Enterobacter hormaechei  subsp.
 hoffmannii  subsp. nov.,
 Enterobacter hormaechei subsp.
 xiangfangensis  comb. nov.,
 Enterobacter roggenkampii  sp. nov., and
 Enterobacter muelleri  is a later heterotypic synonym of
 Enterobacter asburiae  based on computational analysis of sequenced
 Enterobacter  genomes.

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Abstract

Background: The predominant species in clinical Enterobacter isolates is E. hormaechei. Many articles, clinicians, and GenBank submissions misname these strains as E. cloacae. The lack of sequenced type strains or named species/subspecies for some clades in the E. cloacae complex complicate the issue.

Methods: The genomes of the type strains for Enterobacter hormaechei subsp. oharae, E. hormaechei subsp. steigerwaltii, and E. xiangfangensis, and two strains from Hoffmann clusters III and IV of the E. cloacae complex were sequenced. These genomes, the E. hormaechei subsp. hormaechei type strain, and other available Enterobacter type strains were analysed in conjunction with all extant Enterobacter genomes in NCBI’s RefSeq using Average Nucleotide Identity (ANI).

Results: There were five recognizable subspecies of E. hormaechei: E. hormaechei subsp. hoffmannii subsp. nov., E. hormaechei subsp. xiangfangensis comb. nov., and the three previously known subspecies. One of the strains sequenced from the E. cloacae complex was not a novel E. hormaechei subspecies but rather a member of a clade of a novel species: E. roggenkampii sp. nov.. E. muelleri was determined to be a later heterotypic synonym of E. asburiae which should take precedence.

Conclusion: The phylogeny of the Enterobacter genus, particularly the cloacae complex, was re-evaluated based on the type strain genome sequences and all other available Enterobacter genomes in RefSeq.

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Most cited references 47

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APE: Analyses of Phylogenetics and Evolution in R language.

E Paradis, J. Claude, K Strimmer (2004)

Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.

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Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Ivica Letunic, Peer Bork (2016)

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users.

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Genome sequence-based species delimitation with confidence intervals and improved distance functions

Jan Meier-Kolthoff, Alexander Auch, Hans-Peter Klenk … (2013)

Background For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes. Its application as an in-silico replacement for DDH was recently introduced. The main challenge in the implementation of such an application is to produce digital DDH values that must mimic the wet-lab DDH values as close as possible to ensure consistency in the Prokaryotic species concept. Results Correlation and regression analyses were used to determine the best-performing methods and the most influential parameters. GBDP was further enriched with a set of new features such as confidence intervals for intergenomic distances obtained via resampling or via the statistical models for DDH prediction and an additional family of distance functions. As in previous analyses, GBDP obtained the highest agreement with wet-lab DDH among all tested methods, but improved models led to a further increase in the accuracy of DDH prediction. Confidence intervals yielded stable results when inferred from the statistical models, whereas those obtained via resampling showed marked differences between the underlying distance functions. Conclusions Despite the high accuracy of GBDP-based DDH prediction, inferences from limited empirical data are always associated with a certain degree of uncertainty. It is thus crucial to enrich in-silico DDH replacements with confidence-interval estimation, enabling the user to statistically evaluate the outcomes. Such methodological advancements, easily accessible through the web service at http://ggdc.dsmz.de, are crucial steps towards a consistent and truly genome sequence-based classification of microorganisms.

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Author and article information

Contributors

Granger G. Sutton: Role: ConceptualizationRole: Data CurationRole: Formal AnalysisRole: Funding AcquisitionRole: InvestigationRole: MethodologyRole: SoftwareRole: ValidationRole: Writing – Original Draft PreparationRole: Writing – Review & Editing

ORCID: https://orcid.org/0000-0001-7498-8048

Lauren M. Brinkac: Role: Data CurationRole: MethodologyRole: VisualizationRole: Writing – Review & Editing

Thomas H. Clarke: Role: Formal AnalysisRole: MethodologyRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – Review & Editing

Derrick E. Fouts: Role: ConceptualizationRole: Data CurationRole: Formal AnalysisRole: Funding AcquisitionRole: InvestigationRole: MethodologyRole: Project AdministrationRole: SoftwareRole: SupervisionRole: Writing – Review & Editing

Journal

Journal ID (nlm-ta): F1000Res

Journal ID (iso-abbrev): F1000Res

Journal ID (pmc): F1000Research

Title: F1000Research

Publisher: F1000 Research Limited (London, UK )

ISSN (Electronic): 2046-1402

Publication date (Electronic): 29 June 2018

Publication date Collection: 2018

Volume: 7

Electronic Location Identifier: 521

Affiliations

[1 ]J Craig Venter Institute, Rockville, MD, 20850, USA

[1 ]Institute of Medical Microbiology, Justus-Liebig University Giessen, Giessen, Germany

J. Craig Venter Institute, USA

[1 ]Quadram Institute, Norwich, UK

[1 ]Institute of Medical Microbiology, Justus-Liebig University Giessen, Giessen, Germany

J. Craig Venter Institute, USA

[1 ]Quadram Institute, Norwich, UK

J. Craig Venter Institute, USA

Author notes

[a ] GSutton@ 123456jcvi.org

No competing interests were disclosed.

Competing interests: No competing interests were disclosed.

Author information

Granger G. Sutton https://orcid.org/0000-0001-7498-8048

Article

DOI: 10.12688/f1000research.14566.2

PMC ID: 6097438

PubMed ID: 30430006

SO-VID: 687f5d71-0aba-49ee-913e-e66494ffe4c4

License:

This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

History

Date accepted : 27 June 2018

Funding

Funded by: U.S. Department of Health and Human Services

Award ID: U19AI110819

Funded by: National Institutes of Health

Award ID: U19AI110819

This work has been funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services under award number U19AI110819.

The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Enterobacter hormaechei subsp. hoffmannii subsp. nov., Enterobacter hormaechei subsp. xiangfangensis comb. nov., Enterobacter roggenkampii sp. nov., and Enterobacter muelleri is a later heterotypic synonym of Enterobacter asburiae based on computational analysis of sequenced Enterobacter genomes.

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G3: Genes|Genomes|Genetics

Most cited references 47

APE: Analyses of Phylogenetics and Evolution in R language.

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Genome sequence-based species delimitation with confidence intervals and improved distance functions

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