Klebsiella pneumoniae subsp. pneumoniae (DSM 9376, ATCC 12657, CDC 383-68)

Name: Klebsiella pneumoniae subsp. pneumoniae (DSM 9376, ATCC 12657, CDC 383-68)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 4953

Type strain

Strain Designation A3

Culture col. no. DSM 9376 ATCC 12657 CDC 383-68 NCIB 8805 A3

NCBI tax ID(s) 72407

Special Collections DSMZ

Links

Klebsiella pneumoniae subsp. pneumoniae A3 is a mesophilic human pathogen that produces polysaccharides and was isolated from human faeces.

polysaccharide production mesophilic human pathogen genome sequence

Name and taxonomic classification

SI-ID 3116

LMG 3136,ATCC 12657,NCIB 8805,DSM 9376,NCIMB 8805,BCRC 12284,CCRC 12284

@ref 20215

Last LPSN update 2025-12-16 09:47:57

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Enterobacterales

Family Enterobacteriaceae

Genus Klebsiella

Species Klebsiella pneumoniae subsp. pneumoniae

Full scientific name Klebsiella pneumoniae subsp. pneumoniae (Schroeter 1886) Ørskov 1984

BacDive ID	Other strains from **Klebsiella pneumoniae subsp. pneumoniae** (8)	Type strain
4959	K. pneumoniae subsp. pneumoniae 298-53, 298/53, CCUG 225, NCDC 410-68, DSM ... (type strain)
4954	K. pneumoniae subsp. pneumoniae DSM 9377, ATCC 13887, CDC 421-68, NCTC 9496, ...
4955	K. pneumoniae subsp. pneumoniae C122, DSM 11678, ATCC 33495
4958	K. pneumoniae subsp. pneumoniae C37, LRA 024 11 73, DSM 30102, ATCC 13882, ...
4960	K. pneumoniae subsp. pneumoniae DSM 30105, ATCC 9997, CIP 104034, NCDC 400-68
130304	K. pneumoniae subsp. pneumoniae KlpnKS648, KS648, DSM 29417
162705	K. pneumoniae subsp. pneumoniae JCM 20034, ATCC 8308, IAM 1063, IFO 3319, ...
162983	K. pneumoniae subsp. pneumoniae JCM 20694, ATCC 15574, CDC 414-68, IAM 12626

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.2
125438	negative	100

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
3559	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
3559	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3559	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	aerobe	91.4

Spore formation

@ref	Spore formation	Confidence
125439		91.3

Compound production

@ref	Compound
3559	extracellular polysaccharides
3559	polyphosphate

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
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

Metabolite production

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

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68368	arginine dihydrolase	-	3.5.3.6	from API 20E
68368	beta-galactosidase	+	3.2.1.23	from API 20E
68368	cytochrome oxidase	-	1.9.3.1	from API 20E
68368	gelatinase	-		from API 20E
68368	lysine decarboxylase	+	4.1.1.18	from API 20E
68368	ornithine decarboxylase	-	4.1.1.17	from API 20E

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
3559	+	-	+	-	+	-	+	+	-	+	-	+	+	+	+	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.
3559	+	-	+	-	+	-	-	-	-	+	-	+	+	+	+	+	+	+	+	+	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Human
#Host Body Product	#Gastrointestinal tract

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
3559	human faeces	United Kingdom	GBR	Europe

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Pathogenicity animal	Biosafety level	Biosafety level comment
3559			2	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	NCBI tax ID	Score
66792	ASM1318051v1 assembly for Klebsiella pneumoniae subsp. pneumoniae A3	scaffold	GCA_013180515	72407.1440	72407	64.12
66792	ASM2619775v1 assembly for Klebsiella pneumoniae A3	contig	GCA_026197755	573.52617	573	59.49
66792	ASM990729v1 assembly for Klebsiella pneumoniae A3	contig	GCA_009907295	573.29553	573	48.6
66792	ASM1339014v1 assembly for Klebsiella pneumoniae A3	contig	GCA_013390145	573.32092	573	37.01
66792	ASM285676v1 assembly for Klebsiella pneumoniae A3	contig	GCA_002856765	573.52340	573

Genome browser: GCA_013180515

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Klebsiella pneumoniae subsp. pneumoniae A3
NCBI: GCA_013180515

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	91.30	no
125439	motility	BacteriaNetⓘ	yes	74.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	91.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Klebsiella pneumoniae subsp. pneumoniae A3
NCBI: GCA_013180515.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	97.30	no
125438	aerobic	aerobicⓘ	no	53.97	no
125438	spore-forming	spore-formingⓘ	no	88.50	no
125438	thermophilic	thermophileⓘ	no	99.50	no
125438	flagellated	motile2+ⓘ	no	77.84	no

Literature

Title	Authors	Journal	DOI	Year
KpSC-ID: a multiplex real-time PCR assay for the simultaneous detection of the Klebsiella pneumoniae species complex and specific identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae and Klebsiella variicola.	McAndrew G, Barbier E, Rodrigues C, Piveteau P, Brisse S, Reddington K.	Microbiology (Reading)	10.1099/mic.0.001587	2025
Subminimum Inhibitory Concentrations Tetracycline Antibiotics Induce Biofilm Formation in Minocycline-Resistant Klebsiella pneumonia by Affecting Bacterial Physical and Chemical Properties and Associated Genes Expression.	Guo T, Yang L, Zhou N, Wang Z, Huan C, Zhou J, Lin T, Bao G, Hu J, Li G.	ACS Infect Dis	10.1021/acsinfecdis.4c00280	2024
Multiple Cross Displacement Amplification Coupled with Lateral Flow Biosensor (MCDA-LFB) for rapid detection of Legionella pneumophila.	Jiang L, Gu R, Li X, Song M, Huang X, Mu D.	BMC Microbiol	10.1186/s12866-021-02363-3	2022
Ethnobotany, Phytochemistry, and Biological Activities of the Genus Cordyline.	Tematio Fouedjou R, Tsakem B, Siwe-Noundou X, Dongmo Fogang HP, Tiombou Donkia A, Kemvoufo Ponou B, Poka M, Demana PH, Teponno RB, Azefack Tapondjou L.	Biomolecules	10.3390/biom13121783	2023
Salamandamide Lipodipeptides Are Biosynthetic Intermediate Shunt Products of the Nonamodular Nonribosomal Peptide Assembly Lines of the Viscosin Family.	Bhattarai K, Majer T, Haussmann M, Schollmeyer D, Kramer M, Oni FE, Hofte M, Voget R, Gutschow M, Ruetalo N, Schindler M, Straetener J, Wannenwetsch T, Brotz-Oesterhelt H, Karongo R, Masberg B, Lammerhofer M, Hennessy RC, Muletz-Wolz CR, Gross H.	J Nat Prod	10.1021/acs.jnatprod.5c00084	2025
Improved production of propionic acid in Propionibacterium jensenii via combinational overexpression of glycerol dehydrogenase and malate dehydrogenase from Klebsiella pneumoniae.	Liu L, Zhuge X, Shin HD, Chen RR, Li J, Du G, Chen J.	Appl Environ Microbiol	10.1128/aem.03572-14	2015
Fucose-containing bacterial exopolysaccharides: Sources, biological activities, and food applications.	Xiao M, Ren X, Yu Y, Gao W, Zhu C, Sun H, Kong Q, Fu X, Mou H.	Food Chem X	10.1016/j.fochx.2022.100233	2022
Potent Antibacterial Prenylated Acetophenones from the Australian Endemic Plant Acronychia crassipetala.	Tran TD, Olsson MA, McMillan DJ, Cullen JK, Parsons PG, Reddell PW, Ogbourne SM.	Antibiotics (Basel)	10.3390/antibiotics9080487	2020
Pathway engineering of Propionibacterium jensenii for improved production of propionic acid.	Liu L, Guan N, Zhu G, Li J, Shin HD, Du G, Chen J.	Sci Rep	10.1038/srep19963	2016
Discovery of Ircinianin Lactones B and C-Two New Cyclic Sesterterpenes from the Marine Sponge Ircinia wistarii.	Majer T, Bhattarai K, Straetener J, Pohlmann J, Cahill P, Zimmermann MO, Hubner MP, Kaiser M, Svenson J, Schindler M, Brotz-Oesterhelt H, Boeckler FM, Gross H.	Mar Drugs	10.3390/md20080532	2022
Development of a Propionibacterium-Escherichia coli shuttle vector for metabolic engineering of Propionibacterium jensenii, an efficient producer of propionic acid.	Zhuge X, Liu L, Shin HD, Chen RR, Li J, Du G, Chen J.	Appl Environ Microbiol	10.1128/aem.00737-13	2013
New Nocobactin Derivatives with Antimuscarinic Activity, Terpenibactins A-C, Revealed by Genome Mining of Nocardia terpenica IFM 0406.	Chen J, Frediansyah A, Mannle D, Straetener J, Brotz-Oesterhelt H, Ziemert N, Kaysser L, Gross H.	Chembiochem	10.1002/cbic.202000062	2020
The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota L-carnitine catabolism.	Buffa JA, Romano KA, Copeland MF, Cody DB, Zhu W, Galvez R, Fu X, Ward K, Ferrell M, Dai HJ, Skye S, Hu P, Li L, Parlov M, McMillan A, Wei X, Nemet I, Koeth RA, Li XS, Wang Z, Sangwan N, Hajjar AM, Dwidar M, Weeks TL, Bergeron N, Krauss RM, Tang WHW, Rey FE, DiDonato JA, Gogonea V, Gerberick GF, Garcia-Garcia JC, Hazen SL.	Nat Microbiol	10.1038/s41564-021-01010-x	2022
Study of growth requirements other than cysteine of naturally occurring Escherichia coli and Klebsiella spp. auxotrophic for cysteine.	McIver CJ, Tapsall JW.	J Clin Microbiol	10.1128/jcm.31.10.2790-2793.1993	1993
Epidemiology of Klebsiella antibiotic resistance and serotypes.	Smith SM, Digori JT, Eng RH.	J Clin Microbiol	10.1128/jcm.16.5.868-873.1982	1982
Assessment of conventional and commercial methods for identification of clinical isolates of cysteine-requiring strains of Escherichia coli and Klebsiella species.	McIver CJ, Tapsall JW.	J Clin Microbiol	10.1128/jcm.28.9.1947-1951.1990	1990

References

#3559	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 9376
#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 )
#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 .
#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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Klebsiella pneumoniae subsp. pneumoniae (DSM 9376, ATCC 12657, CDC 383-68)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Compound production

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20E

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_013180515

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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