Name: Cocleimonas flava Sh2
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17918

Type strain:

Species: Cocleimonas flava

Strain Designation: Sh2

Culture col. no.: DSM 24830, JCM 16494, KMM 3898, NRIC 0757

Strain history: N. Tanaka <-- L. A. Romanenko Sh2 (=KMM 3898).

NCBI tax ID(s): 634765 (species)

SI-ID 404219

DSM 24830

Section

Cocleimonas flava Sh2 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from internal tissue of sand snail, Umbonium costatum.

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

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Beggiatoales*
	Family	*Leucotrichaceae*
	Genus	*Cocleimonas*
	Species	**Cocleimonas flava**
	Full Scientific Name (LPSN)	Cocleimonas flava Tanaka et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29760]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #29760]	Cell length	2.8 µm

[Ref.: #29760]	Cell width	0.9 µm

[Ref.: #29760]	Cell shape	rod-shaped

[Ref.: #29760]	Motility	no

[Ref.: #29760]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17782]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)

[Ref.: #17782]

Culture medium growth

[Ref.: #17782]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17782]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17782]	growth	28 °C
[Ref.: #29760]	growth	04-33 °C
[Ref.: #29760]	optimum	26.5 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #17782]	Temperature range	mesophilic
[Ref.: #29760]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29760]			optimum	9
[Ref.: #29760]			growth	5.5-11

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29760]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.947

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29760]		NaCl		growth	02-05	%
[Ref.: #29760]		NaCl		optimum	3.5	%

[Ref.: #67770]

Observation

quinones: Q-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29760]	alanine ChEBI	+	carbon source
[Ref.: #29760]	asparagine ChEBI	+	carbon source
[Ref.: #29760]	citrate ChEBI	+	carbon source
[Ref.: #29760]	galactose ChEBI	+	carbon source
[Ref.: #29760]	glucose ChEBI	+	carbon source
[Ref.: #29760]	mannitol ChEBI	+	carbon source
[Ref.: #29760]	rhamnose ChEBI	+	carbon source
[Ref.: #29760]	tween 20 ChEBI	+	carbon source
[Ref.: #29760]	tween 40 ChEBI	+	carbon source
[Ref.: #29760]	tween 80 ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #29760]	acid phosphatase	+	3.1.3.2
[Ref.: #29760]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29760]	catalase	+	1.11.1.6
[Ref.: #29760]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29760]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	glycolate and glyoxylate degradation	100	6 of 6
[Ref.: #66794]	photosynthesis	100	14 of 14
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	cysteine metabolism	77.78	14 of 18
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	vitamin B1 metabolism	61.54	8 of 13
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	oxidative phosphorylation	58.24	53 of 91
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	lysine metabolism	54.76	23 of 42
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	phenol degradation	50	10 of 20
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	arachidonic acid metabolism	44.44	8 of 18
[Ref.: #66794]	degradation of sugar acids	44	11 of 25
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	vitamin B12 metabolism	35.29	12 of 34
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	methanogenesis from CO2	33.33	4 of 12
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
		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.: #17782]	Sample type/isolated from	internal tissue of sand snail, Umbonium costatum
[Ref.: #17782]	Host species	Umbonium costatum
[Ref.: #17782]	Geographic location (country and/or sea, region)	shallow sediments of the Sea of Japan
[Ref.: #17782]	Country	Russia
[Ref.: #17782]	Country ISO 3 Code	RUS
[Ref.: #17782]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Shallow sediments of the Sea of Japan
[Ref.: #67770]	Country	Russia
[Ref.: #67770]	Country ISO 3 Code	RUS
* marker position based on {}

Isolation sources categories

#Host

#Invertebrates (Other)

#Mollusca

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB495251 (>99% sequence identity) for Cocleimonas flava subclade from Microbeatlas

Aquatic Samples	720
Soil Samples	9
Animal Samples	44
Plant Samples
Total Samples	773

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

[Ref.: #17782]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #17782]	Cocleimonas flava gene for 16S ribosomal RNA, partial sequence	AB495251	1512	ENA	634765 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Cocleimonas flava DSM 24830	GCA_004339015	scaffold	GenBank	634765 tax ID
[Ref.: #66792]	Cocleimonas flava strain DSM 24830	634765.3	wgs	PATRIC	634765 tax ID	*
[Ref.: #66792]	Cocleimonas flava DSM 24830	2802428810	draft	JGI IMG/M	634765 tax ID	*

[Ref.: #17782]	GC-content	43.4 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #29760]	GC-content	43.4 mol%
[Ref.: #67770]	GC-content	43.4 mol%	high performance liquid chromatography (HPLC)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Cocleimonas flava DSM 24830 NCBI: GCA_004339015.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Cocleimonas flava strain DSM 24830 PATRIC: 634765.3
[Ref.: #69480]	gram-positive	no	99.216	no
[Ref.: #69480]	anaerobic	no	96.886	yes
[Ref.: #69480]	halophile	no	59.574	no
[Ref.: #69480]	spore-forming	no	96.329	no
[Ref.: #69480]	glucose-util	yes	79.712	yes
[Ref.: #69480]	thermophile	no	99.635	yes
[Ref.: #69480]	flagellated	no	88.993	yes
[Ref.: #69480]	aerobic	yes	89.115	yes
[Ref.: #69480]	motile	no	85.077	no
[Ref.: #69480]	glucose-ferment	no	87.887	no

Availability in culture collections External links

[Ref.: #17782]

Culture collection no.

DSM 24830, JCM 16494, KMM 3898, NRIC 0757

[Ref.: #86907]

SI-ID 404219

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Cocleimonas flava gen. nov., sp. nov., a gammaproteobacterium isolated from sand snail (Umbonium costatum).	Tanaka N, Romanenko LA, Iino T, Frolova GM, Mikhailov VV	Int J Syst Evol Microbiol	10.1099/ijs.0.020263-0	2010	*

References

#17782

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24830

#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 )

#29760

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 #26141 (see below)

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86907

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-ID404219.1 )

#26141

IJSEM 412 2011 ( DOI 10.1099/ijs.0.020263-0 , PubMed 20348322 )

* These data were automatically processed and therefore are not curated

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Cocleimonas flava DSM 24830

Cocleimonas flava strain DSM 24830

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