801
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Vincent AT, Trudel MV, Freschi L, Nagar V, Gagné-Thivierge C, Levesque RC, Charette SJ. Increasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida. BMC Genomics 2016; 17:44. [PMID: 26753691 PMCID: PMC4709979 DOI: 10.1186/s12864-016-2381-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/06/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date. RESULTS We sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy. CONCLUSION Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.
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Affiliation(s)
- Antony T Vincent
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
| | - Mélanie V Trudel
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
| | - Luca Freschi
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Quebec City, QC, Canada.
| | - Vandan Nagar
- Food Technology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
| | - Cynthia Gagné-Thivierge
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
| | - Roger C Levesque
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Département de microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Quebec City, QC, Canada.
| | - Steve J Charette
- Institut de biologie intégrative et des systèmes, Pavillon Charles-Eugène-Marchand, Université Laval, 1030 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
- Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Québec (Hôpital Laval), 2725 Chemin Sainte-Foy, Quebec City, G1V 4G5, QC, Canada.
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, 1045 avenue de la Médecine, Quebec City, G1V 0A6, QC, Canada.
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802
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Genome Sequences of Three Pseudoalteromonas Strains (P1-8, P1-11, and P1-30), Isolated from the Marine Hydroid Hydractinia echinata. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01380-15. [PMID: 26659670 PMCID: PMC4675935 DOI: 10.1128/genomea.01380-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The genomes of three Pseudoalteromonas strains (P1-8, P1-11, and P1-30) were sequenced and assembled. These genomes will inform future study of the genes responsible for the production of biologically active compounds responsible for these strains’ antimicrobial, biofouling, and algicidal activities.
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803
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Draft Whole-Genome Sequence of Serratia marcescens Strain RM66262, Isolated from a Patient with a Urinary Tract Infection. GENOME ANNOUNCEMENTS 2015; 3:3/6/e01423-15. [PMID: 26634764 PMCID: PMC4669405 DOI: 10.1128/genomea.01423-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Serratia marcescens strains are ubiquitous bacteria isolated from environmental niches and also constitute emergent nosocomial opportunistic pathogens. Here, we report on the draft genome sequence of S. marcescens strain RM66262, which was isolated from a patient with urinary tract infection in the Bacteriology Service of the Rosario National University, Rosario, Argentina.
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804
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Prospective Whole-Genome Sequencing Enhances National Surveillance of Listeria monocytogenes. J Clin Microbiol 2015; 54:333-42. [PMID: 26607978 PMCID: PMC4733179 DOI: 10.1128/jcm.02344-15] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/10/2015] [Indexed: 12/31/2022] Open
Abstract
Whole-genome sequencing (WGS) has emerged as a powerful tool for comparing bacterial isolates in outbreak detection and investigation. Here we demonstrate that WGS performed prospectively for national epidemiologic surveillance of Listeria monocytogenes has the capacity to be superior to our current approaches using pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable-number tandem-repeat analysis (MLVA), binary typing, and serotyping. Initially 423 L. monocytogenes isolates underwent WGS, and comparisons uncovered a diverse genetic population structure derived from three distinct lineages. MLST, binary typing, and serotyping results inferred in silico from the WGS data were highly concordant (>99%) with laboratory typing performed in parallel. However, WGS was able to identify distinct nested clusters within groups of isolates that were otherwise indistinguishable using our current typing methods. Routine WGS was then used for prospective epidemiologic surveillance on a further 97 L. monocytogenes isolates over a 12-month period, which provided a greater level of discrimination than that of conventional typing for inferring linkage to point source outbreaks. A risk-based alert system based on WGS similarity was used to inform epidemiologists required to act on the data. Our experience shows that WGS can be adopted for prospective L. monocytogenes surveillance and investigated for other pathogens relevant to public health.
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805
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Skarp CPA, Akinrinade O, Nilsson AJE, Ellström P, Myllykangas S, Rautelin H. Comparative genomics and genome biology of invasive Campylobacter jejuni. Sci Rep 2015; 5:17300. [PMID: 26603914 PMCID: PMC4658567 DOI: 10.1038/srep17300] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 10/28/2015] [Indexed: 12/28/2022] Open
Abstract
Campylobacter jejuni is a major pathogen in bacterial gastroenteritis worldwide and can cause bacteremia in severe cases. C. jejuni is highly structured into clonal lineages of which the ST677CC lineage has been overrepresented among C. jejuni isolates derived from blood. In this study, we characterized the genomes of 31 C. jejuni blood isolates and 24 faecal isolates belonging to ST677CC in order to study the genome biology related to C. jejuni invasiveness. We combined the genome analyses with phenotypical evidence on serum resistance which was associated with phase variation of wcbK; a GDP-mannose 4,6-dehydratase involved in capsular biosynthesis. We also describe the finding of a Type III restriction-modification system unique to the ST-794 sublineage. However, features previously considered to be related to pathogenesis of C. jejuni were either absent or disrupted among our strains. Our results refine the role of capsule features associated with invasive disease and accentuate the possibility of methylation and restriction enzymes in the potential of C. jejuni to establish invasive infections. Our findings underline the importance of studying clinically relevant well-characterized bacterial strains in order to understand pathogenesis mechanisms important in human infections.
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Affiliation(s)
- C. P. A. Skarp
- Department of Medical Sciences, Clinical Microbiology, Uppsala
University, Uppsala, Sweden
| | - O. Akinrinade
- Institute of Clinical Medicine, University of Helsinki,
Helsinki, Finland
- Institute of Biomedicine, University of Helsinki,
Helsinki, Finland
| | - A. J. E. Nilsson
- Department of Medical Sciences, Clinical Microbiology, Uppsala
University, Uppsala, Sweden
| | - P. Ellström
- Department of Medical Sciences, Clinical Microbiology, Uppsala
University, Uppsala, Sweden
| | - S. Myllykangas
- Institute of Biomedicine, University of Helsinki,
Helsinki, Finland
| | - H. Rautelin
- Department of Medical Sciences, Clinical Microbiology, Uppsala
University, Uppsala, Sweden
- Department of Bacteriology and Immunology, University of
Helsinki, Helsinki, Finland
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806
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Attéré SA, Vincent AT, Trudel MV, Chanut R, Charette SJ. Diversity and Homogeneity among Small Plasmids of Aeromonas salmonicida subsp. salmonicida Linked with Geographical Origin. Front Microbiol 2015; 6:1274. [PMID: 26635745 PMCID: PMC4655240 DOI: 10.3389/fmicb.2015.01274] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 10/31/2015] [Indexed: 01/31/2023] Open
Abstract
Furunculosis, which is caused by Aeromonas salmonicida subsp. salmonicida, is a major salmonid disease in fish farms worldwide. Several plasmids found in this bacterium confer phenotypes such drug resistance and virulence. Small plasmids (pAsa1, pAsa2, pAsa3, and pAsal1) related to ColE1- and ColE2-type replicons are usually present in its normal plasmidome. In the present study, with the objective to investigate if these plasmids display particularities related to the origin of the isolates bearing them, a total of 153 isolates, including 78 new and 75 previously described, were analyzed for the presence of small plasmids by PCR and DNA restriction fragment profiling. A geographical dichotomy between Canadian and European isolates for their propensity to do not have pAsa3 or pAsal1 was found. In addition, the genotyping analysis led to the identification of two European isolates harboring an unusual pAsal1. An investigation by next-generation sequencing (NGS) of these two isolates shed light on two pAsal1 variants (pAsal1C and pAsal1D). As with pAsal1B, another pAsal1 variant previously described, these two new variants bore a second insertion sequence (ISAS5) in addition to the usual ISAS11. The characterization of these variants suggested that they could predominate over the wild-type pAsal1 in stressful conditions such as growth at temperatures of 25°C and above. To obtain a comprehensive portrait of the mutational pressure on small plasmids, 26 isolates whose DNA had been sequenced by NGS were investigated. pAsa3 and pAsal1 were more prone to mutations than pAsa1 and pAsa2, especially in the mobA gene, which encodes a relaxase and a primase. Lastly, the average copy number of each plasmid per cell was assessed using raw sequencing data. A clear trend with respect to the relative proportion per cell of each plasmid was identified. Our large-scale study revealed a geographical dichotomy in small plasmid repertoire in addition to a clear trend for pAsa3 and pAsal1 to be more frequently altered. Moreover, we present the discovery of two new variants of pAsal1: pAsal1C and pAsal1D.
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Affiliation(s)
- Sabrina A Attéré
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Antony T Vincent
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Mélanie V Trudel
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Romain Chanut
- Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
| | - Steve J Charette
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval Quebec City, QC, Canada ; Institut de Biologie Intégrative et des Systèmes, Université Laval Quebec City, QC, Canada ; Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec Quebec City, QC, Canada
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807
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Draft Genome Sequence of Pseudomonas aeruginosa ATCC 9027 (DSM 1128), an Important Rhamnolipid Surfactant Producer and Sterility Testing Strain. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01259-15. [PMID: 26514765 PMCID: PMC4626611 DOI: 10.1128/genomea.01259-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Pseudomonas aeruginosa ATCC 9027 (DSM1128) is often used as a quality-control strain for sterility and microbial contamination testing and is an important biosurfactant producer. Here, we present the 6.4-Mb draft genome sequence and highlight some genomic differences to its closest relative, P. aeruginosa strain PA7.
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808
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Draft Genome Sequence of Bacillus licheniformis S127, Isolated from a Sheep Udder Clinical Infection. GENOME ANNOUNCEMENTS 2015; 3:3/5/e00971-15. [PMID: 26430024 PMCID: PMC4574362 DOI: 10.1128/genomea.00971-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Bacillus licheniformis is a Gram-positive biofilm- and endospore-forming bacterium, which contaminates dairy products and can be pathogenic to humans. The draft genome sequencing for B. licheniformis strain S127 is reported here, providing genetic data relevant to the ability of this strain to sustain its survival in the dairy industry.
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809
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Complete Genome Sequence of Bifidobacterium actinocoloniiforme Type Strain DSM 22766T, Isolated from Bumblebee Digestive Tracts. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01084-15. [PMID: 26404606 PMCID: PMC4582582 DOI: 10.1128/genomea.01084-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bifidobacteria are one of the most important beneficial bacteria in the gut of mammals and insects. We sequenced the genome of B. actinocoloniiforme DSM 22766, which was isolated from the digestive tracts of bumblebees. The genome contains 1,548 protein-coding genes, 49 RNAs and two CRISPR repeats.
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810
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Draft Genome Sequence of the First Hypermucoviscous Klebsiella quasipneumoniae subsp. quasipneumoniae Isolate from a Bloodstream Infection. GENOME ANNOUNCEMENTS 2015; 3:3/5/e00952-15. [PMID: 26383657 PMCID: PMC4574361 DOI: 10.1128/genomea.00952-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Klebsiella quasipneumoniae is a recently described species, formerly identified as K. pneumoniae phylogroup KpII. Information on pathogenic and virulence potential of this species are lacking. We sequenced the genome of a hypermucoviscous K. quasipneumoniae clinical isolate showing a virulence genes content (allABCDRS, kfuABC, and mrkABCDFHIJ) peculiar to hypervirulent K. pneumoniae strains.
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811
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Draft Genome Sequence of the Beer Spoilage Bacterium Megasphaera cerevisiae Strain PAT 1T. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01045-15. [PMID: 26358606 PMCID: PMC4566188 DOI: 10.1128/genomea.01045-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genus Megasphaera harbors important spoilage organisms that cause beer spoilage by producing off flavors, undesirable aroma, and turbidity. Megasphaera cerevisiae is mainly found in nonpasteurized low-alcohol beer. In this study, we report the draft genome of the type strain of the genus, M. cerevisiae strain PAT 1(T).
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812
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Draft Genome Sequence of Desulfocarbo indianensis SCBM, a New Genus of Sulfate-Reducing Bacteria, Isolated from Water Extracted from an Active Coalbed Methane Gas Well. GENOME ANNOUNCEMENTS 2015; 3:3/5/e00970-15. [PMID: 26337881 PMCID: PMC4559730 DOI: 10.1128/genomea.00970-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We used Illumina MiSeq technology to sequence the whole genome of Desulfocarbo indianensis SCBM, a new genus of sulfate-reducing bacteria isolated from a coal bed in Indiana, USA. This draft genome represents the first sequenced genome of the genus Desulfocarbo and the second known genome of the order Desulfarculales.
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813
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Draft Genome Sequence and Annotation of Phyllosphere-Persisting Salmonella enterica subsp. enterica Serovar Livingstone Strain CKY-S4, Isolated from an Urban Lake in Regina, Canada. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00884-15. [PMID: 26272568 PMCID: PMC4536679 DOI: 10.1128/genomea.00884-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Here, we report the first draft genome sequence of Salmonella enterica subsp. enterica serovar Livingstone. This S. Livingstone strain CKY-S4 displayed biofilm formation and cellulose production and could persist on lettuce. This genome may help the study of mechanisms by which enteric pathogens colonize food crops.
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814
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Complete Genome Sequence of Staphylococcus aureus FCFHV36, a Methicillin-Resistant Strain Heterogeneously Resistant to Vancomycin. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00893-15. [PMID: 26272570 PMCID: PMC4536681 DOI: 10.1128/genomea.00893-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the sequence of the entire chromosome of Staphylococcus aureus strain FCFHV36, a methicillin-resistant strain heterogeneously intermediate to vancomycin, bearing a type II staphylococcal chromosome cassette mec element (SCCmec), belonging to multilocus sequence type (MLST) 105, and isolated from a vertebra of a patient with osteomyelitis.
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815
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Mansor M, Hamilton TL, Fantle MS, Macalady JL. Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing. Front Microbiol 2015; 6:822. [PMID: 26322031 PMCID: PMC4530308 DOI: 10.3389/fmicb.2015.00822] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/27/2015] [Indexed: 11/13/2022] Open
Abstract
Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces at sites throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs (WMS), FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity). The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V)-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.
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Affiliation(s)
- Muammar Mansor
- Geosciences Department, Pennsylvania State University University Park, PA, USA
| | - Trinity L Hamilton
- Department of Biological Sciences, University of Cincinnati Cincinnati, OH, USA
| | - Matthew S Fantle
- Geosciences Department, Pennsylvania State University University Park, PA, USA
| | - Jennifer L Macalady
- Geosciences Department, Pennsylvania State University University Park, PA, USA
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816
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Characterization of a Novel Putative Xer-Dependent Integrative Mobile Element Carrying the bla(NMC-A) Carbapenemase Gene, Inserted into the Chromosome of Members of the Enterobacter cloacae Complex. Antimicrob Agents Chemother 2015; 59:6620-4. [PMID: 26248383 DOI: 10.1128/aac.01452-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/18/2015] [Indexed: 11/20/2022] Open
Abstract
An Enterobacter ludwigii strain was isolated during routine screening of a Japanese patient for carriage of carbapenem-resistant Enterobacteriaceae. PCR analysis revealed the blaNMC-A carbapenemase gene. Whole-genome sequencing revealed that blaNMC-A was inserted in the chromosome and associated with a novel 29.1-kb putative Xer-dependent integrative mobile element, named EludIMEX-1. Bioinformatic analysis identified similar elements in the genomes of an Enterobacter asburiae strain and of other Enterobacter cloacae complex strains, confirming the mobile nature of this element.
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817
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Fonseca EL, Marin MA, Encinas F, Vicente ACP. Full characterization of the integrative and conjugative element carrying the metallo-β-lactamaseblaSPM-1and bicyclomycinbcr1resistance genes found in the pandemicPseudomonas aeruginosaclone SP/ST277 : Figure 1. J Antimicrob Chemother 2015; 70:2547-50. [DOI: 10.1093/jac/dkv152] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 05/14/2015] [Indexed: 11/14/2022] Open
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818
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Genome Sequences of Pseudomonas amygdali pv. tabaci Strain ATCC 11528 and pv. lachrymans Strain 98A-744. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00683-15. [PMID: 26089433 PMCID: PMC4472910 DOI: 10.1128/genomea.00683-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Certain pathovars of Pseudomonas amygdali, which is newly reclassified from Pseudomonas syringae by DNA-DNA hybridization and ribotyping, cause many serious diseases of major crop plants. Herein, we present draft genome sequences of P. amygdali pv. tabaci strain ATCC 11528 and P. amygdali pv. lachrymans strain 98A-744.
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819
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Genome Sequence of a Klebsiella pneumoniae Sequence Type 258 Isolate with Prophage-Encoded K. pneumoniae Carbapenemase. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00659-15. [PMID: 26089425 PMCID: PMC4472902 DOI: 10.1128/genomea.00659-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We present the draft genome sequence of a Klebsiella pneumoniae carbapenemase (KPC)-producing sequence type 258 (ST258) K. pneumoniae strain, ST258_FL. Uniquely, strain ST258_FL harbors two copies of the blaKPC gene on the chromosome, one of which is integrated into a prophage.
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820
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Draft Genome Sequence of the Bacterium Pseudomonas putida CBB5, Which Can Utilize Caffeine as a Sole Carbon and Nitrogen Source. GENOME ANNOUNCEMENTS 2015; 3:3/3/e00640-15. [PMID: 26067973 PMCID: PMC4463537 DOI: 10.1128/genomea.00640-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Pseudomonas putida CBB5
was isolated from soil by enriching for growth on caffeine (1,3,7-trimethylxanthine). The draft genome of this strain is 6.9 Mb, with 5,941 predicted coding sequences. It includes the previously studied Alx gene cluster encoding alkylxanthine N-demethylase enzymes and other genes that enable the degradation of purine alkaloids.
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821
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Emond-Rheault JG, Vincent AT, Trudel MV, Frey J, Frenette M, Charette SJ. AsaGEI2b: a new variant of a genomic island identified in theAeromonas salmonicidasubsp.salmonicidaJF3224 strain isolated from a wild fish in Switzerland. FEMS Microbiol Lett 2015; 362:fnv093. [DOI: 10.1093/femsle/fnv093] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2015] [Indexed: 12/24/2022] Open
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822
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Murphy RR, O'Connell J, Cox AJ, Schulz-Trieglaff O. NxRepair: error correction in de novo sequence assembly using Nextera mate pairs. PeerJ 2015; 3:e996. [PMID: 26056623 PMCID: PMC4458127 DOI: 10.7717/peerj.996] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 05/13/2015] [Indexed: 02/03/2023] Open
Abstract
Scaffolding errors and incorrect repeat disambiguation during de novo assembly can result in large scale misassemblies in draft genomes. Nextera mate pair sequencing data provide additional information to resolve assembly ambiguities during scaffolding. Here, we introduce NxRepair, an open source toolkit for error correction in de novo assemblies that uses Nextera mate pair libraries to identify and correct large-scale errors. We show that NxRepair can identify and correct large scaffolding errors, without use of a reference sequence, resulting in quantitative improvements in the assembly quality. NxRepair can be downloaded from GitHub or PyPI, the Python Package Index; a tutorial and user documentation are also available.
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Affiliation(s)
| | | | - Anthony J Cox
- Illumina Cambridge, Chesterford Research Park , Essex , UK
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823
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Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. Swabs to genomes: a comprehensive workflow. PeerJ 2015; 3:e960. [PMID: 26020012 PMCID: PMC4435499 DOI: 10.7717/peerj.960] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/24/2015] [Indexed: 02/04/2023] Open
Abstract
The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.
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824
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The ecology of pelagic freshwater methylotrophs assessed by a high-resolution monitoring and isolation campaign. ISME JOURNAL 2015; 9:2442-53. [PMID: 25942006 DOI: 10.1038/ismej.2015.55] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 02/19/2015] [Accepted: 03/06/2015] [Indexed: 11/08/2022]
Abstract
Methylotrophic planktonic bacteria fulfill a particular role in the carbon cycle of lakes via the turnover of single-carbon compounds. We studied two planktonic freshwater lineages (LD28 and PRD01a001B) affiliated with Methylophilaceae (Betaproteobacteria) in Lake Zurich, Switzerland, by a combination of molecular and cultivation-based approaches. Their spatio-temporal distribution was monitored at high resolution (n=992 samples) for 4 consecutive years. LD28 methylotrophs constituted up to 11 × 10(7) cells l(-1) with pronounced peaks in spring and autumn-winter, concomitant with blooms of primary producers. They were rare in the warm water layers during summer but abundant in the cold hypolimnion, hinting at psychrophilic growth. Members of the PRD01a001B lineage were generally less abundant but also had maxima in spring. More than 120 axenic strains from these so far uncultivated lineages were isolated from the pelagic zone by dilution to extinction. Phylogenetic analysis separated isolates into two distinct genotypes. Isolates grew slowly (μmax=0.4 d(-1)), were of conspicuously small size, and were indeed psychrophilic, with higher growth yield at low temperatures. Growth was enhanced upon addition of methanol and methylamine to sterile lake water. Genomic analyses of two strains confirmed a methylotrophic lifestyle with a reduced set of genes involved in C1 metabolism. The very small and streamlined genomes (1.36 and 1.75 Mb) shared several pathways with the marine OM43 lineage. As the closest described taxa (Methylotenera sp.) are only distantly related to either set of isolates, we propose a new genus with two species, that is, 'Candidatus Methylopumilus planktonicus' (LD28) and 'Candidatus Methylopumilus turicensis' (PRD01a001B).
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825
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First report of an OXA-48-producing multidrug-resistant Proteus mirabilis strain from Gaza, Palestine. Antimicrob Agents Chemother 2015; 59:4305-7. [PMID: 25896692 DOI: 10.1128/aac.00565-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/11/2015] [Indexed: 01/11/2023] Open
Abstract
We report the first multidrug-resistant Proteus mirabilis strain producing the carbapenemase OXA-48 (Pm-OXA-48) isolated at Al-Shifa hospital in Gaza, Palestine. Draft genome sequencing of Pm-OXA-48 identified 16 antimicrobial resistance genes, encoding resistance to β-lactams, aminoglycosides, fluoroquinolones, phenicols, streptothricin, tetracycline, and trimethoprim-sulfamethoxazole. Complete sequencing of the bla(OXA-48)-harboring plasmid revealed that it is a 72 kb long IncL/M plasmid, harboring carbapenemase gene bla(OXA-48), extended spectrum β-lactamase gene bla(CTX-M-14), and aminoglycoside resistance genes strA, strB, and aph(3')-VIb.
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826
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Szövényi P, Frangedakis E, Ricca M, Quandt D, Wicke S, Langdale JA. Establishment of Anthoceros agrestis as a model species for studying the biology of hornworts. BMC PLANT BIOLOGY 2015; 15:98. [PMID: 25886741 PMCID: PMC4393856 DOI: 10.1186/s12870-015-0481-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/24/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Plants colonized terrestrial environments approximately 480 million years ago and have contributed significantly to the diversification of life on Earth. Phylogenetic analyses position a subset of charophyte algae as the sister group to land plants, and distinguish two land plant groups that diverged around 450 million years ago - the bryophytes and the vascular plants. Relationships between liverworts, mosses hornworts and vascular plants have proven difficult to resolve, and as such it is not clear which bryophyte lineage is the sister group to all other land plants and which is the sister to vascular plants. The lack of comparative molecular studies in representatives of all three lineages exacerbates this uncertainty. Such comparisons can be made between mosses and liverworts because representative model organisms are well established in these two bryophyte lineages. To date, however, a model hornwort species has not been available. RESULTS Here we report the establishment of Anthoceros agrestis as a model hornwort species for laboratory experiments. Axenic culture conditions for maintenance and vegetative propagation have been determined, and treatments for the induction of sexual reproduction and sporophyte development have been established. In addition, protocols have been developed for the extraction of DNA and RNA that is of a quality suitable for molecular analyses. Analysis of haploid-derived genome sequence data of two A. agrestis isolates revealed single nucleotide polymorphisms at multiple loci, and thus these two strains are suitable starting material for classical genetic and mapping experiments. CONCLUSIONS Methods and resources have been developed to enable A. agrestis to be used as a model species for developmental, molecular, genomic, and genetic studies. This advance provides an unprecedented opportunity to investigate the biology of hornworts.
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Affiliation(s)
- Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Institute of Systematic Botany, University of Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.
- MTA-ELTE-MTM Ecology Research Group, ELTE, Biological Institute, Budapest, Hungary.
| | - Eftychios Frangedakis
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, UK.
- Current Address: Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113 0033, Japan.
| | - Mariana Ricca
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland.
| | - Dietmar Quandt
- Nees-Institut für Biodiversität der Pflanzen, University of Bonn, Meckenheimer Allee 170, D - 53115, Bonn, Germany.
| | - Susann Wicke
- Nees-Institut für Biodiversität der Pflanzen, University of Bonn, Meckenheimer Allee 170, D - 53115, Bonn, Germany.
- Institute for Evolution and Biodiversity, University of Muenster, Huefferstr. 1, 48149, Muenster, Germany.
| | - Jane A Langdale
- Department of Plant Sciences, University of Oxford, South Parks Rd, Oxford, UK.
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827
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Genome Sequence of Bacillus mycoides B38V, a Growth-Promoting Bacterium of Sunflower. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00245-15. [PMID: 25838494 PMCID: PMC4384498 DOI: 10.1128/genomea.00245-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacillus mycoides B38V is a bacterium isolated from the sunflower rhizosphere that is able to promote plant growth and N uptake. The genome of the isolate has approximately 5.80 Mb and presents sequence codifiers for plant growth-promoting characteristics, such as nitrate reduction and ammonification and iron-siderophore uptake.
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828
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de Souza R, Sant'Anna FH, Ambrosini A, Tadra-Sfeir M, Faoro H, Pedrosa FO, Souza EM, Passaglia LMP. Genome of Pseudomonas sp. FeS53a, a Putative Plant Growth-Promoting Bacterium Associated with Rice Grown in Iron-Stressed Soils. GENOME ANNOUNCEMENTS 2015; 3:e00248-15. [PMID: 25838496 PMCID: PMC4384500 DOI: 10.1128/genomea.00248-15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 02/23/2015] [Indexed: 11/24/2022]
Abstract
Pseudomonas sp. FeS53a was isolated from the roots of rice plants cultivated in one area with a well-established history of iron toxicity. The FeS53a genome sequence provides the genetic basis for understanding its lifestyle and survival in association with rice in conditions of iron toxicity.
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Affiliation(s)
- Rocheli de Souza
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Fernando Hayashi Sant'Anna
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Adriana Ambrosini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Michele Tadra-Sfeir
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR, Brazil
| | - Helisson Faoro
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR, Brazil
| | - Fabio Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR, Brazil
| | - Emanuel Maltempi Souza
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná (UFPR), Centro Politécnico, Curitiba, PR, Brazil
| | - Luciane M P Passaglia
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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829
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Whole-Genome Shotgun Sequence of the Keratinolytic Bacterium Lysobacter sp. A03, Isolated from the Antarctic Environment. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00246-15. [PMID: 25838495 PMCID: PMC4384499 DOI: 10.1128/genomea.00246-15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lysobacter sp. strain A03 is a protease-producing bacterium isolated from decomposing-penguin feathers collected in the Antarctic environment. This strain has the ability to degrade keratin at low temperatures. The A03 genome sequence provides the possibility of finding new genes with biotechnological potential to better understand its cold-adaptation mechanism and survival in cold environments.
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830
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Genome of Rhizobium sp. UR51a, Isolated from Rice Cropped in Southern Brazilian Fields. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00249-15. [PMID: 25838497 PMCID: PMC4384501 DOI: 10.1128/genomea.00249-15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Rhizobium sp. UR51a is a Gram-negative bacterium isolated from roots of rice plants, and it presents plant growth-promoting abilities. The nutrient uptake in rice plants inoculated with UR51a was satisfactory. The genome of strain UR51a is composed of 5,233,443-bp and harbors 5,079 coding sequences.
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831
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Draft Genome Sequence of Halomonas sp. KHS3, a Polyaromatic Hydrocarbon-Chemotactic Strain. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00020-15. [PMID: 25767220 PMCID: PMC4357742 DOI: 10.1128/genomea.00020-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The draft genome sequence of Halomonas sp. KHS3, isolated from seawater from Mar del Plata harbor, is reported. This strain is able to grow using aromatic compounds as a carbon source and shows strong chemotactic response toward these substrates. Genes involved in motility, chemotaxis, and degradation of aromatic hydrocarbons were identified.
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832
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Draft Genome Sequence of the Terrestrial Cyanobacterium Scytonema millei VB511283, Isolated from Eastern India. GENOME ANNOUNCEMENTS 2015; 3:3/2/e00009-15. [PMID: 25744984 PMCID: PMC4358371 DOI: 10.1128/genomea.00009-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We report here the draft genome sequence of Scytonema millei VB511283, a cyanobacterium isolated from biofilms on the exterior of stone monuments in Santiniketan, eastern India. The draft genome is 11,627,246 bp long (11.63 Mb), with 118 scaffolds. About 9,011 protein-coding genes, 117 tRNAs, and 12 rRNAs are predicted from this assembly.
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833
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Draft Genome Sequences of Two Drug-Resistant Isolates of Pseudomonas aeruginosa Obtained from Keratitis Patients in India. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01404-14. [PMID: 25573941 PMCID: PMC4290992 DOI: 10.1128/genomea.01404-14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report here the draft genomes of two drug (fluoroquinolone)-resistant clinical isolates of Pseudomonas aeruginosa obtained from the corneal scrapings of keratitis patients from India. The two annotated genomes are 6.31 Mb and 6.41 Mb in size. These genomes are expected to facilitate the identification and understanding of the genes associated with acquired multidrug resistance.
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834
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Draft Genome Sequences of Six Ruminant Coxiella burnetii Isolates of European Origin. GENOME ANNOUNCEMENTS 2014; 2:genomeA.00285-14. [PMID: 24831135 PMCID: PMC4022799 DOI: 10.1128/genomea.00285-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Coxiella burnetii is responsible for Q fever, a worldwide zoonosis attributed to the inhalation of aerosols contaminated by livestock birth products. Six draft genome sequences of European C. burnetii isolates from ruminants are presented here. The availability of these genomes will help in understanding the potential host specificity and pathogenicity and in identifying pertinent markers for surveillance and tracing.
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835
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Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Automated ensemble assembly and validation of microbial genomes. BMC Bioinformatics 2014; 15:126. [PMID: 24884846 PMCID: PMC4030574 DOI: 10.1186/1471-2105-15-126] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/24/2014] [Indexed: 11/12/2022] Open
Abstract
Background The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. Results To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Conclusions Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to select an assembly best tailored to their specific needs.
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Affiliation(s)
- Sergey Koren
- National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, MD 21702, USA.
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836
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Darling AE, Worden P, Chapman TA, Roy Chowdhury P, Charles IG, Djordjevic SP. The genome of Clostridium difficile 5.3. Gut Pathog 2014; 6:4. [PMID: 24565059 PMCID: PMC4234979 DOI: 10.1186/1757-4749-6-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 02/01/2014] [Indexed: 12/26/2022] Open
Abstract
Background Clostridium difficile is the leading cause of infectious diarrhea in humans and responsible for large outbreaks of enteritis in neonatal pigs in both North America and Europe. Disease caused by C. difficile typically occurs during antibiotic therapy and its emergence over the past 40 years is linked with the widespread use of broad-spectrum antibiotics in both human and veterinary medicine. Results We sequenced the genome of Clostridium difficile 5.3 using the Illumina Nextera XT and MiSeq technologies. Assembly of the sequence data reconstructed a 4,009,318 bp genome in 27 scaffolds with an N50 of 786 kbp. The genome has extensive similarity to other sequenced C. difficile genomes, but also has several genes that are potentially related to virulence and pathogenicity that are not present in the reference C. difficile strain. Conclusion Genome sequencing of human and animal isolates is needed to understand the molecular events driving the emergence of C. difficile as a gastrointestinal pathogen of humans and food animals and to better define its zoonotic potential.
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Affiliation(s)
- Aaron E Darling
- ithree institute, University of Technology Sydney, Broadway Street, 2007 Ultimo, Australia.
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