scholarly journals A Microbial Metagenome (Leucobacter sp.) in Caenorhabditis Whole Genome Sequences

2013 ◽  
Vol 7 ◽  
pp. BBI.S11064 ◽  
Author(s):  
Riccardo Percudani
Keyword(s):  
Genetic Information ◽  
Bacterial Species ◽  
Draft Genome ◽  
Single Species ◽  
Public Database ◽  
Genome Sequences ◽  
The Public ◽  
Caenorhabditis Remanei ◽  
Insight Into ◽  
Annotation Errors

DNA of apparently recent bacterial origin is found in the genomic sequences of Caenorhabditis angaria and Caenorhabditis remanei. Here we present evidence that the DNA belongs to a single species of the genus Leucobacter (high-GC Gram+Actinobacteria). Metagenomic tools enabled the assembly of the contaminating sequences in a draft genome of 3.2 Mb harboring 2,826 genes. This information provides insight into a microbial organism intimately associated with Caenorhabditis as well as a solid basis for the reassignment of 3,373 metazoan entries of the public database to a novel bacterial species ( Leucobacter sp. AEAR). The application of metagenomic techniques can thus prevent annotation errors and reveal unexpected genetic information in data obtained by conventional genomics.

scholarly journals Draft Genome Sequences of 1,183 Salmonella Strains from the 100K Pathogen Genome Project

2017 ◽  
Vol 5 (28) ◽  
Author(s):  
Nguyet Kong ◽  
Matthew Davis ◽  
Narine Arabyan ◽  
Bihua C. Huang ◽  
Allison M. Weis ◽  
...  
Keyword(s):  
Human Health ◽  
Global Economy ◽  
Draft Genome ◽  
Genome Project ◽  
Genomic Diversity ◽  
Genome Sequences ◽  
Substantial Impact ◽  
The Public ◽  
Common Food ◽  
Pathogen Genome

ABSTRACT Salmonella is a common food-associated bacterium that has substantial impact on worldwide human health and the global economy. This is the public release of 1,183 Salmonella draft genome sequences as part of the 100K Pathogen Genome Project. These isolates represent global genomic diversity in the Salmonella genus.

scholarly journals Labour sharing promotes coexistence in atrazine degrading bacterial communities

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Loren Billet ◽  
Marion Devers ◽  
Nadine Rouard ◽  
Fabrice Martin-Laurent ◽  
Aymé Spor
Keyword(s):  
Bacterial Communities ◽  
Gene Loss ◽  
Bacterial Species ◽  
Single Species ◽  
Microbial Consortia ◽  
The Public ◽  
Herbicide Atrazine ◽  
Set Up ◽  
Multiple Species ◽  
Isolated Species

AbstractMicrobial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.

scholarly journals Complete and Draft Genome Sequences of Eight Oceanic Pseudomonas aeruginosa Strains

2017 ◽  
Vol 5 (44) ◽  
Author(s):  
Yohei Kumagai ◽  
Susumu Yoshizawa ◽  
Keiji Nakamura ◽  
Yoshitoshi Ogura ◽  
Tetsuya Hayashi ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Species ◽  
Draft Genome ◽  
Open Ocean ◽  
Genome Sequences ◽  
Content Type

ABSTRACT Pseudomonas aeruginosa is one of the most common model bacterial species, and genomes of hundreds of strains of this species have been sequenced to date. However, currently there is only one available genome of an oceanic isolate. Here, we report two complete and six draft genome sequences of P. aeruginosa isolates from the open ocean.

scholarly journals RFPlasmid: Predicting plasmid sequences from short read assembly data using machine learning

2020 ◽  
Author(s):  
Linda van der Graaf van Bloois ◽  
Jaap A. Wagenaar ◽  
Aldert L. Zomer
Keyword(s):  
Bacterial Species ◽  
Draft Genome ◽  
Single Copy ◽  
Chromosomal Marker ◽  
Web Interface ◽  
Large Single Copy ◽  
Genome Sequences ◽  
Multiple Features ◽  
E Coli ◽  
Marker Proteins

AbstractAntimicrobial resistance (AMR) genes in bacteria are often carried on plasmids and these plasmids can transfer AMR genes between bacteria. For molecular epidemiology purposes and risk assessment, it is important to know if the genes are located on highly transferable plasmids or in the more stable chromosomes. However, draft whole genome sequences are fragmented, making it difficult to discriminate plasmid and chromosomal contigs. Current methods that predict plasmid sequences from draft genome sequences rely on single features, like k-mer composition, circularity of the DNA molecule, copy number or sequence identity to plasmid replication genes, all of which have their drawbacks, especially when faced with large single copy plasmids, which often carry resistance genes. With our newly developed prediction tool RFPlasmid, we use a combination of multiple features, including k-mer composition and databases with plasmid and chromosomal marker proteins, to predict if the likely source of a contig is plasmid or chromosomal. The tool RFPlasmid supports models for 17 different bacterial species, including Campylobacter, E. coli, and Salmonella, and has a species agnostic model for metagenomic assemblies or unsupported organisms. RFPlasmid is available both as standalone tool and via web interface.

scholarly journals Draft Genome Sequences of Four Aeromonas salmonicida subsp. achromogenes Strains, 23051, 23053, 23055, and 23056, Isolated from Senegalese Sole (Solea senegalensis)

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Antony T. Vincent ◽  
Alain Le Breton ◽  
Alex Bernatchez ◽  
Cynthia Gagné-Thivierge ◽  
Valérie E. Paquet ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Draft Genome ◽  
Aeromonas Salmonicida ◽  
Large Majority ◽  
Genomic Sequences ◽  
Solea Senegalensis ◽  
Senegalese Sole ◽  
Genome Sequences ◽  
Content Type ◽  
Genomic Analyses

The bacterial species Aeromonas salmonicida officially has five subspecies. A large majority of the currently available sequences come from Aeromonas salmonicida subsp. salmonicida, which causes furunculosis in salmonids. We present the genomic sequences of four Aeromonas salmonicida subsp. achromogenes strains. This will help increase the robustness of genomic analyses for this subspecies.

scholarly journals Draft Genome Sequences of Six Yersinia kristensenii Strains

2022 ◽  
Author(s):  
Angelina A. Kislichkina ◽  
Mikhail E. Platonov ◽  
Yury P. Skryabin ◽  
Angelika A. Sizova ◽  
Lidia A. Shishkina ◽  
...  
Keyword(s):  
Yersinia Enterocolitica ◽  
Bacterial Species ◽  
Draft Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Genomic Level

Yersinia kristensenii is one of the Yersinia enterocolitica -like bacterial species, which are considered nonpathogenic to humans. In this work, we reported the draft genome sequences of six Yersinia kristensenii strains. These draft genomes will help to better characterize Yersinia kristensenii at the genomic level.

scholarly journals Draft Genome Sequences of 12 Monophasic Salmonella enterica subsp. enterica Serotype Typhimurium 1,4,[5],12:i:− Strains Isolated from Wild Griffon Vultures in Eastern Spain

2019 ◽  
Vol 8 (42) ◽  
Author(s):  
Clara Marin ◽  
Giuseppe D’Auria ◽  
Llúcia Martínez-Priego ◽  
Francisco Marco-Jiménez
Keyword(s):  
Salmonella Enterica ◽  
Draft Genome ◽  
Wild Animals ◽  
Genome Sequences ◽  
Host Pathogen Interactions ◽  
Content Type ◽  
Zoonotic Pathogens ◽  
Host Pathogen ◽  
Serovar Typhimurium ◽  
Insight Into

Monophasic Salmonella enterica subsp. enterica serovar Typhimurium is one of the most common zoonotic pathogens. Salmonella species reside in a wide variety of hosts, including wild animals. Thus, we report here the genome sequences of 12 monophasic S. Typhimurium strains isolated from healthy wild vultures to gain better insight into their epidemiology and host-pathogen interactions.

scholarly journals Genome Sequences of Three Nocardia cyriacigeorgica Strains and One Nocardia asteroides Strain

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Florian Vautrin ◽  
Emmanuelle Bergeron ◽  
Audrey Dubost ◽  
Danis Abrouk ◽  
Christophe Martin ◽  
...  
Keyword(s):  
Type Strain ◽  
Draft Genome ◽  
Nocardia Asteroides ◽  
Environmental Isolates ◽  
Genome Sequences ◽  
Content Type ◽  
Nocardia Cyriacigeorgica ◽  
Insight Into

We report four draft genome sequences of Nocardia spp. The strains are the Nocardia cyriacigeorgica DSM 44484 pathogenic type strain; two environmental isolates, Nocardia cyriacigeorgica EML446 and EML1456; and the Nocardia asteroides ATCC 19247 nonpathogenic type strain, with estimated genome sizes of 6.3 to 6.8 Mb. The study of these isolates will provide insight into physiology, evolution, and pathogenicity of Nocardia spp.

scholarly journals Genome Resources of Three West African Strains of Pantoea ananatis Causing Bacterial Blight and Grain Discoloration of Rice

2020 ◽  
Vol 110 (9) ◽  
pp. 1500-1502
Author(s):  
Kossi Kini ◽  
Pierre Lefeuvre ◽  
Lucie Poulin ◽  
Drissa Silué ◽  
Ralf Koebnik
Keyword(s):  
Bacterial Blight ◽  
Molecular Level ◽  
Draft Genome ◽  
West African ◽  
Molecular Diagnostic ◽  
Diagnostic Tools ◽  
Genome Sequences ◽  
Pantoea Ananatis ◽  
Genome Data ◽  
Insight Into

Members of the genus Pantoea have been reported as pathogens for many economically important crops, including rice. Little is known about their host−pathogen interactions at the molecular level and the lack of comprehensive genome data impedes targeted breeding strategies toward resistant rice cultivars. Here, we describe the structural and functional annotation of the draft genome sequences of three rice-pathogenic Pantoea ananatis strains, ARC272, ARC310, and ARC311, which were isolated in Burkina Faso, Togo, and Benin, respectively. The genome sequences of these strains will help in developing molecular diagnostic tools and provide new insight into common traits that may enable P. ananatis to infect rice.

Sign in / Sign up

Export Citation Format

Share Document