Strain identifier
BacDive ID: 132371
Type strain: 
Species: Haematospirillum jordaniae
Strain Designation: H5569
Strain history: <- B. Humrighouse, CDC <- Division of Consolidated Laboratory Services, Richmond, VA, USA <- unknown, HealthPartners Laboratories; H5569
NCBI tax ID(s): 1549855 (species)
version 8.1 (current version)
General
@ref: 24160
BacDive-ID: 132371
DSM-Number: 28903
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, human pathogen
description: Haematospirillum jordaniae H5569 is a microaerophile, mesophilic, Gram-negative human pathogen that was isolated from human blood, 59-year-old male.
NCBI tax id
- NCBI tax id: 1549855
- Matching level: species
strain history
- @ref: 24160
- history: <- B. Humrighouse, CDC <- Division of Consolidated Laboratory Services, Richmond, VA, USA <- unknown, HealthPartners Laboratories; H5569
doi: 10.13145/bacdive132371.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodospirillales
- family: Rhodospirillaceae
- genus: Haematospirillum
- species: Haematospirillum jordaniae
- full scientific name: Haematospirillum jordaniae Humrighouse et al. 2016
@ref: 24160
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodospirillales
family: Rhodospirillaceae
genus: Haematospirillum
species: Haematospirillum jordaniae
full scientific name: Haematospirillum jordaniae Humrighouse et al. 2016
strain designation: H5569
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.999
colony morphology
- @ref: 63361
- incubation period: 2 days
Culture and growth conditions
culture medium
- @ref: 24160
- name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)
- growth: yes
- link: https://mediadive.dsmz.de/medium/693
- composition: Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 63361 | positive | growth | 37 | mesophilic |
| 24160 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 63361
- oxygen tolerance: microaerophile
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.997 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68373 | 16199 | urea | - | hydrolysis |
| 68373 | 17632 | nitrate | - | reduction |
| 68373 | 606565 | hippurate | - | hydrolysis |
| 68373 | 78019 | triphenyltetrazolium chloride | - | reduction |
| 68373 | 17634 | D-glucose | - | assimilation |
| 68373 | 30031 | succinate | - | assimilation |
| 68373 | 30089 | acetate | - | assimilation |
| 68373 | 17272 | propionate | - | assimilation |
| 68373 | 25115 | malate | - | assimilation |
| 68373 | 16947 | citrate | - | assimilation |
antibiotic resistance
| @ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. |
|---|---|---|---|---|---|
| 68373 | 48923 | erythromycin | yes | yes | 14 µg |
| 68373 | 474053 | cefazolin | yes | yes | 224 µg |
| 68373 | 100147 | nalidixic acid | yes | yes | 84 µg |
metabolite production
- @ref: 68373
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: no
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 68373 | alkaline phosphatase | + | 3.1.3.1 |
| 68373 | L-aspartate arylamidase | - | 3.4.11.21 |
| 68373 | L-arginine arylamidase | - | |
| 68373 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
| 68373 | gamma-glutamyltransferase | - | 2.3.2.2 |
| 68373 | esterase | - | |
| 68373 | urease | - | 3.5.1.5 |
API CAM
| @ref | URE | NIT | EST | HIP | GGT | TTC | PYRA | ArgA | AspA | PAL | H2S | GLU | SUT | NAL | CFZ | ACE | PROP | MLT | CIT | ERO |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 24160 | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 24160 | human blood, 59-year-old male | Virginia | USA | USA | North America | |
| 63361 | Human blood | Virginia | USA | USA | North America | 2000 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Human | #Male |
| #Host Body Product | #Fluids | #Blood |
taxonmaps
- @ref: 69479
- File name: preview.99_2081.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_292;96_1143;97_1341;98_1625;99_2081&stattab=map
- Last taxonomy: Haematospirillum jordaniae subclade
- 16S sequence: KM083603
- Sequence Identity:
- Total samples: 6872
- soil counts: 1366
- aquatic counts: 4504
- animal counts: 753
- plant counts: 249
Safety information
risk assessment
- @ref: 24160
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24160
- description: Haematospirillum jordaniae strain H5569 16S ribosomal RNA gene, partial sequence
- accession: KM083603
- length: 1408
- database: ena
- NCBI tax ID: 1549855
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Haematospirillum jordaniae H5569 | GCA_001611975 | complete | ncbi | 1549855 |
| 66792 | Haematospirillum jordaniae H5569 | GCA_012102615 | contig | ncbi | 1549855 |
| 66792 | Haematospirillum jordaniae H5569 | 2718217839 | complete | img | 1549855 |
GC content
- @ref: 24160
- GC-content: 49.9
- method: sequence analysis
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| flagellated | yes | 75.584 | no |
| gram-positive | no | 99.219 | no |
| anaerobic | no | 95.877 | yes |
| aerobic | no | 81.199 | no |
| halophile | no | 65.865 | no |
| spore-forming | no | 93.994 | no |
| glucose-util | yes | 52.677 | yes |
| motile | yes | 88.734 | no |
| thermophile | no | 85.429 | no |
| glucose-ferment | no | 83.344 | no |
External links
@ref: 24160
culture collection no.: DSM 28903, CCUG 66838
straininfo link
- @ref: 90715
- straininfo: 406791
literature
- topic: Phylogeny
- Pubmed-ID: 26857139
- title: Haematospirillum jordaniae gen. nov., sp. nov., isolated from human blood samples.
- authors: Humrighouse BW, Emery BD, Kelly AJ, Metcalfe MG, Mbizo J, McQuiston JR
- journal: Antonie Van Leeuwenhoek
- DOI: 10.1007/s10482-016-0654-0
- year: 2016
- mesh: Adult, Aged, Base Composition, Base Sequence, Blood/*microbiology, Cells, Cultured, DNA, Bacterial/genetics, Gram-Negative Bacterial Infections/*blood/*microbiology, Humans, Male, Middle Aged, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodospirillaceae/classification/genetics/*isolation & purification, Sequence Analysis, DNA
- topic2: Pathogenicity
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | |||
| 24160 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28903 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28903) | |||
| 63361 | Curators of the CCUG | https://www.ccug.se/strain?id=66838 | Culture Collection University of Gothenburg (CCUG) (CCUG 66838) | |||
| 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 | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 68373 | Automatically annotated from API CAM | |||||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 90715 | 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-ID406791.1 |