Nocardioides caeni (DSM 23134, CCUG 57506, KCTC 19600)

Name: Nocardioides caeni (DSM 23134, CCUG 57506, KCTC 19600)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 11145

Type strain

Strain Designation MN8

Culture col. no. DSM 23134 CCUG 57506 KCTC 19600 JCM 19119 MN8

NCBI tax ID(s) 574700

Special Collections DSMZ CCUG JCM KCTC Wink compendium Literature strains

History DSMZ <- KCTC <- J. H. Yoon, KRIBB JCM <-- CCUG 57506 <-- J.-H. Yoon MN8. KCTC <- JH Yoon, KRIBB

Links

Nocardioides caeni MN8 is an aerobe, Gram-positive, rod-shaped bacterium that was isolated from sludge of domestic wastewater.

Gram-positive rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 397370

KCTC 19600,DSM 23134,CCUG 57506

@ref 20215

Last LPSN update 2026-05-29 08:27:29

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Propionibacteriales

Family Nocardioidaceae

Genus Nocardioides

Species Nocardioides caeni

Full scientific name Nocardioides caeni Yoon et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29281	positive	1.6 µm	0.5 µm	rod-shaped
67771	positive
125439	positive				99.475

Colony morphology

@ref	Colony color	Incubation period	Medium used
19803	Sand yellow	10-14 days	ISP 2
61352		7 days

Multicellular morphology

@ref	Forms multicellular complex	Medium name
19803		ISP 2

Pigmentation

29281

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
16724	R2A MEDIUM (DSMZ Medium 830)	Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
19803	ISP 2		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
16724	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16724	positive	growth	28
19803	positive	optimum	28
29281	positive	growth	10-35
29281	positive	optimum	30
61352	positive	growth	30
67770	positive	growth	28
67771	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
29281	positive	optimum	7
29281	positive	growth	6-9.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29281	aerobe
61352	aerobe
67771	aerobe
125439	obligate aerobe	99.263

Spore formation

29281

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29281	NaCl	positive	growth	0-1 %
29281	NaCl	positive	optimum	0.5 %

Observation

67770

Observationquinones: MK-8(H₄)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29281	22599 ChEBI	arabinose	+	carbon source
29281	17057 ChEBI	cellobiose	+	carbon source
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
29281	4853 ChEBI	esculin	+	hydrolysis
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	-	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
29281	26546 ChEBI	rhamnose	+	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
29281	53424 ChEBI	tween 20	+	carbon source
29281	53423 ChEBI	tween 40	+	carbon source
29281	53425 ChEBI	tween 60	+	carbon source
29281	53426 ChEBI	tween 80	+	carbon source
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29281	16136 ChEBI	hydrogen sulfide
29281	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
29281	35581 ChEBI	indole	+

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
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68382	cystine arylamidase	+	3.4.11.3	from API zym
29281	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
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
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
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
68382	valine arylamidase	+		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	butanoate fermentation	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	vitamin K metabolism	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	adipate degradation	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	Entner Doudoroff pathway	100	10 of 10
66794	threonine metabolism	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	octane oxidation	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	ppGpp biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	coenzyme A metabolism	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	aerobactin biosynthesis	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	teichoic acid biosynthesis	100	1 of 1
66794	cellulose degradation	100	5 of 5
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	phenylalanine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	starch degradation	80	8 of 10
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	factor 420 biosynthesis	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	glycogen metabolism	80	4 of 5
66794	purine metabolism	79.79	75 of 94
66794	alanine metabolism	79.31	23 of 29
66794	photosynthesis	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	heme metabolism	78.57	11 of 14
66794	citric acid cycle	78.57	11 of 14
66794	allantoin degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	glycolysis	76.47	13 of 17
66794	histidine metabolism	75.86	22 of 29
66794	gluconeogenesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	toluene degradation	75	3 of 4
66794	glutamate and glutamine metabolism	75	21 of 28
66794	vitamin B12 metabolism	73.53	25 of 34
66794	pyrimidine metabolism	73.33	33 of 45
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	propanol degradation	71.43	5 of 7
66794	4-hydroxyphenylacetate degradation	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	vitamin B1 metabolism	69.23	9 of 13
66794	urea cycle	69.23	9 of 13
66794	cyanate degradation	66.67	2 of 3
66794	enterobactin biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	oxidative phosphorylation	65.93	60 of 91
66794	tryptophan metabolism	65.79	25 of 38
66794	non-pathway related	65.79	25 of 38
66794	lipid metabolism	64.52	20 of 31
66794	tyrosine metabolism	64.29	9 of 14
66794	metabolism of disaccharids	63.64	7 of 11
66794	d-xylose degradation	63.64	7 of 11
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	C4 and CAM-carbon fixation	62.5	5 of 8
66794	androgen and estrogen metabolism	62.5	10 of 16
66794	isoleucine metabolism	62.5	5 of 8
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	lysine metabolism	61.9	26 of 42
66794	methionine metabolism	61.54	16 of 26
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	lipoate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	glutathione metabolism	57.14	8 of 14
66794	nitrate assimilation	55.56	5 of 9
66794	degradation of hexoses	55.56	10 of 18
66794	cysteine metabolism	55.56	10 of 18
66794	aspartate and asparagine metabolism	55.56	5 of 9
66794	phenol degradation	55	11 of 20
66794	degradation of pentoses	53.57	15 of 28
66794	bile acid biosynthesis, neutral pathway	52.94	9 of 17
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	quinate degradation	50	1 of 2
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	carnitine metabolism	50	4 of 8
66794	cyclohexanol degradation	50	2 of 4
66794	glycogen biosynthesis	50	2 of 4
66794	glycine metabolism	50	5 of 10
66794	phenylmercury acetate degradation	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	cholesterol biosynthesis	45.45	5 of 11
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	lipid A biosynthesis	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	ascorbate metabolism	40.91	9 of 22
66794	arachidonate biosynthesis	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	coenzyme M biosynthesis	40	4 of 10
66794	myo-inositol biosynthesis	40	4 of 10
66794	glycine betaine biosynthesis	40	2 of 5
66794	dTDPLrhamnose biosynthesis	37.5	3 of 8
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	degradation of sugar acids	28	7 of 25
66794	chlorophyll metabolism	27.78	5 of 18
66794	arachidonic acid metabolism	27.78	5 of 18
66794	carotenoid biosynthesis	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	lactate fermentation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	polyamine pathway	21.74	5 of 23

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
19803	-	-	+	+	-	-	+	-	-	-	-	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
19803	not determinedn.d.	+	+	+	+	+	+	+	-	-	+	+	-	-	-	+	+	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Wastewater
#Environmental	#Terrestrial	#Mud (Sludge)

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
16724	sludge of domestic wastewater		Daejeon	Republic of Korea	KOR	Asia
61352	Sludge of a domestic wastewater	2006-01-01	Taejon	Republic of Korea	KOR	Asia
67770	Sludge of domestic wastewater			Republic of Korea	KOR	Asia
67771	From wastewater		Daejeon	Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ423551 (>99% sequence identity) for Nocardioides caeni from Microbeatlas

Aquatic Samples	3
Soil Samples	14
Animal Samples	7
Plant Samples	0
Total Samples	24

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16724	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	ASM4267666v1 assembly for Nocardioides caeni CCUG 57506	scaffold	GCA_042676665			574700	74.23
124043	ASM3954447v1 assembly for Nocardioides caeni JCM 19119	scaffold	GCA_039544475			574700	73.21
67770	ASM491219v1 assembly for Nocardioides caeni DSM 23134	scaffold	GCA_004912195	574700.3	2989575051	574700	58.52

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16724	Nocardioides sp. MN8 16S ribosomal RNA gene, partial sequence	FJ423551	1474		574700

GC content

@ref	GC-content (mol%)	Method
16724	71.5	high performance liquid chromatography (HPLC)
29281	71.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM4267666v1 assembly for Nocardioides caeni CCUG 57506
NCBI: GCA_042676665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.26	no
125439	gram_stain	BacteriaNetⓘ	positive	99.48	no
125439	spore_formation	BacteriaNetⓘ	no	75.83	no
125439	motility	BacteriaNetⓘ	no	84.83	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Nocardioides caeni strain DSM 23134
PATRIC: 574700.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	87.09	yes
125438	anaerobic	anaerobicⓘ	no	93.47	yes
125438	spore-forming	spore-formingⓘ	no	60.44	yes
125438	aerobic	aerobicⓘ	yes	86.59	yes
125438	thermophilic	thermophileⓘ	no	97.11	no
125438	flagellated	motile2+ⓘ	no	62.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Nocardioides pelophilus sp. nov., isolated from freshwater mud.	Yan ZF, Lin P, Li CT, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002776	2018
Phylogeny	Nocardioides flava sp. nov., isolated from rhizosphere of poppy plant, Republic of Korea.	Singh H, Yin CS	Arch Microbiol	10.1007/s00203-015-1178-0	2016
Phylogeny	Nocardioides albidus sp. nov., an actinobacterium isolated from garden soil.	Singh H, Du J, Trinh H, Won K, Yang JE, Yin C, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijsem.0.000730	2015
Phylogeny	Nocardioides caeni sp. nov., isolated from wastewater.	Yoon JH, Kang SJ, Park S, Kim W, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.010124-0	2009

References

#16724	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23134
#19803	Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .
#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 )
#25697	IJSEM 2794 2009 ( DOI 10.1099/ijs.0.010124-0 , PubMed 19628618 )
#29281	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #25697
#61352	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 57506
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#68379	Automatically annotated from API Coryne .
#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 .
#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 )

Content

About us

Nocardioides caeni (DSM 23134, CCUG 57506, KCTC 19600)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Multicellular morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

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_042676665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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