Marixanthomonas ophiurae (NRIC 0684, JCM 14121, KMM 3046)

Name: Marixanthomonas ophiurae (NRIC 0684, JCM 14121, KMM 3046)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134220

Type strain

Culture col. no. NRIC 0684 JCM 14121 KMM 3046 CIP 109555

NCBI tax ID(s) 387659

Special Collections JCM CIP Literature strains

History JCM <-- M. Uchino <-- L. A. Romanenko KMM 3046. CIP <- 2007, JCM <- 2006, M. Uchino, Tokyo Agricult. Univ., Tokyo, Japan <- L.A. Romanenko, Vladivostok, Russia

Links

Marixanthomonas ophiurae NRIC 0684 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from Ophiuroid specimen collected from the Fiji Sea at a depth of 480 m.

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

Name and taxonomic classification

SI-ID 297232

JCM 14121,CIP 109555

@ref 20215

Last LPSN update 2026-05-29 08:38:16

Domain Bacteria

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Marixanthomonas

Species Marixanthomonas ophiurae

Full scientific name Marixanthomonas ophiurae Romanenko et al. 2007

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31925	negative	2.5 µm	0.45 µm	rod-shaped
121426	negative			rod-shaped
125438					94.5
125438	negative				99.481
125439	negative				98.876

Pigmentation

31925

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
37764	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
121426	CIP Medium 13			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
31925	positive	growth	05-32
31925	positive	optimum	26.5
37764	positive	growth	30
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH	PH range
31925	positive	optimum	7.5
31925	positive	growth	6.5-8.5	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31925	aerobe
125439	obligate aerobe	98.764

Spore formation

@ref	Spore formation	Confidence
31925
125438		91.275
125439		99.453

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31925	NaCl	positive	growth	1.0-12 %
31925	NaCl	positive	optimum	4 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
121426	17632 ChEBI	nitrate	-	reduction
121426	16301 ChEBI	nitrite	-	reduction
31925	53424 ChEBI	tween 20	+	carbon source
31925	53423 ChEBI	tween 40	+	carbon source
31925	53426 ChEBI	tween 80	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
121426	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
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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
31925	catalase	+	1.11.1.6
121426	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31925	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
31925	gelatinase	+
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
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121426	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
121426	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
121426	-	+	+	+	-	+	+	-	-	+	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
67770	Ophiuroid specimen collected from the Fiji Sea at a depth of 480 m
121426	Environment, Deep sea, brittle star	Fiji Sea	Fiji	FJI	Australia and Oceania

Taxonmaps

69479

Global distribution of 16S sequence AB261012 (>99% sequence identity) for Marixanthomonas ophiurae subclade from Microbeatlas

Aquatic Samples	1240
Soil Samples	64
Animal Samples	217
Plant Samples	4
Total Samples	1525

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
121426	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM341374v1 assembly for Marixanthomonas ophiurae KMM 3046	contig	GCA_003413745	387659.5	2887695450	387659	78.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31925	Marixanthomonas ophiurae gene for 16S rRNA, partial sequence, strain: KMM 3046	AB261012	1397		387659

GC content

@ref	GC-content (mol%)	Method
31925	37.3
67770	37.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM341374v1 assembly for Marixanthomonas ophiurae KMM 3046
NCBI: GCA_003413745

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.76	no
125439	motility	BacteriaNetⓘ	no	78.65	no
125439	gram_stain	BacteriaNetⓘ	negative	98.88	no
125439	spore_formation	BacteriaNetⓘ	no	99.45	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Marixanthomonas ophiurae strain KMM 3046
PATRIC: 387659.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.48	yes
125438	anaerobic	anaerobicⓘ	no	97.31	no
125438	spore-forming	spore-formingⓘ	no	91.28	yes
125438	aerobic	aerobicⓘ	yes	85.04	yes
125438	thermophilic	thermophileⓘ	no	95.77	yes
125438	flagellated	motile2+ⓘ	no	94.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov.	Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK.	Front Microbiol	10.3389/fmicb.2022.738205	2022
Metabolism	Extracellular Vesicle Signatures and Post-Translational Protein Deimination in Purple Sea Urchin (Strongylocentrotus purpuratus) Coelomic Fluid-Novel Insights into Echinodermata Biology.	D'Alessio S, Buckley KM, Kraev I, Hayes P, Lange S.	Biology (Basel)	10.3390/biology10090866	2021
	Luteirhabdus pelagi gen. nov., sp. nov., a novel member of the family Flavobacteriaceae, isolated from the West Pacific Ocean.	Ren WT, Meng FX, Guo LL, Sun L, Xu XW, Zhou P, Wu YH.	Arch Microbiol	10.1007/s00203-021-02557-3	2021
Phylogeny	Constantimarinum furrinae gen. nov., sp. nov., a marine bacterium isolated from saline volcanic rock aquifer (lava seawater) at Jeju Island, Republic of Korea.	Yang SH, Oh HM, Park MJ, Jang D, Kwon KK	J Microbiol	10.1007/s12275-022-1468-6	2021
Phylogeny	Marixanthomonas spongiae sp. nov., isolated from marine sponge.	Zhuang L, Pang H, Xu L, Chen D	Int J Syst Evol Microbiol	10.1099/ijsem.0.004968	2021
Phylogeny	Marixanthomonas ophiurae gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from a deep-sea brittle star.	Romanenko LA, Uchino M, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.64662-0	2007

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 )
#28182	IJSEM 457 2007 ( DOI 10.1099/ijs.0.64662-0 , PubMed 17329768 )
#31925	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 #28182
#37764	; Curators of the CIP;
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#121426	Collection of Institut Pasteur ; Curators of the CIP; CIP 109555
#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

Marixanthomonas ophiurae (NRIC 0684, JCM 14121, KMM 3046)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

API zym

Isolation, sampling and environmental information

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003413745

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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