We report here the genome sequence of a multidrug-resistant Klebsiella pneumoniae strain, which caused an outbreak in a neonatal ward in 2011. The genome consists of a single chromosome (5,278 kb) and three plasmids (362 kb, 5 kb, and 4 kb). Copyright © 2015 Becker et al.
Bacillus subtilis, which belongs to the phylum Firmicutes, is the most widely studied Gram-positive model organism. It is found in a wide variety of environments and is particularly abundant in soils and in the gastrointestinal tracts of ruminants and humans. Here, we present the complete genome sequence of the newly described B. subtilis strain UD1022. The UD1022 genome consists of a 4.025-Mbp chromosome, and other major findings from our analysis will provide insights into the genomic basis of it being a plant growth-promoting rhizobacterium (PGPR) with biocontrol potential. Copyright © 2015 Bishnoi et al.
Edwardsiella tarda is a Gram-negative facultative anaerobe that has been isolated from fish, reptiles, amphibians, and mammals, including humans. This is a report of the complete and annotated genome of isolate FL95-01, recovered from channel catfish (Ictalurus punctatus). Copyright © 2015 Reichley et al.
Among the Enterobacteriacea Klebsiella pneumoniae is for the most part obtained from clinical samples and most probable cause of a typical form of primary pneumonia. It can also responsible for a variety of extrapulmonary infections, counting enteritis and meningitis in infants, urinary tract infections in children and adults and septicaemia in all age groups. Like wise these pathogens are significant cause of hospital acquired infections right through the world. The remarkable increase in the prevalence of antibiotic resistance in bacteria noticed in recent years represents a considerable challenge to public health microbiology worldwide. Klebsiellae have a tendency to possess antibiotic resistant plasmids; as a result, infections with multiple antibiotic-resistant strains can be likely. Only some degree of studies had been accounted in this regard from Nepal. The study was performed from January 1999 to March 2001. To come upon the existing dated antibiotic resistance pattern of Klebsiella pneumoniae. The study was carried out at TUTH laboratory with the objectives to ascertain the prevalence of Klebsiella pneumoniae in conjunction with to calculate the significance antibiotic resistance correlation between various antibiotics. By which the later 15 years analysis of antibiotic resistance was evaluated with comparison to this study.In this scrutiny the result was established that the numbers of total isolates including both klebsiella pneumoniae and other Kebsiella species were 62 from urine samples, 78 from pus samples and 96 from sputum samples and 34 from other miscellaneous samples. In this study positive culture for Klebsiella pneumoniae was 32.83% for sputum samples, 23.62.% for urine samples and 24.57% for pus samples. Majority of the strains isolated were sensitive to ß- lactamases, Floroquinolones, Aminoglycosides, Tetracycline and Cotrimoxazole, combined antibiotics. The current review study from 1999 to 2014 discloses the frequency of infections due to klebsiella pneumoniae strains in the hospitalized patients and their tendency towards antibiotic resistance was on the increase. Large quantity of antibiotics exploited for human therapy has resulted in the selection of pathogenic bacteria resistant to multiple antimicrobial drugs. This has become a vital clinical and infection control challenge, particularly in resource-limited settings with far above the ground a raising rate of antimicrobial resistance.
Burkholderia pyrrocinia 2327(T) (=DSM 10685(T), having an origin history as a strain Fujisawa Pharm 2327(T) from Fujisawa Pharmaceutical Co., Ltd.) is the first industrial bacterium for the isolation of antifungal antibiotic pyrrolnitrin. Herein, we present the first complete genome sequence of strain 2327(T), which consists of three circular chromosomes with one plasmid for the total 7,961,346bp sized genome with a GC content of 66.5%. This information will provide better understanding of molecular mechanisms in strain 2327(T), leading the insight of whole-cell system for the practical application of strain with the virtue of antibiotic capacity. Copyright © 2015 Elsevier B.V. All rights reserved.
We introduce FinisherSC, a repeat-aware and scalable tool for upgrading de novo assembly using long reads. Experiments with real data suggest that FinisherSC can provide longer and higher quality contigs than existing tools while maintaining high concordance.The tool and data are available and will be maintained at http://kakitone.github.io/finishingTool/: dntse@stanford.eduSupplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Pseudomonas stutzeri SLG510A3-8, isolated from oil-contaminated soil in Shengli Oilfield, China, has the potential to be applied for microbial enhanced oil recovery. Here, we reported the complete genome sequence of this bacterium. It has a 4,650,155bp circular chromosome encoding 4450 genes, and the genome consists of genes that are involved in denitrification, chemotaxis, benzoate degradation, molecule transportation, and other functions. The genome contains a complete set of genes for type I secretion system in comparison with sequences of other P. stutzeri strains. Copyright © 2015 Elsevier B.V. All rights reserved.
Lactobacillus salivarius Ren (LsR) (CGMCC No. 3606) is a probiotic strain that was isolated from the feces of a healthy centenarian living in Bama, Guangxi, China. Previous studies have shown that this strain decreases 4-nitroquinoline 1-oxide (4-NQO)-induced genotoxicity in vitro. It also suppresses 4-NQO-induced oral carcinogenesis and 1,2-dimethylhydrazine (DMH)-induced colorectal carcinogenesis, and therefore may be used as an adjuvant therapeutic agent for cancer. Here, we report the complete genome sequence of LsR that consists of a circular chromosome of 1751,565bp and two plasmids (pR1, 176,951bp; pR2, 49,848bp). Copyright © 2015 Elsevier B.V. All rights reserved.
Lactobacillus helveticus MB2-1 is a probiotic bacterium producing exopolysaccharides (EPS), which was isolated from traditional Sayram ropy fermented milk in southern Xinjiang, China. The genome consists of a circular 2,084,058bp chromosome with no plasmid. The genome sequence indicated that this strain includes a 15.20kb gene cluster involved in EPS biosynthesis. Genome sequencing information has provided the basis for understanding the potential molecular mechanism behind the EPS production. Copyright © 2015 Elsevier B.V. All rights reserved.
A hybrid sequence assembly of the complete Mycoplasma synoviae type strain WVU 1853T genome was compared to that of strain MS53. The findings support prior conclusions about M. synoviae, based on the genome of that otherwise uncharacterized field strain, and provide the first evidence of epigenetic modifications in M. synoviae.
Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.
Bordetella pertussis is the causative agent of whooping cough, a highly contagious, acute respiratory illness that has seen resurgence despite the use of vaccines. We present the complete genome sequence of a clinical strain of B. pertussis, D420, which is representative of a currently circulating clade of this pathogen. Copyright © 2015 Boinett et al.
Aliivibrio wodanis and Moritella viscosa have often been isolated concurrently from fish with winter-ulcer disease. Little is known about the interaction between the two bacterial species and how the presence of one bacterial species affects the behaviour of the other.The impact on bacterial growth in co-culture was investigated in vitro, and the presence of A. wodanis has an inhibitorial effect on M. viscosa. Further, we have sequenced the complete genomes of these two marine Gram-negative species, and have performed transcriptome analysis of the bacterial gene expression levels from in vivo samples. Using bacterial implants in the fish abdomen, we demonstrate that the presence of A. wodanis is altering the gene expression levels of M. viscosa compared to when the bacteria are implanted separately.From expression profiling of the transcriptomes, it is evident that the presence of A. wodanis is altering the global gene expression of M. viscosa. Co-cultivation studies showed that A. wodanis is impeding the growth of M. viscosa, and that the inhibitorial effect is not contact-dependent.
Streptomyces leeuwenhoekii, isolated from the hyperarid Atacama Desert, produces the new ansamycin-like compounds chaxamycins A to D, which possess potent antibacterial activity and moderate antiproliferative activity. We report the development of genetic tools to manipulate S. leeuwenhoekii and the identification and partial characterization of the 80.2-kb chaxamycin biosynthesis gene cluster, which was achieved by both mutational analysis in the natural producer and heterologous expression in Streptomyces coelicolor A3(2) strain M1152. Restoration of chaxamycin production in a nonproducing ?cxmK mutant (cxmK encodes 3-amino-5-hydroxybenzoic acid [AHBA] synthase) was achieved by supplementing the growth medium with AHBA, suggesting that mutasynthesis may be a viable approach for the generation of novel chaxamycin derivatives. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
Bacillus thuringiensis is an important microbial biopesticide for controlling agricultural pests by the production of toxic parasporal crystals proteins.Here,we report the finished annotated genome sequence of B. thuringiensis YC-10,which is highly toxic to nematodes.The complete genome sequence consists of a circular chromosome and nine circular plasmids,which the biggest plasmid harbors six parasporal crystals proteins genes consisting of cry1Aa, cry1Ac, cry1Ia, cry2Aa, cry2Ab and cryB1. The crystals proteins of Cry1Ia and Cry1Aa have high nematicidal activity against Meloidogyne incognita. Copyright © 2015 Elsevier B.V. All rights reserved.
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