Name: Agarivorans albus IAM 14998
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133657

Type strain:

Species: Agarivorans albus

Culture col. no.: IAM 14998, LMG 21761, MKT 106, JCM 21469, NBRC 102603, CIP 108457

Strain history: CIP <- 2004, M. Kurahashi, Tokyo Univ., Tokyo, Japan: strain MKT 106

NCBI tax ID(s): 1331007 (strain), 182262 (species)

SI-ID 93908

LMG21761, IAM 14998, JCM 21469, NBRC 102603, CIP 108457

Special Collections

Other strains from Agarivorans albus

Section

When using BacDive for research please cite our paper

Agarivorans albus IAM 14998 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Omphalius pfeifferi pfeifferi Banda.

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Alteromonadales*
	Family	*Alteromonadaceae*
	Genus	*Agarivorans*
	Species	**Agarivorans albus**
	Full Scientific Name (LPSN)	Agarivorans albus Kurahashi and Yokota 2004

Information on morphological and physiological properties Morphology

[Ref.: #29979]	Gram stain	negative
[Ref.: #116196]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %100
[Ref.: #125439]	Gram stain	negative Confidence in %99.4

[Ref.: #29979]	Cell length	1.7 µm

[Ref.: #29979]	Cell width	0.8 µm

[Ref.: #29979]	Cell shape	rod-shaped
[Ref.: #116196]	Cell shape	rod-shaped

[Ref.: #29979]	Motility	yes
[Ref.: #116196]	Motility	no

[Ref.: #29979]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #32699]

Culture medium

Marine agar (MA)

[Ref.: #32699]

Culture medium growth

[Ref.: #32699]

Culture medium composition

expand / minimize

[Ref.: #116196]

Culture medium

CIP Medium 13

[Ref.: #116196]

Culture medium growth

[Ref.: #116196]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #29979]		optimum	37 °C
[Ref.: #32699]		growth	25 °C
[Ref.: #67770]		growth	25 °C
[Ref.: #116196]		growth	10-30 °C
[Ref.: #116196]	negative	growth	5 °C
[Ref.: #116196]	negative	growth	37 °C
[Ref.: #116196]	negative	growth	41 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29979]	Oxygen tolerance	aerobe
[Ref.: #116196]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %98.2

[Ref.: #29979]	Ability of spore formation	no
[Ref.: #125438]	Ability of spore formation	no Confidence in %91.149
[Ref.: #125439]	Ability of spore formation	no Confidence in %97.1

	Salt	Tested relation		Salt conc.
[Ref.: #29979]	NaCl		growth	>0	%
[Ref.: #116196]	NaCl		growth	0-8	%
[Ref.: #116196]	NaCl	no	growth	10	%

[Ref.: #67770]

Observation

quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29979]	esculin ChEBI	+	hydrolysis
[Ref.: #116196]	esculin ChEBI	-	hydrolysis
[Ref.: #29979]	glucose ChEBI	+	carbon source
[Ref.: #29979]	maltose ChEBI	+	carbon source
[Ref.: #29979]	mannitol ChEBI	+	carbon source
[Ref.: #116196]	nitrate ChEBI	-	reduction
[Ref.: #116196]	nitrate ChEBI	-	respiration
[Ref.: #116196]	nitrite ChEBI	-	reduction
[Ref.: #116196]	sodium thiosulfate ChEBI	-	builds gas from
[Ref.: #29979]	xylose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #116196]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #116196]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	+	3.2.1.24	* from API zym
[Ref.: #116196]	amylase	-
[Ref.: #116196]	beta-galactosidase	+	3.2.1.23
[Ref.: #68382]	beta-galactosidase	+	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	+	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	+	3.2.1.31	* from API zym
[Ref.: #116196]	caseinase	+	3.4.21.50
[Ref.: #116196]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #116196]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #116196]	gelatinase	+
[Ref.: #116196]	lecithinase	+
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #116196]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116196]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #116196]	oxidase	-
[Ref.: #116196]	protease	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #116196]	tryptophan deaminase	-
[Ref.: #116196]	tween esterase	+
[Ref.: #116196]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	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
[Ref.: #116196]	2756	not determinedn.d.	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	-	+	-	+	-	-	-	-	+	+	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	+	+	-	-	+	+	-	+	-	-	+	+	+	-	-	-	+	-	-	-	-	-	-	+	-	+	+	-	+	+	+	+	-	-	-	-	-	+	-	-	+	+	-	+	+	+	-	+	+	-

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116196]	11200	-	+	+	+	-	+	-	-	+	-	+	+	-	+	+	-	+	-	+	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #67770]	Sample type/isolated from	Omphalius pfeifferi pfeifferi Banda
[Ref.: #67770]	Host species	Omphalius pfeifferi pfeifferi
[Ref.: #67770]	Geographic location (country and/or sea, region)	Tateyama, Chiba
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #116196]	Sample type/isolated from	Mollusca, limpet
[Ref.: #116196]	Geographic location (country and/or sea, region)	Tateyama chiba
[Ref.: #116196]	Country	Japan
[Ref.: #116196]	Country ISO 3 Code	JPN
[Ref.: #116196]	Continent	Asia
[Ref.: #116196]	Isolation date	1999
* marker position based on {}

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #116196]

Biosafety level

Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #29979]	Agarivorans albus gene for 16S rRNA, partial sequene, strain:MKT106	AB076561	1454	GenBank ENA	1331007 tax ID
[Ref.: #124043]	Agarivorans albus gene for 16S rRNA, partial sequence, strain: NBRC 102603.	AB681878	1406	GenBank ENA	182262 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Agarivorans albus MKT 106	GCA_000414175	contig	GenBank ENA	1331007 tax ID
[Ref.: #66792]	Agarivorans albus JCM 21469	GCA_019670105	complete	GenBank ENA	182262 tax ID	*
[Ref.: #66792]	Agarivorans albus strain JCM 21469	182262.5	complete	PATRIC	182262 tax ID	*

[Ref.: #29979]	GC-content	49.5 mol%
[Ref.: #67770]	GC-content	49.5 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Agarivorans albus JCM 21469 NCBI: GCA_019670105.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	100	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	91.344	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	61.45	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	91.149	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.5	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	85.381	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Agarivorans albus strain JCM 21469 PATRIC: 182262.5
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	97.1
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	83.1
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.4
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	98.2

Availability in culture collections External links

[Ref.: #29979]

Culture collection no.

IAM 14998, LMG 21761, MKT 106, JCM 21469, NBRC 102603, CIP 108457

[Ref.: #91546]

SI-ID 93908

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Cloning, Expression, and Biochemical Characterization of a Novel Acidic GH16 beta-Agarase, AgaJ11, from Gayadomonas joobiniege G7.	Jung S, Jeong BC, Hong SK, Lee CR	Appl Biochem Biotechnol	10.1007/s12010-016-2262-x	2016	*
Phylogeny	Agarivorans litoreus sp. nov., a novel gammaproteobacterium isolated from seawater and emended description of the genus Agarivorans.	Park S, Park JM, Jung YT, Yoon JH	Antonie Van Leeuwenhoek	10.1007/s10482-014-0273-6	2014	*
Genetics	Draft Genome Sequence of Agarivorans albus Strain MKT 106T, an Agarolytic Marine Bacterium.	Yasuike M, Nakamura Y, Kai W, Fujiwara A, Fukui Y, Satomi M, Sano M	Genome Announc	10.1128/genomeA.00367-13	2013	*
Phylogeny	Agarivorans gilvus sp. nov. isolated from seaweed.	Du ZJ, Lv GQ, Rooney AP, Miao TT, Xu QQ, Chen GJ	Int J Syst Evol Microbiol	10.1099/ijs.0.019810-0	2010	*
Phylogeny	Agarivorans albus gen. nov., sp. nov., a gamma-proteobacterium isolated from marine animals.	Kurahashi M, Yokota A	Int J Syst Evol Microbiol	10.1099/ijs.0.02778-0	2004	*

References

#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 )

#29979

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 #26347 (see below)

#32699 ; Curators of the CIP;

#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;

#68382

Automatically annotated from API zym .

#91546

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID93908.1 )

#116196 Collection of Institut Pasteur ; Curators of the CIP; CIP 108457

#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 .

#26347

IJSEM 693 2004 ( DOI 10.1099/ijs.0.02778-0 , PubMed 15143010 )

* These data were automatically processed and therefore are not curated

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Agarivorans albus JCM 21469

Agarivorans albus strain JCM 21469

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