Strain identifier
BacDive ID: 130955
Type strain: 
Species: Hafnia alvei
Strain Designation: 1004
Strain history: <- M. Jünger, Universitätsmedizin Göttingen, Abt. Anaesthesiologie, Georg-August-Universität,Germany; 1004 <- Abt. Medizinische Mikrobiologie
NCBI tax ID(s): 569 (species)
version 9.3 (current version)
General
@ref: 22247
BacDive-ID: 130955
DSM-Number: 24119
keywords: genome sequence, Bacteria, mesophilic, Gram-negative, human pathogen
description: Hafnia alvei 1004 is a mesophilic, Gram-negative human pathogen that was isolated from tracheal aspirate.
NCBI tax id
- NCBI tax id: 569
- Matching level: species
strain history
- @ref: 22247
- history: <- M. Jünger, Universitätsmedizin Göttingen, Abt. Anaesthesiologie, Georg-August-Universität,Germany; 1004 <- Abt. Medizinische Mikrobiologie
doi: 10.13145/bacdive130955.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Hafniaceae
- genus: Hafnia
- species: Hafnia alvei
- full scientific name: Hafnia alvei Møller 1954 (Approved Lists 1980)
@ref: 22247
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Hafniaceae
genus: Hafnia
species: Hafnia alvei
full scientific name: Hafnia alvei Møller 1954
strain designation: 1004
type strain: no
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 97.6 |
| 125438 | negative | 99.5 |
multimedia
- @ref: 22247
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_24119.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 22247
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
- @ref: 22247
- growth: positive
- type: growth
- temperature: 37
Physiology and metabolism
oxygen tolerance
- @ref: 125439
- oxygen tolerance: aerobe
- confidence: 92.8
spore formation
- @ref: 125439
- spore formation: no
- confidence: 93.3
compound production
- @ref: 22247
- compound: volatile organic compounds
Isolation, sampling and environmental information
isolation
- @ref: 22247
- sample type: tracheal aspirate
- geographic location: Göttingen
- country: Germany
- origin.country: DEU
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host Body-Site | #Oral cavity and airways | #Trachea |
| #Host Body Product | #Fluids | #Aspirate |
Safety information
risk assessment
- @ref: 22247
- pathogenicity human: yes
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Hafnia paralvei strain FDAARGOS_1502 | 546367.114 | complete | patric | 546367 |
| 66792 | Hafnia paralvei strain FDAARGOS_1502 | 546367.116 | complete | patric | 546367 |
| 66792 | Hafnia paralvei strain FDAARGOS_1502 | 546367.115 | complete | patric | 546367 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.5 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 96.017 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 88.79 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 60.285 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 99 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 73.6 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 93.3 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 72 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 97.6 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 92.8 |
External links
@ref: 22247
culture collection no.: DSM 24119
straininfo link
- @ref: 89432
- straininfo: 404921
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 22247 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-24119 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24119) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 89432 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID404921.1 | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 10.1101/2024.08.12.607695 | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 | https://github.com/GenomeNet/deepG |