Strain identifier
BacDive ID: 381
Type strain:
Species: Bordetella holmesii
Strain Designation: 5589, F5101
Strain history: CIP <- 1995, R.S. Weyant, CDC: strain F5101 <- E. Gorzynski: strain 5589
NCBI tax ID(s): 1247649 (strain), 35814 (species)
General
@ref: 5044
BacDive-ID: 381
DSM-Number: 13416
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative
description: Bordetella holmesii 5589 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from human blood.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1247649 | strain |
35814 | species |
strain history
@ref | history |
---|---|
5044 | <- CCUG <- R. S. Weyant, CDC |
119931 | CIP <- 1995, R.S. Weyant, CDC: strain F5101 <- E. Gorzynski: strain 5589 |
doi: 10.13145/bacdive381.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Alcaligenaceae
- genus: Bordetella
- species: Bordetella holmesii
- full scientific name: Bordetella holmesii Weyant et al. 1995
@ref: 5044
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Alcaligenaceae
genus: Bordetella
species: Bordetella holmesii
full scientific name: Bordetella holmesii Weyant et al. 1995
strain designation: 5589, F5101
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.992 | ||
119931 | negative | oval-shaped | no |
colony morphology
- @ref: 5044
- incubation period: 2-3 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5044 | COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) | yes | https://mediadive.dsmz.de/medium/693 | Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base |
41151 | MEDIUM 6 - Columbia agar with 10 % horse blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml) | |
5044 | BORDET-GENGOU-MEDIUM (DIFCO) (DSMZ Medium 438) | yes | https://mediadive.dsmz.de/medium/438 | Name: BORDET-GENGOU-MEDIUM (DIFCO) (DSMZ Medium 438) Composition: Horse blood 150.0 g/l Bordet-Gengou-Agar-Base |
119931 | CIP Medium 6 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5044 | positive | growth | 37 | mesophilic |
41151 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 119931
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 99 |
69480 | no | 99.982 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68368 | 30849 | L-arabinose | - | fermentation |
68368 | 27613 | amygdalin | - | fermentation |
68368 | 28053 | melibiose | - | fermentation |
68368 | 17992 | sucrose | - | fermentation |
68368 | 62345 | L-rhamnose | - | fermentation |
68368 | 30911 | sorbitol | - | fermentation |
68368 | 17268 | myo-inositol | - | fermentation |
68368 | 16899 | D-mannitol | - | fermentation |
68368 | 17634 | D-glucose | - | fermentation |
68368 | 5291 | gelatin | - | hydrolysis |
68368 | 27897 | tryptophan | - | energy source |
68368 | 16199 | urea | - | hydrolysis |
68368 | 16947 | citrate | - | assimilation |
68368 | 18257 | ornithine | - | degradation |
68368 | 25094 | lysine | - | degradation |
68368 | 29016 | arginine | - | hydrolysis |
119931 | 17632 | nitrate | + | reduction |
119931 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68368 | 15688 | acetoin | yes |
68368 | 35581 | indole | no |
68368 | 16136 | hydrogen sulfide | no |
119931 | 35581 | indole | yes |
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | indole test |
---|---|---|---|---|
68368 | 15688 | acetoin | + | |
68368 | 35581 | indole | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
68368 | cytochrome oxidase | - | 1.9.3.1 |
68368 | gelatinase | - | |
68368 | tryptophan deaminase | - | 4.1.99.1 |
68368 | urease | - | 3.5.1.5 |
68368 | ornithine decarboxylase | - | 4.1.1.17 |
68368 | lysine decarboxylase | - | 4.1.1.18 |
68368 | arginine dihydrolase | - | 3.5.3.6 |
68368 | beta-galactosidase | - | 3.2.1.23 |
119931 | oxidase | + | |
119931 | catalase | - | 1.11.1.6 |
119931 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119931 | - | - | + | + | - | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - |
API 20E
@ref | ONPG | ADH Arg | LDC Lys | ODC | CIT | H2S | URE | TDA Trp | IND | VP | GEL | GLU | MAN | INO | Sor | RHA | SAC | MEL | AMY | ARA | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
5044 | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
5044 | human blood | Buffalo, N.Y. | USA | USA | North America | |
45947 | Human periodontitis | |||||
51918 | Human blood,37-yr-old man | N.Y.,Buffalo | USA | USA | North America | |
119931 | Human, Blood | Buffalo, New York | United States of America | USA | North America | 1983 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Human | |
#Host Body Product | #Fluids | #Blood |
taxonmaps
- @ref: 69479
- File name: preview.99_12.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_9;97_9;98_11;99_12&stattab=map
- Last taxonomy: Bordetella pertussis
- 16S sequence: NR_029173
- Sequence Identity:
- Total samples: 23163
- soil counts: 4730
- aquatic counts: 9586
- animal counts: 5464
- plant counts: 3383
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
5044 | 2 | Risk group (German classification) |
119931 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Bordetella holmesii strain LMG 15945 16S ribosomal RNA gene, partial sequence | KF601905 | 1376 | ena | 35814 |
20218 | Bordetella holmesii CDC F5101 16S ribosomal RNA gene, complete sequence | U04820 | 1525 | ena | 1247649 |
5044 | Bordetella holmesii strain CDC F5101 16S ribosomal RNA, partial sequence | NR_029173 | 1525 | nuccore | 35814 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Bordetella holmesii ATCC 51541 | GCA_000612485 | complete | ncbi | 1247649 |
66792 | Bordetella holmesii ATCC 51541 | 1247649.3 | complete | patric | 1247649 |
66792 | Bordetella holmesii ATCC 51541 | 2576861425 | complete | img | 1247649 |
66792 | Bordetella holmesii strain FDAARGOS_1539 | 35814.89 | complete | patric | 35814 |
66792 | Bordetella holmesii strain FDAARGOS_1539 | 35814.88 | complete | patric | 35814 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | yes | 78.459 | no |
flagellated | no | 66.234 | no |
gram-positive | no | 98.603 | no |
anaerobic | no | 98.442 | no |
halophile | no | 79.359 | no |
spore-forming | no | 94.829 | no |
thermophile | no | 99.327 | yes |
glucose-util | no | 82.253 | no |
aerobic | yes | 88.127 | no |
glucose-ferment | no | 92.307 | yes |
External links
@ref: 5044
culture collection no.: DSM 13416, ATCC 51541, CCM 4585, CCUG 13416, CCUG 34073, CDC F5101, LMG 15945, CIP 104394
straininfo link
- @ref: 70061
- straininfo: 9897
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11168088 | Bordetella holmesii isolated from a patient with sickle cell anemia: analysis and comparison with other Bordetella holmesii isolates. | Njamkepo E, Delisle F, Hagege I, Gerbaud G, Guiso N | Clin Microbiol Infect | 10.1046/j.1469-0691.2000.00032.x | 2000 | Adhesins, Bacterial/analysis, Adult, Anemia, Sickle Cell/blood/complications/*microbiology, Bacterial Proteins/*analysis/blood/genetics, Bacterial Toxins/analysis, Bordetella/*classification/genetics/isolation & purification, Bordetella Infections/blood/complications/*microbiology, Humans, Immunoblotting, Species Specificity | Pathogenicity |
Metabolism | 27448237 | BipA Is Associated with Preventing Autoagglutination and Promoting Biofilm Formation in Bordetella holmesii. | Hiramatsu Y, Saito M, Otsuka N, Suzuki E, Watanabe M, Shibayama K, Kamachi K | PLoS One | 10.1371/journal.pone.0159999 | 2016 | Agglutination/*genetics, Agglutination Tests, Amino Acid Sequence, Animals, Bacterial Outer Membrane Proteins/chemistry/*genetics/*metabolism, *Biofilms, Bordetella/*physiology, Bordetella Infections/microbiology, Gene Expression Regulation, Bacterial, Mice, Mutation, Pneumonia, Bacterial/microbiology | |
Pathogenicity | 28524084 | Bordetella holmesii: Lipid A Structures and Corresponding Genomic Sequences Comparison in Three Clinical Isolates and the Reference Strain ATCC 51541. | Bouchez V, AlBitar-Nehme S, Novikov A, Guiso N, Caroff M | Int J Mol Sci | 10.3390/ijms18051080 | 2017 | Bordetella pertussis/*chemistry/*genetics, Endotoxins/chemistry/genetics, Gas Chromatography-Mass Spectrometry, Lipid A/*chemistry/genetics, Mass Spectrometry, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization | |
Metabolism | 32899371 | Bordetella holmesii Lipopolysaccharide Hide and Seek Game with Pertussis: Structural Analysis of the O-Specific Polysaccharide and the Core Oligosaccharide of the Type Strain ATCC 51541. | Ucieklak K, Koj S, Niedziela T | Int J Mol Sci | 10.3390/ijms21176433 | 2020 | Bordetella/*chemistry, Lipopolysaccharides/*chemistry, Mass Spectrometry, O Antigens/*chemistry, Oligosaccharides/*chemistry, Whooping Cough/*metabolism/microbiology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5044 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13416) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-13416 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
41151 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16297 | ||||
45947 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 13416) | https://www.ccug.se/strain?id=13416 | |||
51918 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 34073) | https://www.ccug.se/strain?id=34073 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68368 | Automatically annotated from API 20E | |||||
68382 | Automatically annotated from API zym | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
70061 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID9897.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119931 | Curators of the CIP | Collection of Institut Pasteur (CIP 104394) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104394 |