Name: Bordetella holmesii 5589
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 381

Type strain:

Species: Bordetella holmesii

Strain Designation: 5589, F5101

Culture col. no.: DSM 13416, ATCC 51541, CCM 4585, CCUG 13416, CCUG 34073, CDC F5101, LMG 15945, CIP 104394

Strain history: CIP <- 1995, R.S. Weyant, CDC: strain F5101 <- E. Gorzynski: strain 5589

NCBI tax ID(s): 1247649 (strain), 35814 (species)

SI-ID 9897

LMG 15945, ATCC 51541, CCUG 34073, CIP 104394, CCM 4585, DSM 13416, NCTC 12912

Other strains from Bordetella holmesii

B. holmesii Hol B1, CIP 106630
B. holmesii 149013, G8341, CIP 104396, ATCC ...
B. holmesii G8350, CIP 104397
B. holmesii 92A 2997, G7702, CIP 104395, ATCC ...
B. holmesii CCUG 33848, LMG 15047
B. holmesii CCUG 47500
B. holmesii CCUG 53681
B. holmesii CCUG 59107
B. holmesii CCUG 59194

Section

Bordetella holmesii 5589 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from human blood.

Gram-negative
mesophilic
obligate aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Alcaligenaceae*
	Genus	*Bordetella*
	Species	**Bordetella holmesii**
	Full Scientific Name (LPSN)	Bordetella holmesii Weyant et al. 1995

Information on morphological and physiological properties Morphology

[Ref.: #119931]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.992

[Ref.: #119931]	Cell shape	oval-shaped

[Ref.: #119931]	Motility	no

[Ref.: #5044]

Incubation period

2-3 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5044]

Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

[Ref.: #5044]

Culture medium growth

[Ref.: #5044]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5044]

Culture medium composition

expand / minimize

[Ref.: #41151]

Culture medium

MEDIUM 6 - Columbia agar with 10 % horse blood

[Ref.: #41151]

Culture medium growth

[Ref.: #41151]

Culture medium composition

expand / minimize

[Ref.: #5044]

Culture medium

BORDET-GENGOU-MEDIUM (DIFCO) (DSMZ Medium 438)

[Ref.: #5044]

Culture medium growth

[Ref.: #5044]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5044]

Culture medium composition

expand / minimize

[Ref.: #119931]

Culture medium

CIP Medium 6

[Ref.: #119931]

Culture medium growth

[Ref.: #119931]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #5044]			growth	37 °C
[Ref.: #41151]			growth	37 °C

[Ref.: #5044]	Temperature range	mesophilic
[Ref.: #41151]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #119931]

Oxygen tolerance

obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.982

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68368]	amygdalin ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	arginine ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	citrate ChEBI	-	assimilation	* from API 20E
[Ref.: #68368]	D-glucose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	D-mannitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	gelatin ChEBI	-	hydrolysis	* from API 20E
[Ref.: #68368]	L-arabinose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	L-rhamnose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	lysine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	melibiose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	myo-inositol ChEBI	-	fermentation	* from API 20E
[Ref.: #119931]	nitrate ChEBI	+	reduction
[Ref.: #119931]	nitrite ChEBI	-	reduction
[Ref.: #68368]	ornithine ChEBI	-	degradation	* from API 20E
[Ref.: #68368]	sorbitol ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	sucrose ChEBI	-	fermentation	* from API 20E
[Ref.: #68368]	tryptophan ChEBI	-	energy source	* from API 20E
[Ref.: #68368]	urea ChEBI	-	hydrolysis	* from API 20E
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #119931]	indole ChEBI	yes
[Ref.: #68368]	acetoin ChEBI	yes	* from API 20E
[Ref.: #68368]	hydrogen sulfide ChEBI	no	* from API 20E
[Ref.: #68368]	indole ChEBI	no	* from API 20E

	Physiological tests	Metabolite	Voges-Proskauer-test	Indole test
[Ref.: #68368]		acetoin ChEBI	+		* from API 20E
[Ref.: #68368]		indole ChEBI		-	* from API 20E

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68368]	arginine dihydrolase	-	3.5.3.6	* from API 20E
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym, API 20E
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #119931]	catalase	-	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68368]	cytochrome oxidase	-	1.9.3.1	* from API 20E
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68368]	gelatinase	-		* from API 20E
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68368]	lysine decarboxylase	-	4.1.1.18	* from API 20E
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68368]	ornithine decarboxylase	-	4.1.1.17	* from API 20E
[Ref.: #119931]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68368]	tryptophan deaminase	-	4.1.99.1	* from API 20E
[Ref.: #119931]	urease	-	3.5.1.5
[Ref.: #68368]	urease	-	3.5.1.5	* from API 20E
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20E:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	beta-GalactosidaseONPG	Arginine dihydrolaseADH (Arg)	Lysine decarboxylaseLDC (Lys)	Ornithine decarboxylaseODC	Citrate utilizationCIT	H2S productionH2S	Urease/urea hydrolysisURE	Tryptophan deaminaseTDA (Trp)	Indole productionIND	Acetoin production (Voges Proskauer test)VP	Gelatinase/gelatin hydrolysisGEL	Fermentation/oxidation of D-glucoseGLU	Fermentation/oxidation of D-mannitolMAN	Fermentation/oxidation of inositolINO	Fermentation/oxidation of sorbitolSor	Fermentation/oxidation of L-rhamnoseRHA	Fermentation/oxidation of sucroseSAC	Fermentation/oxidation of melibioseMEL	Fermentation/oxidation of amygdalinAMY	Fermentation/oxidation of L-arabinoseARA	Cytochrome oxidaseOX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	Oxidative catabolisation of D-glucoseOF-O	Fermentation of D-glucoseOF-F
[Ref.: #5044]	17945	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #119931]	7925	-	-	+	+	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #5044]	Sample type/isolated from	human blood
[Ref.: #5044]	Geographic location (country and/or sea, region)	Buffalo, N.Y.
[Ref.: #5044]	Country	USA
[Ref.: #5044]	Country ISO 3 Code	USA
[Ref.: #5044]	Continent	North America

[Ref.: #45947]	Sample type/isolated from	Human periodontitis

[Ref.: #51918]	Sample type/isolated from	Human blood,37-yr-old man
[Ref.: #51918]	Geographic location (country and/or sea, region)	N.Y.,Buffalo
[Ref.: #51918]	Country	USA
[Ref.: #51918]	Country ISO 3 Code	USA
[Ref.: #51918]	Continent	North America

[Ref.: #119931]	Sample type/isolated from	Human, Blood
[Ref.: #119931]	Geographic location (country and/or sea, region)	Buffalo, New York
[Ref.: #119931]	Country	United States of America
[Ref.: #119931]	Country ISO 3 Code	USA
[Ref.: #119931]	Continent	North America
[Ref.: #119931]	Isolation date	1983
* marker position based on {}

Isolation sources categories

#Host	#Human	-
#Host Body Product	#Fluids	#Blood

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence NR_029173 (>99% sequence identity) for Bordetella pertussis from Microbeatlas

Aquatic Samples	9586
Soil Samples	4730
Animal Samples	5464
Plant Samples	3383
Total Samples	23163

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #5044]	Biosafety level	2	Risk group (German classification) According to TRBA 466
[Ref.: #119931]	Biosafety level	2	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #5044]	Bordetella holmesii strain CDC F5101 16S ribosomal RNA, partial sequence	NR_029173	1525	GenBank	35814 tax ID
[Ref.: #20218]	Bordetella holmesii CDC F5101 16S ribosomal RNA gene, complete sequence	U04820	1525	ENA	1247649 tax ID	*
[Ref.: #20218]	Bordetella holmesii strain LMG 15945 16S ribosomal RNA gene, partial sequence	KF601905	1376	ENA	35814 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Bordetella holmesii ATCC 51541	GCA_000612485	complete	GenBank	1247649 tax ID	*
[Ref.: #66792]	Bordetella holmesii ATCC 51541	1247649.3	complete	PATRIC	1247649 tax ID	*
[Ref.: #66792]	Bordetella holmesii ATCC 51541	2576861425	complete	JGI IMG/M	1247649 tax ID	*
[Ref.: #66792]	Bordetella holmesii strain FDAARGOS_1539	35814.89	complete	PATRIC	35814 tax ID	*
[Ref.: #66792]	Bordetella holmesii strain FDAARGOS_1539	35814.88	complete	PATRIC	35814 tax ID	*

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Bordetella holmesii ATCC 51541 ATCC 51541 NCBI: GCA_000612485.1
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Bordetella holmesii ATCC 51541 ATCC 51541 NCBI: GCA_000612485.1
[Ref.: #69480]	motile	yes	78.459	no
[Ref.: #69480]	flagellated	no	66.234	no
[Ref.: #69480]	gram-positive	no	98.603	no
[Ref.: #69480]	anaerobic	no	98.442	no
[Ref.: #69480]	halophile	no	79.359	no
[Ref.: #69480]	spore-forming	no	94.829	no
[Ref.: #69480]	thermophile	no	99.327	yes
[Ref.: #69480]	glucose-util	no	82.253	no
[Ref.: #69480]	aerobic	yes	88.127	no
[Ref.: #69480]	glucose-ferment	no	92.307	yes

Availability in culture collections External links

[Ref.: #5044]

Culture collection no.

DSM 13416, ATCC 51541, CCM 4585, CCUG 13416, CCUG 34073, CDC F5101, LMG 15945, CIP 104394

[Ref.: #70061]

SI-ID 9897

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	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	*
Pathogenicity	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	*
Metabolism	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	*
Phylogeny	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	*

References

#5044

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13416

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#41151 ; Curators of the CIP;
#45947 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 13416
#51918 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 34073

#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) .

#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.: MicrobeAtlas 1.0 beta .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#70061

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 . ( DOI 10.60712/SI-ID9897.1 )

#119931 Collection of Institut Pasteur ; Curators of the CIP; CIP 104394
* These data were automatically processed and therefore are not curated

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Bordetella holmesii ATCC 51541 ATCC 51541

Bordetella holmesii ATCC 51541 ATCC 51541

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