Name: Croceivirga lutea CSW06
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133397

Type strain:

Species: Croceivirga lutea

Strain Designation: CSW06

Culture col. no.: CGMCC 1.15761, JCM 31455, KCTC 52375, MCCC 1K03195

Strain history: X.-H. Zhang and Y. Wang; Ocean Univ. of China, China; CSW06.

Special Collections

Section

When using BacDive for research please cite our paper

Croceivirga lutea CSW06 is an obligate aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from surface seawater of the Bohai Sea of China.

colony-forming
Gram-negative
rod-shaped
obligate aerobe
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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Croceivirga*
	Species	**Croceivirga lutea**
	Full Scientific Name (LPSN)	Croceivirga lutea (Wang et al. 2017) Zhang et al. 2020

	Synonym	Muricauda lutea
	Synonym	Allomuricauda lutea

Information on morphological and physiological properties Morphology

[Ref.: #25249]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.6
[Ref.: #125438]	Gram stain	negative Confidence in %98

[Ref.: #25249]	Cell length	2.4-8.2 µm

[Ref.: #25249]	Cell width	0.4 µm

[Ref.: #25249]	Cell shape	rod-shaped

[Ref.: #25249]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %91.5

[Ref.: #25249]	Colony size	0.5 mm
[Ref.: #25249]	Colony color	orange
[Ref.: #25249]	Colony shape	circular
[Ref.: #25249]	Incubation period	1 day
[Ref.: #25249]	Cultivation medium used	MA

[Ref.: #25249]	Pigment production	yes
[Ref.: #25249]	Pigment name	Flexirubin-type

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25249]

Culture medium

Marine agar (MA)

[Ref.: #25249]

Culture medium growth

		Temperature
[Ref.: #25249]	growth	16-40 °C
[Ref.: #25249]	optimum	28 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #25249]			optimum	7
[Ref.: #25249]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25249]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99.3

[Ref.: #125439]	Ability of spore formation	no Confidence in %96
[Ref.: #125438]	Ability of spore formation	no Confidence in %93.757

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25249]		NaCl		growth	1.0-7.0	%(w/v)
[Ref.: #25249]		NaCl		optimum	4	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25249]	2-oxoglutarate ChEBI	+	respiration
[Ref.: #25249]	4-hydroxy-L-proline ChEBI	+	respiration
[Ref.: #25249]	5-dehydro-D-gluconate ChEBI	+	fermentation
[Ref.: #25249]	acetate ChEBI	+	respiration
[Ref.: #25249]	alginate ChEBI	-	hydrolysis
[Ref.: #25249]	alpha-cyclodextrin ChEBI	+	respiration
[Ref.: #25249]	alpha-D-glucose ChEBI	+	respiration
[Ref.: #25249]	amygdalin ChEBI	+	fermentation
[Ref.: #25249]	arbutin ChEBI	+	fermentation
[Ref.: #25249]	beta-hydroxybutyrate ChEBI	+	respiration
[Ref.: #25249]	carboxymethylcellulose ChEBI	+	hydrolysis
[Ref.: #25249]	casein	-	hydrolysis
[Ref.: #25249]	cellobiose ChEBI	+	fermentation
[Ref.: #25249]	cellobiose ChEBI	+	respiration
[Ref.: #25249]	chitin ChEBI	-	hydrolysis
[Ref.: #25249]	citrate ChEBI	+	respiration
[Ref.: #25249]	D-arabitol ChEBI	+	fermentation
[Ref.: #25249]	D-fructose ChEBI	+	fermentation
[Ref.: #25249]	D-fructose ChEBI	+	respiration
[Ref.: #25249]	D-fructose ChEBI	+	builds acid from
[Ref.: #25249]	D-fucose ChEBI	+	fermentation
[Ref.: #25249]	D-galactose ChEBI	+	fermentation
[Ref.: #25249]	D-galactose ChEBI	+	builds acid from
[Ref.: #25249]	D-glucarate ChEBI	+	respiration
[Ref.: #25249]	D-gluconate ChEBI	+	respiration
[Ref.: #25249]	D-glucosaminic acid ChEBI	-	respiration
[Ref.: #25249]	D-glucose ChEBI	+	fermentation
[Ref.: #25249]	D-glucose 6-phosphate ChEBI	+	respiration
[Ref.: #25249]	D-glucuronate ChEBI	+	respiration
[Ref.: #25249]	D-mannose ChEBI	+	assimilation
[Ref.: #25249]	D-mannose ChEBI	+	fermentation
[Ref.: #25249]	D-mannose ChEBI	+	respiration
[Ref.: #25249]	D-psicose ChEBI	+	respiration
[Ref.: #25249]	D-tagatose ChEBI	+	fermentation
[Ref.: #25249]	D-xylose ChEBI	+	fermentation
[Ref.: #25249]	dextrin ChEBI	-	respiration
[Ref.: #25249]	dna ChEBI	-	hydrolysis
[Ref.: #25249]	esculin ChEBI	+	hydrolysis
[Ref.: #25249]	esculin ChEBI	+	fermentation
[Ref.: #25249]	gelatin ChEBI	+	hydrolysis
[Ref.: #25249]	gentiobiose ChEBI	+	fermentation
[Ref.: #25249]	gentiobiose ChEBI	+	respiration
[Ref.: #25249]	glucose 1-phosphate ChEBI	+	respiration
[Ref.: #25249]	glycogen ChEBI	+	fermentation
[Ref.: #25249]	glycogen ChEBI	+	respiration
[Ref.: #25249]	glycyl L-aspartic acid ChEBI	+	respiration
[Ref.: #25249]	glycyl-L-bromosuccinic glutamic acid	+	respiration
[Ref.: #25249]	inosine ChEBI	+	respiration
[Ref.: #25249]	inulin ChEBI	+	fermentation
[Ref.: #25249]	inulin ChEBI	+	builds acid from
[Ref.: #25249]	L-alaninamide ChEBI	+	respiration
[Ref.: #25249]	L-alanine ChEBI	+	respiration
[Ref.: #25249]	L-alanylglycine ChEBI	+	respiration
[Ref.: #25249]	L-arabinose ChEBI	-	builds acid from
[Ref.: #25249]	L-arabitol ChEBI	+	fermentation
[Ref.: #25249]	L-asparagine ChEBI	+	respiration
[Ref.: #25249]	L-aspartate ChEBI	+	respiration
[Ref.: #25249]	L-fucose ChEBI	+	fermentation
[Ref.: #25249]	L-glutamate ChEBI	+	respiration
[Ref.: #25249]	L-ornithine ChEBI	+	respiration
[Ref.: #25249]	L-pyroglutamic acid ChEBI	+	respiration
[Ref.: #25249]	L-serine ChEBI	+	respiration
[Ref.: #25249]	lactate ChEBI	+	respiration
[Ref.: #25249]	lactose ChEBI	+	fermentation
[Ref.: #25249]	lactose ChEBI	+	respiration
[Ref.: #25249]	lactulose ChEBI	+	respiration
[Ref.: #25249]	malonate ChEBI	+	respiration
[Ref.: #25249]	maltose ChEBI	+	fermentation
[Ref.: #25249]	maltose ChEBI	+	respiration
[Ref.: #25249]	melezitose ChEBI	+	fermentation
[Ref.: #25249]	melibiose ChEBI	+	fermentation
[Ref.: #25249]	melibiose ChEBI	+	respiration
[Ref.: #25249]	methyl alpha-D-glucopyranoside ChEBI	+	fermentation
[Ref.: #25249]	methyl alpha-D-glucopyranoside ChEBI	+	builds acid from
[Ref.: #25249]	methyl alpha-D-mannoside ChEBI	+	fermentation
[Ref.: #25249]	methyl D-glucoside ChEBI	+	respiration
[Ref.: #25249]	monomethyl succinate ChEBI	-	respiration
[Ref.: #25249]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #25249]	N-acetylglucosamine ChEBI	+	fermentation
[Ref.: #25249]	N-acetylglucosamine ChEBI	+	respiration
[Ref.: #25249]	N-acetylglucosamine ChEBI	+	builds acid from
[Ref.: #25249]	nitrate ChEBI	+	reduction
[Ref.: #25249]	phenylacetate ChEBI	+	assimilation
[Ref.: #25249]	propionate ChEBI	+	respiration
[Ref.: #25249]	raffinose ChEBI	+	fermentation
[Ref.: #25249]	raffinose ChEBI	+	respiration
[Ref.: #25249]	salicin ChEBI	+	fermentation
[Ref.: #25249]	sodium citrate ChEBI	+	assimilation
[Ref.: #25249]	starch ChEBI	+	hydrolysis
[Ref.: #25249]	starch ChEBI	+	fermentation
[Ref.: #25249]	succinate ChEBI	+	respiration
[Ref.: #25249]	sucrose ChEBI	+	fermentation
[Ref.: #25249]	sucrose ChEBI	+	respiration
[Ref.: #25249]	trehalose ChEBI	+	fermentation
[Ref.: #25249]	trehalose ChEBI	+	respiration
[Ref.: #25249]	turanose ChEBI	+	fermentation
[Ref.: #25249]	turanose ChEBI	+	respiration
[Ref.: #25249]	tween 20 ChEBI	+	hydrolysis
[Ref.: #25249]	tween 40 ChEBI	+	hydrolysis
[Ref.: #25249]	tween 80 ChEBI	+	hydrolysis
[Ref.: #25249]	uridine ChEBI	+	respiration
[Ref.: #25249]	xylitol ChEBI	+	fermentation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25249]		acetoin ChEBI	no
[Ref.: #25249]		hydrogen sulfide ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test
[Ref.: #25249]		acetoin ChEBI	-

	Enzyme	Enzyme activity	EC number
[Ref.: #25249]	acid phosphatase	+	3.1.3.2
[Ref.: #25249]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25249]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25249]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25249]	arginine dihydrolase	+	3.5.3.6
[Ref.: #25249]	beta-galactosidase	+	3.2.1.23
[Ref.: #25249]	beta-glucosidase	+	3.2.1.21
[Ref.: #25249]	catalase	+	1.11.1.6
[Ref.: #25249]	cytochrome oxidase	-	1.9.3.1
[Ref.: #25249]	esterase (C 4)	-
[Ref.: #25249]	esterase Lipase (C 8)	+
[Ref.: #25249]	leucine arylamidase	+	3.4.11.1
[Ref.: #25249]	lysine decarboxylase	+	4.1.1.18
[Ref.: #25249]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #25249]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25249]	ornithine decarboxylase	+	4.1.1.17
[Ref.: #25249]	trypsin	-	3.4.21.4
[Ref.: #25249]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #25249]	Sample type/isolated from	surface seawater of the Bohai Sea of China
[Ref.: #25249]	Geographic location (country and/or sea, region)	the Bohai Sea of China
[Ref.: #25249]	Country	China
[Ref.: #25249]	Country ISO 3 Code	CHN
[Ref.: #25249]	Continent	Asia
[Ref.: #25249]	Geographic location	28.0000°/122.0000°

[Ref.: #67770]	Sample type/isolated from	Surface seawater of the Bohai Sea
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Surface water

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU315485 (>99% sequence identity) for Croceivirga lutea subclade from Microbeatlas

Aquatic Samples	1414
Soil Samples	35
Animal Samples	286
Plant Samples	42
Total Samples	1777

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.: #25249]	Croceivirga lutea 16S ribosomal RNA gene, partial sequence	KU315485	1482	GenBank ENA	1775167 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Croceivirga lutea CSW06	GCA_014235875	contig	GenBank ENA	1775167 tax ID
[Ref.: #66792]	Croceivirga lutea CGMCC 1.15761	GCA_014643615	scaffold	GenBank ENA	1775167 tax ID	*
[Ref.: #66792]	Muricauda lutea strain CGMCC 1.15761	1775167.4	wgs	PATRIC	1775167 tax ID	*

[Ref.: #25249]	GC-content	50.3 mol%	high performance liquid chromatography (HPLC)
[Ref.: #67770]	GC-content	35 mol%	genome sequence analysis

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: Croceivirga lutea CGMCC 1.15761 NCBI: GCA_014643615.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.72	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	88.349	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	93.757	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.472	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	91.5	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Croceivirga lutea CGMCC 1.15761 NCBI: GCA_014643615
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	96
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	75.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.6
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.3

Availability in culture collections External links

[Ref.: #25249]

Culture collection no.

CGMCC 1.15761, JCM 31455, KCTC 52375, MCCC 1K03195

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Identification and classification of Croceivirga thetidis sp. nov., a marine Flavobacteriaceae isolated from the hard coral Acropora.	Yoon J, Yasumoto-Hirose M, Kasai H	Antonie Van Leeuwenhoek	10.1007/s10482-021-01611-w	2021	*
Phylogeny	Croceivirga litoralis sp. nov., isolated from coastal surface water, and reclassification of Muricauda lutea as Croceivirga lutea comb. nov.	Zhang J, Xu Y, Chen X, Liu D, Song H, Liu J, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004541	2020	*

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 )

#25249

Y. Y. Wang, X.,Liu, J.,Wu, Y.,Zhang, X. H.: Muricauda lutea sp. nov., isolated from seawater. IJSEM 67: 1064 - 1069 2017 ( DOI 10.1099/ijsem.0.001792 , PubMed 28086077 )

#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;

#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 .

#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 .

* These data were automatically processed and therefore are not curated

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Croceivirga lutea CGMCC 1.15761

Croceivirga lutea CGMCC 1.15761

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