For Publishers
DiscoveryMetadataPeer reviewHostingPublishing
For Researchers
JoinPublishReviewCollect
Register
Blog
About
Search
Advanced search
My ScienceOpen
Search
For Publishers
For Researchers
Blog
About
1
views
10
references
 Top references
cited by
1
    
0 reviews
 Review
0
comments
 Comment
0
recommends
+1 Recommend
0 collections
    0
    shares
      0
      similar
       All similar
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Draft Genome Sequence of Enterobacter cloacae 3D9 (Phylum Proteobacteria)

      brief-report

      Read this article at

      ScienceOpenPublisherPMC
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Presented here is the draft genome sequence of Enterobacter cloacae 3D9. This candidate seed endophyte was isolated from Zea nicaraguensis.

          ABSTRACT

          Presented here is the draft genome sequence of Enterobacter cloacae 3D9. This candidate seed endophyte was isolated from Zea nicaraguensis. The genome contains 4,653,375 bp in 28 contigs.

          Related collections

          Most cited references10

          • Record: found
          • Abstract: found
          • Article: not found

          Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples.

          Dhany Saputra, Christina A. Svendsen, Frank Aarestrup … (2013)
          Whole-genome sequencing (WGS) is becoming available as a routine tool for clinical microbiology. If applied directly on clinical samples, this could further reduce diagnostic times and thereby improve control and treatment. A major bottleneck is the availability of fast and reliable bioinformatic tools. This study was conducted to evaluate the applicability of WGS directly on clinical samples and to develop easy-to-use bioinformatic tools for the analysis of sequencing data. Thirty-five random urine samples from patients with suspected urinary tract infections were examined using conventional microbiology, WGS of isolated bacteria, and direct sequencing on pellets from the urine samples. A rapid method for analyzing the sequence data was developed. Bacteria were cultivated from 19 samples but in pure cultures from only 17 samples. WGS improved the identification of the cultivated bacteria, and almost complete agreement was observed between phenotypic and predicted antimicrobial susceptibilities. Complete agreement was observed between species identification, multilocus sequence typing, and phylogenetic relationships for Escherichia coli and Enterococcus faecalis isolates when the results of WGS of cultured isolates and urine samples were directly compared. Sequencing directly from the urine enabled bacterial identification in polymicrobial samples. Additional putative pathogenic strains were observed in some culture-negative samples. WGS directly on clinical samples can provide clinically relevant information and drastically reduce diagnostic times. This may prove very useful, but the need for data analysis is still a hurdle to clinical implementation. To overcome this problem, a publicly available bioinformatic tool was developed in this study.
          Article 0 comments Cited 195 times – based on 0 reviews     Review now
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            Benchmarking of methods for genomic taxonomy.

            Oksana Lukjancenko, Salvatore Cosentino, Thomas Sicheritz-Pontén … (2014)
            One of the first issues that emerges when a prokaryotic organism of interest is encountered is the question of what it is--that is, which species it is. The 16S rRNA gene formed the basis of the first method for sequence-based taxonomy and has had a tremendous impact on the field of microbiology. Nevertheless, the method has been found to have a number of shortcomings. In the current study, we trained and benchmarked five methods for whole-genome sequence-based prokaryotic species identification on a common data set of complete genomes: (i) SpeciesFinder, which is based on the complete 16S rRNA gene; (ii) Reads2Type that searches for species-specific 50-mers in either the 16S rRNA gene or the gyrB gene (for the Enterobacteraceae family); (iii) the ribosomal multilocus sequence typing (rMLST) method that samples up to 53 ribosomal genes; (iv) TaxonomyFinder, which is based on species-specific functional protein domain profiles; and finally (v) KmerFinder, which examines the number of cooccurring k-mers (substrings of k nucleotides in DNA sequence data). The performances of the methods were subsequently evaluated on three data sets of short sequence reads or draft genomes from public databases. In total, the evaluation sets constituted sequence data from more than 11,000 isolates covering 159 genera and 243 species. Our results indicate that methods that sample only chromosomal, core genes have difficulties in distinguishing closely related species which only recently diverged. The KmerFinder method had the overall highest accuracy and correctly identified from 93% to 97% of the isolates in the evaluations sets.
            Article 0 comments Cited 141 times – based on 0 reviews     Review now
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Role of root microbiota in plant productivity.

              Andrzej Tkacz, Philip Poole (2015)
              The growing human population requires increasing amounts of food, but modern agriculture has limited possibilities for increasing yields. New crop varieties may be bred to have increased yields and be more resistant to environmental stress and pests. However, they still require fertilization to supplement essential nutrients that are normally limited in the soil. Soil microorganisms present an opportunity to reduce the requirement for inorganic fertilization in agriculture. Microorganisms, due to their enormous genetic pool, are also a potential source of biochemical reactions that recycle essential nutrients for plant growth. Microbes that associate with plants can be considered to be part of the plant's pan-genome. Therefore, it is essential for us to understand microbial community structure and their 'metagenome' and how it is influenced by different soil types and crop varieties. In the future we may be able to modify and better utilize the soil microbiota potential for promoting plant growth.
              Article 0 comments Cited 75 times – based on 0 reviews     Review now
                Bookmark
                All references

                Author and article information

                Contributors
                Jason Stajich: Role: Editor
                Journal
                Journal ID (nlm-ta): Microbiol Resour Announc
                Journal ID (iso-abbrev): Microbiol Resour Announc
                Journal ID (hwp): ga
                Journal ID (pmc): mra
                Journal ID (publisher-id): MRA
                Title: Microbiology Resource Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2576-098X
                Publication date (Electronic): 25 October 2018
                Publication date Collection: October 2018
                Volume: 7
                Issue: 16
                Electronic Location Identifier: e00902-18
                Affiliations
                [a ]Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
                University of California, Riverside
                Author notes
                Address correspondence to Manish N. Raizada, raizada@ 123456uoguelph.ca .

                Citation Dumigan CR, Perry GE, Pauls KP, Raizada MN. 2018. Draft genome sequence of Enterobacter cloacae 3D9 (phylum Proteobacteria). Microbiol Resour Announc 7:e00902-18. https://doi.org/10.1128/MRA.00902-18.

                Article
                Publisher ID: MRA00902-18
                DOI: 10.1128/MRA.00902-18
                PMC ID: 6256583
                PubMed ID: 30533747
                SO-VID: 5abb1cdc-095f-46ed-9471-e8cb677f3808
                Copyright © Copyright © 2018 Dumigan et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 26 June 2018
                Date accepted : 1 October 2018
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 12, Pages: 2, Words: 1237
                Funding
                Funded by: Canadian Foundation for Innovation (CFI);
                Award ID: 460635
                Award Recipient :
                Funded by: Canada First Research Excellence Fund, https://doi.org/10.13039/501100010785;
                Award ID: LAAIR grant 499049
                Award Recipient :
                Funded by: Ontario Ministry of Agriculture, Food and Rural Affairs (OMAFRA), https://doi.org/10.13039/501100000094;
                Award ID: LAAIR grant 499049
                Award Recipient :
                Categories
                Subject: Genome Sequences
                Custom metadata
                cover-date October 2018

                Data availability:

                Comments

                Comment on this article