Arenibacter certesii (DSM 19833, CCUG 48006, JCM 13507)

Name: Arenibacter certesii (DSM 19833, CCUG 48006, JCM 13507)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5484

Type strain

Culture col. no. DSM 19833 CCUG 48006 JCM 13507 KCTC 12113 KMM 3941 2 more

NCBI tax ID(s) 1121011 228955

Special Collections DSMZ CCUG JCM KCTC CIP Literature strains

History <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok; KMM 3941 KMM 3941 <-- O. I. Nedashkovskaya. <- SB Kim <- OI Nedashkovskaya, KMM, Russia CIP <- 2004, CCUG <- 2003, KMM

Links

Arenibacter certesii DSM 19833 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from green alga Ulva fenestrata.

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

Name and taxonomic classification

SI-ID 99602

KCTC 12113,CCUG 48006,CIP 108496,JCM 13507,DSM 19833

@ref 20215

Last LPSN update 2026-02-09 11:18:58

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Arenibacter

Species Arenibacter certesii

Full scientific name Arenibacter certesii Nedashkovskaya et al. 2004

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
30041	negative	4 µm	0.55 µm	rod-shaped
67771				rod-shaped
67771	negative
118218	negative			rod-shaped
125438					92.5
125438	negative				98.981
125439	negative				99.5

Colony morphology

@ref	Incubation period
57947	2 days
118218

Pigmentation

@ref	Production	Name
30041
118218		flexirubin type pigments

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8341	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
33969	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
118218	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
8341	positive	growth	28
30041	positive	growth	4.0-38
30041	positive	optimum	16
33969	positive	growth	30
57947	positive	growth	30
67770	positive	growth	25
67771	positive	growth	25
118218	positive	growth	5-37
118218	negative	growth	41
118218	negative	growth	45

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
30041	aerobe
57947	aerobe
67771	aerobe
118218	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		94.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30041	NaCl	positive	growth	1.0-10 %
30041	NaCl	positive	optimum	5.5 %
118218	NaCl	positive	growth	2-10 %
118218	NaCl		growth	0 %

Observation

@ref	Observation
67770	quinones: MK-6
67771	quinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30041	22599 ChEBI	arabinose	+	carbon source
30041	17057 ChEBI	cellobiose	+	carbon source
118218	4853 ChEBI	esculin	+	hydrolysis
30041	33984 ChEBI	fucose	+	carbon source
30041	28260 ChEBI	galactose	+	carbon source
30041	17234 ChEBI	glucose	+	carbon source
118218	606565 ChEBI	hippurate	-	hydrolysis
30041	17716 ChEBI	lactose	+	carbon source
118218	15792 ChEBI	malonate	-	assimilation
30041	17306 ChEBI	maltose	+	carbon source
30041	37684 ChEBI	mannose	+	carbon source
30041	28053 ChEBI	melibiose	+	carbon source
30041	506227 ChEBI	N-acetylglucosamine	+	carbon source
30041	17632 ChEBI	nitrate	+	reduction
118218	17632 ChEBI	nitrate	+	reduction
118218	17632 ChEBI	nitrate	-	respiration
118218	16301 ChEBI	nitrite	-	reduction
30041	16634 ChEBI	raffinose	+	carbon source
30041	17992 ChEBI	sucrose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118218	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Voges-proskauer-test	Methylred-test
118218	15688 ChEBI	acetoin	-
118218	17234 ChEBI	glucose		-

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118218	alcohol dehydrogenase	-	1.1.1.1
30041	alkaline phosphatase	+	3.1.3.1
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
118218	amylase	+
68382	beta-galactosidase	-	3.2.1.23	from API zym
118218	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118218	caseinase	-	3.4.21.50
30041	catalase	+	1.11.1.6
118218	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
30041	cytochrome oxidase	+	1.9.3.1
118218	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118218	gamma-glutamyltransferase	+	2.3.2.2
118218	gelatinase	+/-
118218	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118218	lipase	-
68382	lipase (C 14)	-		from API zym
118218	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118218	ornithine decarboxylase	-	4.1.1.17
118218	oxidase	+
118218	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
118218	tryptophan deaminase	-
118218	tween esterase	-
30041	urease	+	3.5.1.5
118218	urease	+	3.5.1.5
68382	valine arylamidase	+		from API zym

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
118218	-	+	+	+	-	+	+	+	+	-	+	+	+	-	-	+	+	+	+	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
118218	not determinedn.d.	+	+	-	+	+	-	+	+	+	+	+	+	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-	-	-	-	-	+	-	-	+	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Algae	#Green algae

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Continent	Host species	Country ISO 3 Code	Isolation date
8341	green alga Ulva fenestrata		Sea of Japan, Gulf of Peter the Great, Troitsa Bay		Asia	Ulva fenestrata
57947	Green alga,Ulva fenestrata	2000-06-01	Troitsa Bay,Gulf of P Great	Sea of Japan	Asia
67770	Green alga, Ulva fenestrata		Troitsa Bay, Gulf of Peter the Great			Ulva fenestrata
67771	From green alga, `Ulva fenestrata`		Sea of Japan	International waters
118218	Green alga, Ulva fenestrata			Japan	Asia		JPN	2000

Taxonmaps

69479

Global distribution of 16S sequence AY271622 (>99% sequence identity) for Arenibacter certesii from Microbeatlas

Aquatic Samples	152
Soil Samples	2
Animal Samples	8
Plant Samples
Total Samples	162

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8341	1	Risk group (German classification) According to TRBA 466
118218	1	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
67770	ASM42954v1 assembly for Arenibacter certesii DSM 19833	scaffold	GCA_000429545	1121011.3	2523231023	1121011	61.31
66792	ASM1465129v1 assembly for Arenibacter certesii KCTC 12113	scaffold	GCA_014651295	228955.3	8066433584	228955	57.55

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
8341	Arenibacter sp. KMM 3941 16S ribosomal RNA gene, partial sequence	AY271622	1438	228955
124043	Arenibacter certesii strain KCTC 12113 16S ribosomal RNA gene, partial sequence.	MT759918	1319	228955
124043	Arenibacter certesii strain KCTC 12113 16S ribosomal RNA gene, partial sequence.	MT758052	1362	228955

GC content

@ref	GC-content (mol%)	Method
8341	37.7
67770	37.7	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: Arenibacter certesii KCTC 12113
NCBI: GCA_014651295

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	94.70	no
125439	motility	BacteriaNetⓘ	no	66.90	no
125439	gram_stain	BacteriaNetⓘ	negative	99.50	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	77.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Arenibacter certesii DSM 19833
PATRIC: 1121011.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.98	no
125438	anaerobic	anaerobicⓘ	no	95.74	yes
125438	spore-forming	spore-formingⓘ	no	87.83	no
125438	aerobic	aerobicⓘ	yes	87.73	yes
125438	thermophilic	thermophileⓘ	no	98.02	no
125438	flagellated	motile2+ⓘ	no	92.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Chronic stress is associated with altered gut microbiota profile and relevant metabolites in adolescents.	Ying L, Yuhao W, Yafang H, Jiao L, Lina D, Qinze S, Chenghai Y, Shaoxiong Z, Yuexi G, Mingwang S, Zelin C, Chuangchuang W, Zihan G, Xin L, Lu M, Lei Z.	BMC Microbiol	10.1186/s12866-025-04094-1	2025
Metabolism	Comparative analysis of glycoside hydrolases activities from phylogenetically diverse marine bacteria of the genus Arenibacter.	Bakunina I, Nedashkovskaya O, Balabanova L, Zvyagintseva T, Rasskasov V, Mikhailov V.	Mar Drugs	10.3390/md11061977	2013
Enzymology	Algae-bacteria association inferred by 16S rDNA similarity in established microalgae cultures.	Schwenk D, Nohynek L, Rischer H.	Microbiologyopen	10.1002/mbo3.175	2014
	The structural diversity of carbohydrate antigens of selected gram-negative marine bacteria.	Nazarenko EL, Crawford RJ, Ivanova EP.	Mar Drugs	10.3390/md9101914	2011
Genetics	Structural characterization of the carbohydrate backbone of the lipooligosaccharide of the marine bacterium Arenibacter certesii strain KMM 3941(T).	Silipo A, Molinaro A, Nazarenko EL, Sturiale L, Garozzo D, Gorshkova RP, Nedashkovskaya OI, Lanzetta R, Parrilli M	Carbohydr Res	10.1016/j.carres.2005.08.021	2005
Phylogeny	Arenibacter amylolyticus sp. nov., an amylase-producing bacterium of the family Flavobacteriaceae isolated from marine water in India.	Sidhu C, Saini MK, Srinivas Tanuku NR, Pinnaka AK	Int J Syst Evol Microbiol	10.1099/ijsem.0.004664	2021
Phylogeny	Arenibacter lacus sp. nov., Isolated from Chilika Lagoon, India.	Kumar D, Smita N, Kumar G, Suresh G, Jagadeeshwari U, Sasikala C, Ramana CV	Curr Microbiol	10.1007/s00284-020-02205-x	2020
Phylogeny	Arenibacter antarcticus sp. nov., isolated from marine sediment.	Li AZ, Lin LZ, Zhang MX, Zhu HH	Int J Syst Evol Microbiol	10.1099/ijsem.0.002340	2017
Phylogeny	Arenibacter certesii sp. nov., a novel marine bacterium isolated from the green alga Ulva fenestrata.	Nedashkovskaya OI, Kim SB, Han SK, Lysenko AM, Mikhailov VV, Bae KS	Int J Syst Evol Microbiol	10.1099/ijs.0.02872-0	2004

References

#8341	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19833
#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 )
#26402	IJSEM 1173 2004 ( DOI 10.1099/ijs.0.02872-0 , PubMed 15280287 )
#30041	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 #26402
#33969	; Curators of the CIP;
#57947	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 48006
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#118218	Collection of Institut Pasteur ; Curators of the CIP; CIP 108496
#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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Arenibacter certesii (DSM 19833, CCUG 48006, JCM 13507)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000429545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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