Name: Flavobacterium crassostreae LPB0076
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 133395

Type strain:

Species: Flavobacterium crassostreae

Strain Designation: LPB0076

Culture col. no.: KACC 18706, JCM 31219

Strain history: H. Yi; Korea Univ., South Korea; LPB0076.

NCBI tax ID(s): 1763534 (species)

Special Collections

Section

When using BacDive for research please cite our paper

Flavobacterium crassostreae LPB0076 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and has a brown diffusible pigmentation.

colony-forming
Gram-negative
pigmented
rod-shaped
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	*Flavobacterium*
	Species	**Flavobacterium crassostreae**
	Full Scientific Name (LPSN)	Flavobacterium crassostreae Choi et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #25263]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.7
[Ref.: #125438]	Gram stain	negative Confidence in %98.182

[Ref.: #25263]	Cell length	1.8-4.0 µm

[Ref.: #25263]	Cell width	0.4-0.5 µm

[Ref.: #25263]	Cell shape	rod-shaped

[Ref.: #25263]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %92

[Ref.: #25263]	Colony color	yellow
[Ref.: #25263]	Colony shape	circular
[Ref.: #25263]	Incubation period	2 days
[Ref.: #25263]	Cultivation medium used	MA

[Ref.: #25263]	Pigment production	no
[Ref.: #25263]	Pigmentation color	brown diffusible
[Ref.: #25263]	Pigment production	no
[Ref.: #25263]	Pigment name	Flexirubin-type

Information on culture and growth conditions Culture and growth conditions

[Ref.: #25263]

Culture medium

Marine agar (MA)

[Ref.: #25263]

Culture medium growth

[Ref.: #25263]

Culture medium

Trypticase Soy Agar (TSA)

[Ref.: #25263]

Culture medium growth

[Ref.: #25263]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #25263]

Culture medium growth

[Ref.: #25263]

Culture medium

NA (nutrient agar)

[Ref.: #25263]

Culture medium growth

		Temperature
[Ref.: #25263]	growth	15-30 °C
[Ref.: #25263]	optimum	25 °C
[Ref.: #67770]	growth	25 °C

	pH	Kind of pH		pH
[Ref.: #25263]			optimum	6.5-7.0
[Ref.: #25263]			growth	5.5-8.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #25263]

Oxygen tolerance

aerobe

[Ref.: #125439]	Ability of spore formation	no Confidence in %99.7
[Ref.: #125438]	Ability of spore formation	no Confidence in %93.785

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25263]		NaCl		growth	0-4	%
[Ref.: #25263]		NaCl		optimum	2-3	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25263]	adipate ChEBI	-	carbon source
[Ref.: #25263]	agar ChEBI	-	degradation
[Ref.: #25263]	alginate ChEBI	-	degradation
[Ref.: #25263]	amygdalin ChEBI	-	builds acid from
[Ref.: #25263]	carboxymethylcellulose ChEBI	-	degradation
[Ref.: #25263]	casein	+	degradation
[Ref.: #25263]	chitin ChEBI	-	degradation
[Ref.: #25263]	citrate ChEBI	-	assimilation
[Ref.: #25263]	D-glucose ChEBI	-	builds acid from
[Ref.: #25263]	D-sorbitol ChEBI	-	builds acid from
[Ref.: #25263]	decanoate ChEBI	-	carbon source
[Ref.: #25263]	dna ChEBI	-	degradation
[Ref.: #25263]	esculin ChEBI	-	degradation
[Ref.: #25263]	gelatin ChEBI	-	degradation
[Ref.: #25263]	hypoxanthine ChEBI	-	degradation
[Ref.: #25263]	L-arabinose ChEBI	-	carbon source
[Ref.: #25263]	L-arabinose ChEBI	-	builds acid from
[Ref.: #25263]	L-rhamnose ChEBI	-	builds acid from
[Ref.: #25263]	L-tyrosine ChEBI	-	degradation
[Ref.: #25263]	malate ChEBI	-	carbon source
[Ref.: #25263]	maltose ChEBI	-	carbon source
[Ref.: #25263]	mannitol ChEBI	+	carbon source
[Ref.: #25263]	mannitol ChEBI	+	builds acid from
[Ref.: #25263]	melibiose ChEBI	-	builds acid from
[Ref.: #25263]	myo-inositol ChEBI	-	builds acid from
[Ref.: #25263]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #25263]	nitrate ChEBI	-	reduction
[Ref.: #25263]	phenylacetate ChEBI	-	carbon source
[Ref.: #25263]	potassium gluconate ChEBI	-	carbon source
[Ref.: #25263]	sodium citrate ChEBI	-	carbon source
[Ref.: #25263]	starch ChEBI	-	degradation
[Ref.: #25263]	sucrose ChEBI	-	builds acid from
[Ref.: #25263]	tween 20 ChEBI	-	degradation
[Ref.: #25263]	tween 40 ChEBI	-	degradation
[Ref.: #25263]	tween 60 ChEBI	-	degradation
[Ref.: #25263]	tween 80 ChEBI	-	degradation
[Ref.: #25263]	xanthine ChEBI	-	degradation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #25263]	acetoin ChEBI	no
[Ref.: #25263]	hydrogen sulfide ChEBI	no
[Ref.: #25263]	indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #25263]	6-phospho-beta-galactosidase	-	3.2.1.85
[Ref.: #25263]	acid phosphatase	+	3.1.3.2
[Ref.: #25263]	alkaline phosphatase	+	3.1.3.1
[Ref.: #25263]	alpha-chymotrypsin	-	3.4.21.1
[Ref.: #25263]	alpha-fucosidase	-	3.2.1.51
[Ref.: #25263]	alpha-galactosidase	-	3.2.1.22
[Ref.: #25263]	alpha-glucosidase	-	3.2.1.20
[Ref.: #25263]	alpha-mannosidase	-	3.2.1.24
[Ref.: #25263]	arginine dihydrolase	-	3.5.3.6
[Ref.: #25263]	beta-glucosidase	-	3.2.1.21
[Ref.: #25263]	beta-glucuronidase	-	3.2.1.31
[Ref.: #25263]	catalase	+	1.11.1.6
[Ref.: #25263]	cystine arylamidase	-	3.4.11.3
[Ref.: #25263]	cytochrome oxidase	+	1.9.3.1
[Ref.: #25263]	esterase (C 4)	-
[Ref.: #25263]	esterase Lipase (C 8)	-
[Ref.: #25263]	leucine arylamidase	+	3.4.11.1
[Ref.: #25263]	lipase (C 14)	-
[Ref.: #25263]	lysine decarboxylase	-	4.1.1.18
[Ref.: #25263]	N-acetyl-beta-glucosaminidase	-	3.2.1.52
[Ref.: #25263]	naphthol-AS-BI-phosphohydrolase	+
[Ref.: #25263]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #25263]	trypsin	-	3.4.21.4
[Ref.: #25263]	tryptophan deaminase	-	4.1.99.1
[Ref.: #25263]	urease	-	3.5.1.5
[Ref.: #25263]	valine arylamidase	+
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	alanine metabolism	65.52	19 of 29
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	phenylalanine metabolism	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	pyrimidine metabolism	57.78	26 of 45
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	mevalonate metabolism	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	purine metabolism	56.38	53 of 94
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	non-pathway related	52.63	20 of 38
[Ref.: #66794]	suberin monomers biosynthesis	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glutamate and glutamine metabolism	50	14 of 28
[Ref.: #66794]	isoprenoid biosynthesis	46.15	12 of 26
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	oxidative phosphorylation	41.76	38 of 91
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	arginine metabolism	37.5	9 of 24
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	formaldehyde oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	urea cycle	30.77	4 of 13
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin B12 metabolism	26.47	9 of 34
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	arachidonic acid metabolism	22.22	4 of 18
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	glutathione metabolism	21.43	3 of 14
[Ref.: #66794]	degradation of pentoses	21.43	6 of 28
		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.: #25263]	Sample type/isolated from	a gut sample of a Pacific oyster (C. gigas) caught at Yeongheung Island, Korea
[Ref.: #25263]	Geographic location (country and/or sea, region)	Yeongheung Island, Korea
[Ref.: #25263]	Country	Republic of Korea
[Ref.: #25263]	Country ISO 3 Code	KOR
[Ref.: #25263]	Continent	Asia
[Ref.: #25263]	Geographic location	37.0000°/126.0000°
[Ref.: #25263]	Isolation date	2016-02-27

[Ref.: #67770]	Sample type/isolated from	Pacific oyster (Crassostrea gigas) caught off Yeongheung Island
[Ref.: #67770]	Host species	Crassostrea gigas
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Invertebrates (Other)	#Mollusca
#Host Body-Site	#Gastrointestinal tract	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KU057346 (>99% sequence identity) for Flavobacterium crassostreae subclade from Microbeatlas

Aquatic Samples	204
Soil Samples	124
Animal Samples	59
Plant Samples	24
Total Samples	411

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.: #25263]	Flavobacterium crassostreae strain LPB0076 16S ribosomal RNA gene, partial sequence	KU057346	1405	GenBank ENA	1763534 tax ID
[Ref.: #25263]	Flavobacterium crassostreae, complete genome	CP017688		GenBank ENA	1763534 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Flavobacterium crassostreae LPB0076	GCA_001831475	complete	GenBank ENA	1763534 tax ID	*
[Ref.: #66792]	Flavobacterium crassostreae LPB0076	GCA_001686945	contig	GenBank ENA	1763534 tax ID	*
[Ref.: #66792]	Flavobacterium crassostreae LPB0076	2772190676	draft	JGI IMG/M	1763534 tax ID	*
[Ref.: #66792]	Flavobacterium crassostreae LPB0076	2721755704	complete	JGI IMG/M	1763534 tax ID	*

[Ref.: #25263]	GC-content	35.9 mol%
[Ref.: #67770]	GC-content	36 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: Flavobacterium crassostreae LPB0076 NCBI: GCA_001831475.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.182	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.42	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	86.839	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	93.785	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	94.013	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	92	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Flavobacterium crassostreae LPB0076 IMG: 2721755704
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	99.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	72.6
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	89.3

Availability in culture collections External links

[Ref.: #25263]

Culture collection no.

KACC 18706, JCM 31219

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Flavobacterium muglaense sp. nov. isolated from internal organs of apparently healthy rainbow trout.	Duman M, Ay H, Altun S, Sahin N, Saticioglu IB	Int J Syst Evol Microbiol	10.1099/ijsem.0.004903	2021	*
Phylogeny	Flavobacterium crassostreae sp. nov., isolated from Pacific oyster.	Choi S, Shin SK, Kim E, Yi H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001728	2017	*

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 )

#25263

S. S. Choi, S. K.,Kim, E.,Yi, H.: Flavobacterium crassostreae sp. nov., isolated from Pacific oyster. IJSEM 67: 988 - 992 2017 ( DOI 10.1099/ijsem.0.001728 , PubMed 27959776 )

#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) .

#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;

#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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