Kocuria carniphila (CCUG 55751, JCM 14118, DSM 16004)

Name: Kocuria carniphila (CCUG 55751, JCM 14118, DSM 16004)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7658

Type strain

Culture col. no. CCUG 55751 JCM 14118 DSM 16004 CCM 132 NBRC 110786

NCBI tax ID(s) 262208

Special Collections DSMZ CCUG JCM Wink compendium

History <- Z. Pácová, CCM <- L. Kotoucková <- J. Arpai (Micrococcus lactis) CCM 132 <-- J. Arpai 188 ("Micrococcus lactis").

Links

Kocuria carniphila CCUG 55751 is a microaerophile bacterium that was isolated from meat.

microaerophile genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 66427

NBRC 110786,CCM 132,DSM 16004,JCM 14118,CCUG 55751

@ref 20215

Last LPSN update 2026-02-09 11:19:31

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Kocuria

Species Kocuria carniphila

Full scientific name Kocuria carniphila Tvrzová et al. 2005

BacDive ID	Other strains from **Kocuria carniphila** (1)	Type strain
154896	K. carniphila CCUG 55574

Morphology

Cell morphology

@ref	Motility	Confidence	Gram stain
125438		93.5
125438		94.189	positive

Colony morphology

@ref	Colony color	Medium used
69276	Ivory (1014)	ISP 3
69276	Lemon yellow (1012)	ISP 2
69276	Lemon yellow (1012)	ISP 6
69276	Sulfur yellow (1016)	ISP 5
69276	Sulfur yellow (1016)	ISP 7
69276	Zinc yellow (1018)	ISP 4
69276	Zinc yellow (1018)	suter with tyrosine
69276	Zinc yellow (1018)	suter without tyrosine

Multicellular morphology

@ref	Complex name	Medium name
69276	Aerial mycelium	ISP 2
69276	Aerial mycelium	ISP 3
69276	Aerial mycelium	ISP 4
69276	Aerial mycelium	ISP 5
69276	Aerial mycelium	ISP 6
69276	Aerial mycelium	ISP 7
69276	Aerial mycelium	suter with tyrosine
69276	Aerial mycelium	suter without tyrosine

Pigmentation

@ref	Production	Name
69276		melanin pigment
69276		soluble pigment

Multimedia

@ref:	69276
multimedia content:	DSM_16004_image3.jpeg
multimedia.multimedia content:	DSM_16004_image3.jpeg
caption:	Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69276
multimedia content:	DSM_16004_image4.jpeg
multimedia.multimedia content:	DSM_16004_image4.jpeg
caption:	Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69276
multimedia content:	DSM_16004_image7.jpeg
multimedia.multimedia content:	DSM_16004_image7.jpeg
caption:	(ISP6, ISP7, SSM+T, SSM-T)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

@ref:	69276
multimedia content:	DSM_16004_image8.jpeg
multimedia.multimedia content:	DSM_16004_image8.jpeg
caption:	(ISP6, ISP7, SSM+T, SSM-T)
intellectual property rights:	Helmholtz-Zentrum für Infektionsforschung GmbH
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
6235	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)
6235	positive	growth	28
60715	positive	growth	37
67770	positive	growth	28

Physiology and metabolism

Oxygen tolerance

60715

Oxygen tolerancemicroaerophile

Spore formation

@ref	Spore formation	Confidence
125439		94.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
69276	NaCl	positive	growth	0-7.5 %

Murein

@ref	Murein short key	Type
6235	A11.06	A3alpha L-Lys-L-Ala₃

Observation

67770

Observationquinones: MK-7(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
69276	22599 ChEBI	arabinose	-	growth
69276	62968 ChEBI	cellulose	-	growth
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
69276	28757 ChEBI	fructose	+	growth
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
69276	17234 ChEBI	glucose	+	growth
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
69276	17268 ChEBI	inositol	+/-	growth
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
69276	37684 ChEBI	mannose	+	growth
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
69276	16634 ChEBI	raffinose	-	growth
69276	26546 ChEBI	rhamnose	-	growth
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
69276	17992 ChEBI	sucrose	+	growth
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
69276	18222 ChEBI	xylose	-	growth

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
68379	alkaline phosphatase	-	3.1.3.1	from API Coryne
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
68379	alpha-glucosidase	+	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	+	3.2.1.23	from API zym
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	esterase lipase (C 8)	+		from API zym
68379	gelatinase	-		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68379	pyrazinamidase	+	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	+	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
69276	+	+	+	-	-	+	+	-	-	-	-	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
69276	not determinedn.d.	-	+/-	+	-	+	+/-	+/-	-	-	-	+/-	-	+	-	+	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Meat

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6235	meat	Slovakia	SVK	Europe
60715	Meat	Slovakia	SVK	Europe
67770	Meat

Taxonmaps

69479

Global distribution of 16S sequence AM237391 (>99% sequence identity) for Kocuria from Microbeatlas

Aquatic Samples	1481
Soil Samples	802
Animal Samples	9515
Plant Samples	388
Total Samples	12186

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6235	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
124043	ASM4264772v1 assembly for Kocuria carniphila CCM 132	contig	GCA_042647725			262208	74.45
67770	ASM413655v1 assembly for Kocuria carniphila CCM 132	contig	GCA_004136555	262208.3	2865693805	262208	68.96

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Kocuria carniphila partial 16S rRNA gene, isolate OS-32.d1	AM237350	1481	262208
20218	Kocuria carniphila partial 16S rRNA gene, isolate OS-32.d2	AM237351	1418	262208
20218	Kocuria carniphila partial 16S rRNA gene, isolate OS-94	AM237379	1420	262208
20218	Kocuria carniphila partial 16S rRNA gene, isolate OS-114	AM237382	1120	262208
20218	Kocuria carniphila partial 16S rRNA gene, isolate OS-130	AM237385	1420	262208
20218	Kocuria carniphila partial 16S rRNA gene, isolate OS-155.b	AM237391	1419	262208
6235	Kocuria carniphila partial 16S rRNA gene, strain CCM 132T	AJ622907	1515	262208
124043	Kocuria carniphila strain CCM 132 16S ribosomal RNA gene, partial sequence.	MT760087	1358	262208

GC content

@ref	GC-content (mol%)	Method
6235	71
67770	71	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Kocuria carniphila CCM 132
NCBI: GCA_004136555

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.30	no
125439	motility	BacteriaNetⓘ	no	59.40	no
125439	gram_stain	BacteriaNetⓘ	negative	66.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	72.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Kocuria carniphila strain CCM 132
PATRIC: 262208.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	94.19	no
125438	anaerobic	anaerobicⓘ	no	98.55	no
125438	spore-forming	spore-formingⓘ	no	73.49	no
125438	aerobic	aerobicⓘ	yes	86.25	no
125438	thermophilic	thermophileⓘ	no	95.47	no
125438	flagellated	motile2+ⓘ	no	93.50	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Occurrence of disinfectant-resistant bacteria in a fresh-cut vegetables processing facility and their role in protecting Salmonella enteritidis.	Xu JG, Meng J, Bao WJ, Kang JM, Chen JY, Han BZ.	RSC Adv	10.1039/d0ra09325d	2021
Enzymology	Two cases of peritonitis caused by Kocuria marina in patients undergoing continuous ambulatory peritoneal dialysis.	Lee JY, Kim SH, Jeong HS, Oh SH, Kim HR, Kim YH, Lee JN, Kook JK, Kho WG, Bae IK, Shin JH.	J Clin Microbiol	10.1128/jcm.00847-09	2009
Phylogeny	Kocuria subflava sp. nov., isolated from marine sediment from the Indian Ocean.	Jiang Z, Zhang WH, Yuan CG, Chen JY, Cao LX, Park DJ, Xiao M, Kim CJ, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-015-0587-z	2015
Phylogeny	Reclassification of strain CCM 132, previously classified as Kocuria varians, as Kocuria carniphila sp. nov.	Tvrzova L, Schumann P, Sedlacek I, Pacova Z, Sproer C, Verbarg S, Kroppenstedt RM	Int J Syst Evol Microbiol	10.1099/ijs.0.63304-0	2005

References

#6235	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16004
#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 )
#60715	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 55751
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68379	Automatically annotated from API Coryne .
#68382	Automatically annotated from API zym .
#69276	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 .
#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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Kocuria carniphila (CCUG 55751, JCM 14118, DSM 16004)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Murein

Observation

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042647725

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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