Bordetella holmesii (DSM 13416, ATCC 51541, CCM 4585)

Name: Bordetella holmesii (DSM 13416, ATCC 51541, CCM 4585)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 381

Type strain

Strain Designation 5589, F5101

Culture col. no. DSM 13416 ATCC 51541 CCM 4585 CCUG 13416 CCUG 34073 5 more

NCBI tax ID(s) 1247649 35814

Special Collections DSMZ CCUG CIP

History DSMZ <- CCUG <- R. S. Weyant, CDC CIP <- 1995, R.S. Weyant, CDC: strain F5101 <- E. Gorzynski: strain 5589

Links

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

Gram-negative oval-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 9897

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

@ref 20215

Last LPSN update 2026-05-29 08:25:01

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Alcaligenaceae

Genus Bordetella

Species Bordetella holmesii

Full scientific name Bordetella holmesii Weyant et al. 1995

BacDive ID	Other strains from **Bordetella holmesii** (9)	Type strain
134581	B. holmesii Hol B1, CIP 106630
135543	B. holmesii 149013, G8341, CIP 104396, ATCC 700053
138611	B. holmesii G8350, CIP 104397
139052	B. holmesii 92A 2997, G7702, CIP 104395, ATCC 700052, ...
147591	B. holmesii CCUG 33848, LMG 15047
152732	B. holmesii CCUG 47500
154454	B. holmesii CCUG 53681
155710	B. holmesii CCUG 59107
155745	B. holmesii CCUG 59194

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119931	negative	oval-shaped
125439	negative		96.64
125438	negative		97.479

Colony morphology

5044

Incubation period2-3 days

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
5044	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	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		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)	Medium recipe at MediaDive	Name: BORDET-GENGOU-MEDIUM (DIFCO) (DSMZ Medium 438) Composition: Horse blood 150.0 g/l Bordet-Gengou-Agar-Base
119931	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
5044	positive	growth	37
41151	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
119931	obligate aerobe
125439	obligate aerobe	97.039

Spore formation

@ref	Spore formation	Confidence
125439		99.488
125438		94.028

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68368	27613 ChEBI	amygdalin	-	fermentation	from API 20E
68368	29016 ChEBI	arginine	-	hydrolysis	from API 20E
68368	16947 ChEBI	citrate	-	assimilation	from API 20E
68368	17634 ChEBI	D-glucose	-	fermentation	from API 20E
68368	16899 ChEBI	D-mannitol	-	fermentation	from API 20E
68368	5291 ChEBI	gelatin	-	hydrolysis	from API 20E
68368	30849 ChEBI	L-arabinose	-	fermentation	from API 20E
68368	62345 ChEBI	L-rhamnose	-	fermentation	from API 20E
68368	25094 ChEBI	lysine	-	degradation	from API 20E
68368	28053 ChEBI	melibiose	-	fermentation	from API 20E
68368	17268 ChEBI	myo-inositol	-	fermentation	from API 20E
119931	17632 ChEBI	nitrate	+	reduction
119931	16301 ChEBI	nitrite	-	reduction
68368	18257 ChEBI	ornithine	-	degradation	from API 20E
68368	30911 ChEBI	sorbitol	-	fermentation	from API 20E
68368	17992 ChEBI	sucrose	-	fermentation	from API 20E
68368	27897 ChEBI	tryptophan	-	energy source	from API 20E
68368	16199 ChEBI	urea	-	hydrolysis	from API 20E

Metabolite production

@ref	Chebi-ID	Metabolite
68368	15688 ChEBI	acetoin	from API 20E
68368	16136 ChEBI	hydrogen sulfide	from API 20E
119931	35581 ChEBI	indole
68368	35581 ChEBI	indole	from API 20E

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Indole test
68368	15688 ChEBI	acetoin	+		from API 20E
68368	35581 ChEBI	indole		-	from API 20E

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68382	beta-galactosidase	-	3.2.1.23	from API zym
68368	beta-galactosidase	-	3.2.1.23	from API 20E
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119931	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68368	gelatinase	-		from API 20E
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68368	lysine decarboxylase	-	4.1.1.18	from API 20E
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E
119931	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
68368	tryptophan deaminase	-	4.1.99.1	from API 20E
119931	urease	-	3.5.1.5
68368	urease	-	3.5.1.5	from API 20E
68382	valine arylamidase	-		from API zym

API 20E

@ref	ONPG	ADH (Arg)	LDC (Lys)	ODC	CIT	H2S productionH2S	URE	TDA (Trp)	IND	Acetoin production (Voges Proskauer test)VP	GEL	GLU	MAN	INO	Sor	RHA	SAC	MEL	AMY	ARA	OX	Nitrite productionNO2	Reduction to N2N2	MotilityMOB	Growth on MacConkey mediumMAC	OF-O	OF-F
5044	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119931	-	-	+	+	-	+	-	-	-	-	-	-	-	-	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Fluids	#Blood

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
5044	human blood	Homo sapiens	Buffalo, N.Y.	USA	USA	North America
45947	Human periodontitis	Homo sapiens
51918	Human blood,37-yr-old man	Homo sapiens	N.Y.,Buffalo	USA	USA	North America
119931	Human, Blood	Homo sapiens	Buffalo, New York	United States of America	USA	North America	1983

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
5044	2	Risk group (German classification) According to TRBA 466
119931	2	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Bordetella holmesii strain FDAARGOS_1539	complete		35814.89		35814	99.65
124043	ASM2073598v1 assembly for Bordetella holmesii FDAARGOS_1539	complete	GCA_020735985	35814.88	8120703930	35814	97.86
124043	ASM4829672v1 assembly for Bordetella holmesii ATCC 51541 CDC F5101	complete	GCA_048296725			1247649	94.63
66792	ASM61248v1 assembly for Bordetella holmesii ATCC 51541	complete	GCA_000612485	1247649.3	2576861425	1247649	68.68

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Bordetella holmesii strain LMG 15945 16S ribosomal RNA gene, partial sequence	KF601905	1376	35814
20218	Bordetella holmesii CDC F5101 16S ribosomal RNA gene, complete sequence	U04820	1525	1247649
5044	Bordetella holmesii strain CDC F5101 16S ribosomal RNA, partial sequence	NR_029173	1525	35814

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Bordetella holmesii strain FDAARGOS_1539
BV-BRC: 35814.89

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.04	no
125439	gram_stain	BacteriaNetⓘ	negative	96.64	no
125439	motility	BacteriaNetⓘ	yes	81.74	no
125439	spore_formation	BacteriaNetⓘ	no	99.49	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Bordetella holmesii ATCC 51541 ATCC 51541
NCBI: GCA_000612485.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.48	no
125438	anaerobic	anaerobicⓘ	no	95.61	no
125438	aerobic	aerobicⓘ	yes	86.71	yes
125438	spore-forming	spore-formingⓘ	no	94.03	no
125438	thermophilic	thermophileⓘ	no	98.00	yes
125438	flagellated	motile2+ⓘ	no	54.36	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Conserved Structural Features of Core Oligosaccharides among the Lipopolysaccharides of Respiratory Pathogens from the Genus Bordetella Analyzed Exclusively by NMR Spectroscopy.	Ucieklak K, Koj S, Niedziela T.	Int J Mol Sci	10.3390/ijms22031029	2021
Phylogeny	Detection and differentiation of Bordetella spp. by real-time PCR.	Koidl C, Bozic M, Burmeister A, Hess M, Marth E, Kessler HH.	J Clin Microbiol	10.1128/jcm.01303-06	2007
	Whole-Genome Sequences of Bacteremia Isolates of Bordetella holmesii.	Tettelin H, Hooven TA, Zhao X, Su Q, Sadzewicz L, Tallon LJ, Fraser CM, Ratner AJ.	Genome Announc	10.1128/genomea.01023-17	2017
	Molecular detection of Bordetella holmesii in two infants with pertussis-like syndrome: the first report from Iran.	Lotfi MN, Nikbin VS, Nasiri O, Badmasti F, Shahcheraghi F.	Iran J Microbiol		2017
Enzymology	Validation and Implementation of a Diagnostic Algorithm for DNA Detection of Bordetella pertussis, B. parapertussis, and B. holmesii in a Pediatric Referral Hospital in Barcelona, Spain.	Valero-Rello A, Henares D, Acosta L, Jane M, Jordan I, Godoy P, Munoz-Almagro C.	J Clin Microbiol	10.1128/jcm.01231-18	2019
Pathogenicity	Environmental Origin of the Genus Bordetella.	Hamidou Soumana I, Linz B, Harvill ET.	Front Microbiol	10.3389/fmicb.2017.00028	2017
	Evaluation of amplification targets for the specific detection of Bordetella pertussis using real-time polymerase chain reaction.	Hasan MR, Tan R, Al-Rawahi GN, Thomas E, Tilley P.	Can J Infect Dis Med Microbiol	10.1155/2014/763128	2014
Phylogeny	Real-time PCR assay targeting IS481 of Bordetella pertussis and molecular basis for detecting Bordetella holmesii.	Reischl U, Lehn N, Sanden GN, Loeffelholz MJ.	J Clin Microbiol	10.1128/jcm.39.5.1963-1966.2001	2001
Genetics	Genomic characterization of Kerstersia gyiorum SWMUKG01, an isolate from a patient with respiratory infection in China.	Li Y, Tang M, Wang G, Li C, Chen W, Luo Y, Zeng J, Hu X, Zhou Y, Gao Y, Zhang L.	PLoS One	10.1371/journal.pone.0214686	2019
Enzymology	Identification of Bordetella pertussis in a critically ill human immunodeficiency virus-infected patient by direct genotypical analysis of Gram-stained material and discrimination from B. holmesii by using a unique recA gene restriction enzyme site.	Vielemeyer O, Crouch JY, Edberg SC, Howe JG.	J Clin Microbiol	10.1128/jcm.42.2.847-849.2004	2004
Phylogeny	Fluorescence in situ hybridization for rapid identification of Achromobacter xylosoxidans and Alcaligenes faecalis recovered from cystic fibrosis patients.	Wellinghausen N, Wirths B, Poppert S.	J Clin Microbiol	10.1128/jcm.00508-06	2006
	Evaluation of real-time PCR for diagnosis of Bordetella pertussis infection.	Knorr L, Fox JD, Tilley PA, Ahmed-Bentley J.	BMC Infect Dis	10.1186/1471-2334-6-62	2006
	Development and evaluation of a loop-mediated isothermal amplification method for rapid diagnosis of Bordetella pertussis infection.	Kamachi K, Toyoizumi-Ajisaka H, Toda K, Soeung SC, Sarath S, Nareth Y, Horiuchi Y, Kojima K, Takahashi M, Arakawa Y.	J Clin Microbiol	10.1128/jcm.44.5.1899-1902.2006	2006
	In silico design and validation of a highly degenerate primer pair: a systematic approach.	Chukwuemeka PO, Umar HI, Olukunle OF, Oretade OM, Olowosoke CB, Akinsola EO, Elabiyi MO, Kurmi UG, Eigbe JO, Oyelere BR, Isunu LE, Oretade OJ.	J Genet Eng Biotechnol	10.1186/s43141-020-00086-y	2020
Enzymology	Evaluation of real-time PCR for detection of and discrimination between Bordetella pertussis, Bordetella parapertussis, and Bordetella holmesii for clinical diagnosis.	Templeton KE, Scheltinga SA, van der Zee A, Diederen BM, van Kruijssen A, Goossens H, Kuijper E, Claas EC.	J Clin Microbiol	10.1128/jcm.41.9.4121-4126.2003	2003
Phylogeny	Multiplex LightCycler PCR assay for detection and differentiation of Bordetella pertussis and Bordetella parapertussis in nasopharyngeal specimens.	Sloan LM, Hopkins MK, Mitchell PS, Vetter EA, Rosenblatt JE, Harmsen WS, Cockerill FR, Patel R.	J Clin Microbiol	10.1128/jcm.40.1.96-100.2002	2002
	Rapid PCR Detection of Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum.	Cunningham SA, Mandrekar JN, Rosenblatt JE, Patel R.	Int J Bacteriol	10.1155/2013/168742	2013
Enzymology	Real-time LightCycler PCR for detection and discrimination of Bordetella pertussis and Bordetella parapertussis.	Kosters K, Reischl U, Schmetz J, Riffelmann M, Wirsing von Konig CH.	J Clin Microbiol	10.1128/jcm.40.5.1719-1722.2002	2002
Phylogeny	Phylogenetic analysis of Ara+ and Ara- Burkholderia pseudomallei isolates and development of a multiplex PCR procedure for rapid discrimination between the two biotypes.	Dharakul T, Tassaneetrithep B, Trakulsomboon S, Songsivilai S.	J Clin Microbiol	10.1128/jcm.37.6.1906-1912.1999	1999
Phylogeny	Genotypic characterization of Bradyrhizobium strains nodulating small Senegalese legumes by 16S-23S rRNA intergenic gene spacers and amplified fragment length polymorphism fingerprint analyses.	Doignon-Bourcier F, Willems A, Coopman R, Laguerre G, Gillis M, de Lajudie P.	Appl Environ Microbiol	10.1128/aem.66.9.3987-3997.2000	2000
	The rtxA toxin gene of Kingella kingae: a pertinent target for molecular diagnosis of osteoarticular infections.	Lehours P, Freydiere AM, Richer O, Burucoa C, Boisset S, Lanotte P, Prere MF, Ferroni A, Lafuente C, Vandenesch F, Megraud F, Menard A.	J Clin Microbiol	10.1128/jcm.01657-10	2011
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
Phylogeny	Bordetella holmesii sp. nov., a new gram-negative species associated with septicemia.	Weyant RS, Hollis DG, Weaver RE, Amin MF, Steigerwalt AG, O'Connor SP, Whitney AM, Daneshvar MI, Moss CW, Brenner DJ.	J Clin Microbiol	10.1128/jcm.33.1.1-7.1995	1995

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 .
#119931	Collection of Institut Pasteur ; Curators of the CIP; CIP 104394
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Bordetella holmesii (DSM 13416, ATCC 51541, CCM 4585)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_020735985

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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