection, and possible transfer of these resistance factors. Horizontal gene transfer may conceivably occur in the food production setting or the gastrointestinal tract after consumption. Copyright © 2017 Marti et al.

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July 7, 2019

Complete genome sequencing of Streptomyces sp. strain MOE7, which produces an extracellular polysaccharide with antioxidant and antitumor activities.

Streptomyces sp. strain MOE7 is a Gram-positive filamentous bacterium isolated from agricultural soil in Columbia, Missouri, USA. Strain MOE7 produces an extracellular polysaccharide with antioxidant and antitumor activities. Through PacBio RSII sequencing, the MOE7 genome was found to be a linear chromosome of 8,399,509 bp with 6,782 protein-coding sequences. Copyright © 2017 Elnahas et al.

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July 7, 2019

Complete genome sequence of Escherichia coli BLR(DE3), a recA-deficient derivative of E. coli BL21(DE3).

Escherichia coli BLR(DE3) is a commercially available recA-deficient derivative of BL21(DE3), one of the most widely used strains for recombinant protein expression. Here, we present the full-genome sequence of BLR(DE3) and highlight additional differences with its parent strain BL21(DE3) which were previously unreported but may affect its physiology. Copyright © 2017 Goffin and Dehottay.

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July 7, 2019

Draft genome sequence of Microbacterium foliorum strain 122 isolated from a plant growing in a chronically hydrocarbon-contaminated site.

Microbacterium foliorum strain 122 is a bacterial endophyte isolated from a Dactylis glomerata plant growing in a natural oil seep soil located in Oil Springs, Ontario, Canada. We present here a draft genome sequence of an endophytic strain that has promising potential in hydrocarbon degradation and plant growth promotion. Copyright © 2017 Lumactud et al.

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