We present here the complete genome sequence of Bacillus subtilis strain DKU_NT_03 isolated from the traditional Korean food chung-gook-jang, which is made from soybeans. This strain was chosen to identify genetic factors with high-quality nattokinase activity. Copyright © 2018 Jeong et al.
Achromobacter spanius is a newly described, non-fermenting, Gram-negative, coccoid pathogen isolated from human blood. Whole-genome sequencing of the A. spanius type strain was performed to investigate the mechanism of pathogenesis of this strain at a genomic level.The complete genome of A. spanius type strain DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing.The complete genome of DSM 23806T consists of one circular DNA chromosome of 6425783bp with a G+C content of 64.26%. The entire genome contains 5804 predicted coding sequences (CDS) and 55 tRNAs. Genomic island (GI) analysis showed that this strain encodes several important pathogenesis- and resistance-related genes.These results strongly suggest that GIs provide some fitness advantages in A. spanius type strain DSM 23806T. This report provides an extensive understanding of A. spanius at a genomic level as well as an understanding of the evolution of A. spanius. Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.
Lactobacillus paracasei EG9 is a strain isolated from well-ripened cheese and accelerates free amino acid production during cheese ripening. Its complete genome sequence was determined using the PacBio RS II platform, revealing a single circular chromosome of 2,927,257 bp, a G+C content of 46.59%, and three plasmids. Copyright © 2018 Asahina et al.
Progesterone (PGT) is not completely removed in conventional treatment plants, and the processing results may have adverse effects on aquatic organisms. In this study, an effective PGT-degradation bacterium, Rhodococcus sp. HYW, was newly isolated from the pharmaceutical plant and was used to augment degradation of PGT. When grown in a mineral medium (MM) containing a trace amount of PGT (500?µg/L) as the sole carbon and energy source, the results show that 99% of PGT was degraded within 1?h and followed the first-order reaction kinetics. Bioaugmentation of PGT-contaminated activated sludge greatly enhanced the PGT degradation rate (~91%) and its derivatives degradation rate were also greatly improved (>83%). The process of PGT degradation in non-bioaugmented PGT-contaminated activated sludge (NBS) and bioaugmentation activated sludge with the bacterial consortium(BS) also conforms to the first-order kinetic model. Furthermore, 12 and 11 biodegradation products for PGT in the NBS and BS were identified using HPLC-LTQ-Orbitrap XL™, respectively. Based on these biodegradation products, two degradation pathways for PGT in NBS and BS were proposed, respectively. Comparing the degradation kinetics and metabolites, it was found that BS degrades PGT more rapidly and can further convert PGT to a small molecular acid. Finally, to reveal the probable cause for the differences in the PGT degradation efficiency and products in the NBS and BS.
Mesorhizobium amorphae CCNWGS0123 was isolated in 2006, from effective nodules of Robinia pseudoacacia L. grown in lead-zinc mine tailing site, in Gansu Province, China. M. amorphae CCNWGS0123 is an aerobic, Gram-negative, non-spore-forming rod strain. This paper characterized M. amorphae CCNWGS0123 and presents its complete genome sequence information and genome annotation. The 7,374,589 bp long genome which encodes 7136 protein-coding genes and 63 RNA coding genes, contains one chromosome and four plasmids. Moreover, a chromosome with no gaps was assembled.
Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. Most existing tools for detecting STR variation with short reads do so within the read length and so are unable to detect the majority of pathogenic expansions. Here we present STRetch, a new genome-wide method to scan for STR expansions at all loci across the human genome. We demonstrate the use of STRetch for detecting STR expansions using short-read whole-genome sequencing data at known pathogenic loci as well as novel STR loci. STRetch is open source software, available from github.com/Oshlack/STRetch .
Lactococcus lactis subsp. lactis is a pathogenic bacterium causing postharvest decay of the cultivated mushroom Pleurotus eryngii, whose pathogenic mechanism is little known. Sequencing of its complete genome is a prerequisite for revealing the molecular mechanism of infection. In this research, the complete genome of SLPE1-3 was obtained using the Single Molecular Real Time (SMRT) sequencing strategy. The genome was analyzed both structurally and functionally. The complete genome of SLPE1-3 consists of a single, circular chromosome (2,522,493 bp; 34.91% GC content) without any plasmid. The results showed the feasibility and superiority of SMRT in bacterial complete-genome research. The genome of SLPE1-3 has the specific features of L. lactis subsp. lactis not just in the phylogenesis and genome structure, but also in functional classification. Compared with L. lactis subsp. lactis IL1403, L. lactis subsp. cremoris MG1363 and L. lactis subsp. lactis KF147, 23 peculiar genes were identified in SLPE1-3 which were involved in lipid metabolism, cell wall biogenesis and some functional enzymes. In addition, 37 potential genes relating to antifungal function were filtered for further mechanism research.
Enterococcus gilvus CR1, isolated from raw cow’s milk, can produce carotenoids. The complete genome sequence of this strain was determined using the PacBio RS II platform. The assembly was found to contain a circular chromosome, including carotenoid biosynthesis genes, and comprises 2,863,043 bp, with a GC content of 41.86% and three plasmids.
Clostridioides (Clostridium) difficile is a spore-forming anaerobic bacte- rium that causes severe intestinal diseases in humans. Here, we report the complete genome sequence of the first C. difficile foodborne type strain (PCR ribotype 078) isolated from food animals in Canada in 2004, which has 100% similarity to the ge- nome sequence of the historic human clinical strain M120.
Salinisphaera sp. strain LB1 was isolated from Lake Brown, Western Aus- tralia, surface water enriched at pH 4.0 and with 5% (wt/vol) NaCl. The complete ge- nome sequence is presented in this report.
The rise of antibiotic resistance in pathogenic bacteria is endangering the efficacy of antibiotics, which consequently results in greater use of silver as a biocide. Chromosomal mapping of the Cus system or plasmid encoded Sil system and their relationship with silver resistance was studied for several gram-negative bacteria. However, only few reports investigated silver detoxification mediated by the Sil system integrated in Escherichia coli chromosome. Accordingly, this work aimed to study the Sil system in E. coli ATCC 8739 and to produce evidence for its role in silver resistance development. Silver resistance was induced in E. coli ATCC 8739 by stepwise passage in culture media containing increasing concentrations of AgNO3. The published genome of E. coli ATCC 8739 contains a region showing strong homology to the Sil system genes. The role of this region in E. coli ATCC 8739 was assessed by monitoring the expression of silC upon silver stress, which resulted in a 350-fold increased expression. De novo sequencing of the whole genome of a silver resistant strain derived from E. coli ATCC 8739 revealed mutations in ORFs putative for SilR and CusR. The silver resistant strain (E. coli AgNO3R) showed constitutive expression of silC which posed a cost of fitness resulting in retarded growth. Furthermore, E. coli AgNO3R exhibited cross-resistance to ciprofloxacin and a slightly increased tolerance to ampicillin. This study demonstrates that E. coli is able to develop resistance to silver, which may pose a threat towards an effective use of silver compounds as antiseptics.
We screened bacteria that use E2 as its sole source of carbon and energy for growth and identified them as Rhodococcus, and we named them DSSKP-R-001. For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. The genomic sketches included a predicted protein-coding gene of approximately 5.4?Mbp with G?+?C content of 68.72% and 5180. The genome of Rhodococcus strain DSSKP-R-001 consists of three replicons: one chromosome and two plasmids of 5.2, 0.09, and 0.09, respectively. The results showed that there were ten steroid-degrading enzymes distributed in the whole genome of the strain. The existence and expression of estradiol-degrading enzymes were verified by PCR and RTPCR. Finally, comparative genomics was used to compare multiple strains of Rhodococcus. It was found that Rhodococcus DSSKP-R-001 had the highest similarity to Rhodococcus sp. P14 and there were 2070 core genes shared with Rhodococcus sp. P14, Rhodococcus jostii RHA1, Rhodococcus opacus B4, and Rhodococcus equi 103S, showing evolutionary homology. In summary, this study provides a comprehensive understanding of the role of Rhodococcus DSSKP-R-001 in estradiol-efficient degradation of these assays for Rhodococcus. DSSKP-R-001 in bioremediation and evolution within Rhodococcus has important meaning.
Acquired genomic structural variants (SVs) are major hallmarks of cancer genomes, but they are challenging to reconstruct from short-read sequencing data. Here we exploited the long reads of the nanopore platform using our customized pipeline, Picky ( https://github.com/TheJacksonLaboratory/Picky ), to reveal SVs of diverse architecture in a breast cancer model. We identified the full spectrum of SVs with superior specificity and sensitivity relative to short-read analyses, and uncovered repetitive DNA as the major source of variation. Examination of genome-wide breakpoints at nucleotide resolution uncovered micro-insertions as the common structural features associated with SVs. Breakpoint density across the genome is associated with the propensity for interchromosomal connectivity and was found to be enriched in promoters and transcribed regions of the genome. Furthermore, we observed an over-representation of reciprocal translocations from chromosomal double-crossovers through phased SVs. We demonstrate that Picky analysis is an effective tool for comprehensive detection of SVs in cancer genomes from long-read data.
Fusarium oxysporum is a pathogenic fungus that infects hundreds of plant species. This paper reports the improved genome assembly of a reference strain, F. oxysporum f. sp. lycopersici Fol4287, a tomato pathogen.
More than half of the genomic landscape in humans and many other organisms is composed of repetitive DNA, which mostly derives from transposable elements (TEs) and viruses. Recent technological advances permit improved assessment of the repetitive content across genomes and newly developed molecular assays have revealed important roles of TEs and viruses in host genome evolution and organization. To update on our current understanding of TE biology and to promote new interdisciplinary strategies for the TE research community, leading experts gathered for the 2nd Uppsala Transposon Symposium on October 4–5, 2018 in Uppsala, Sweden. Using cutting-edge single-molecule and single-cell approaches, research on TEs and other repeats has entered a new era in biological and biomedical research.
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