Name: Kordiimonas lacus S3-22
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17859

Type strain:

Species: Kordiimonas lacus

Strain Designation: S3-22

Culture col. no.: DSM 23258, CGMCC 1.9109, JCM 16261

Strain history: X.-W. Xu S3-22.

NCBI tax ID(s): 637679 (species)

SI-ID 399869

DSM 23258

Section

Kordiimonas lacus S3-22 is a mesophilic, Gram-negative, motile bacterium that was isolated from sediment from a ballast water tank.

Gram-negative
motile
rod-shaped
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	*Alphaproteobacteria*
	Order	*Kordiimonadales*
	Family	*Temperatibacteraceae*
	Genus	*Kordiimonas*
	Species	**Kordiimonas lacus**
	Full Scientific Name (LPSN)	Kordiimonas lacus Xu et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #29662]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.889

[Ref.: #29662]	Cell length	4.5 µm

[Ref.: #29662]	Cell width	0.65 µm

[Ref.: #29662]	Cell shape	rod-shaped

[Ref.: #29662]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.981

[Ref.: #29662]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #16763]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #16763]

Culture medium growth

[Ref.: #16763]

Culture medium link

Medium recipe at MediaDive

[Ref.: #16763]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #16763]	growth	37 °C
[Ref.: #29662]	growth	10-43 °C
[Ref.: #29662]	optimum	33.5 °C
[Ref.: #67770]	growth	35 °C

[Ref.: #16763]	Temperature range	mesophilic
[Ref.: #29662]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #29662]			optimum	7
[Ref.: #29662]			growth	06-09

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29662]		NaCl		growth	0.5-10	%
[Ref.: #29662]		NaCl		optimum	2.5	%

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29662]	acetate ChEBI	+	carbon source
[Ref.: #29662]	alanine ChEBI	+	carbon source
[Ref.: #29662]	arginine ChEBI	+	carbon source
[Ref.: #29662]	asparagine ChEBI	+	carbon source
[Ref.: #29662]	aspartate ChEBI	+	carbon source
[Ref.: #29662]	cellobiose ChEBI	+	carbon source
[Ref.: #29662]	esculin ChEBI	+	hydrolysis
[Ref.: #29662]	gluconate ChEBI	+	carbon source
[Ref.: #29662]	glucose ChEBI	+	carbon source
[Ref.: #29662]	glutamate ChEBI	+	carbon source
[Ref.: #29662]	glycerol ChEBI	+	carbon source
[Ref.: #29662]	histidine ChEBI	+	carbon source
[Ref.: #29662]	lactate ChEBI	+	carbon source
[Ref.: #29662]	malate ChEBI	+	carbon source
[Ref.: #29662]	maltose ChEBI	+	carbon source
[Ref.: #29662]	myo-inositol ChEBI	+	carbon source
[Ref.: #29662]	ornithine ChEBI	+	carbon source
[Ref.: #29662]	salicin ChEBI	+	carbon source
[Ref.: #29662]	serine ChEBI	+	carbon source
[Ref.: #29662]	trehalose ChEBI	+	carbon source
[Ref.: #29662]	tween 20 ChEBI	+	carbon source
[Ref.: #29662]	tween 40 ChEBI	+	carbon source
[Ref.: #29662]	tween 60 ChEBI	+	carbon source
[Ref.: #29662]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #29662]		hydrogen sulfide ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #29662]	acid phosphatase	+	3.1.3.2
[Ref.: #29662]	alkaline phosphatase	+	3.1.3.1
[Ref.: #29662]	catalase	+	1.11.1.6
[Ref.: #29662]	cytochrome oxidase	+	1.9.3.1
[Ref.: #29662]	gelatinase	+

	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]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	proline metabolism	90.91	10 of 11
[Ref.: #66794]	propionate fermentation	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	purine metabolism	78.72	74 of 94
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	78.57	11 of 14
[Ref.: #66794]	allantoin degradation	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	arginine metabolism	75	18 of 24
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	vitamin B6 metabolism	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	lysine metabolism	71.43	30 of 42
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	vitamin B1 metabolism	69.23	9 of 13
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	myo-inositol biosynthesis	60	6 of 10
[Ref.: #66794]	glycolysis	58.82	10 of 17
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	oxidative phosphorylation	46.15	42 of 91
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	androgen and estrogen metabolism	43.75	7 of 16
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	metabolism of disaccharids	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[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]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	vitamin B12 metabolism	32.35	11 of 34
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	d-xylose degradation	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #16763]	Sample type/isolated from	sediment from a ballast water tank
[Ref.: #16763]	Geographic location (country and/or sea, region)	Zhejiang province
[Ref.: #16763]	Country	China
[Ref.: #16763]	Country ISO 3 Code	CHN
[Ref.: #16763]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sediment sample collected from a ballast water tank
* marker position based on {}

Isolation sources categories

#Engineered	#Built environment	#Container (Reservoir)
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ847942 (>99% sequence identity) for Kordiimonas lacus from Microbeatlas

Aquatic Samples	565
Soil Samples	64
Animal Samples	4
Plant Samples	19
Total Samples	652

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

[Ref.: #16763]

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.: #16763]	Kordiimonas lacus strain S3-22 16S ribosomal RNA gene, partial sequence	FJ847942	1419	ENA	637679 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Kordiimonas lacus S3-22	GCA_001550055	scaffold	GenBank	637679 tax ID
[Ref.: #66792]	Kordiimonas lacus CGMCC 1.9109	GCA_900101935	contig	GenBank	637679 tax ID	*
[Ref.: #66792]	Kordiimonas lacus strain CGMCC 1.9109	637679.5	wgs	PATRIC	637679 tax ID	*
[Ref.: #66792]	Kordiimonas lacus CGMCC 1.9109	2617270924	draft	JGI IMG/M	637679 tax ID	*
[Ref.: #66792]	Kordiimonas lacus S3-22	2690315885	draft	JGI IMG/M	637679 tax ID	*

[Ref.: #16763]	GC-content	54.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29662]	GC-content	54.9 mol%
[Ref.: #16763]	GC-content	57.2 mol%	sequence analysis
[Ref.: #67770]	GC-content	54.6-55.2 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: Kordiimonas lacus strain CGMCC 1.9109 PATRIC: 637679.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Kordiimonas lacus strain CGMCC 1.9109 PATRIC: 637679.5
[Ref.: #69480]	gram-positive	no	98.108	yes
[Ref.: #69480]	anaerobic	no	99.513	no
[Ref.: #69480]	halophile	no	52.945	no
[Ref.: #69480]	spore-forming	no	93.791	no
[Ref.: #69480]	glucose-util	yes	90.746	no
[Ref.: #69480]	flagellated	yes	64.923	no
[Ref.: #69480]	aerobic	yes	83.374	no
[Ref.: #69480]	thermophile	no	96.97	yes
[Ref.: #69480]	motile	yes	89.296	yes
[Ref.: #69480]	glucose-ferment	no	90.459	no

Availability in culture collections External links

[Ref.: #16763]

Culture collection no.

DSM 23258, CGMCC 1.9109, JCM 16261

[Ref.: #86850]

SI-ID 399869

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Kordiimonas lipolytica sp. nov., isolated from seawater.	Wu YH, Jian SL, Meng FX, Maripatay, Tohty D, Wang CS, Xu XW	Int J Syst Evol Microbiol	10.1099/ijsem.0.001007	2016	*
Phylogeny	Kordiimonas sediminis sp. nov., isolated from a sea cucumber culture pond.	Zhang HX, Zhao JX, Chen GJ, Du ZJ	Antonie Van Leeuwenhoek	10.1007/s10482-016-0671-z	2016	*
Phylogeny	Eilatimonas milleporae gen. nov., sp. nov., a marine bacterium isolated from the hydrocoral Millepora dichotoma.	Paramasivam N, Ben-Dov E, Arotsker L, Kushmaro A	Int J Syst Evol Microbiol	10.1099/ijs.0.043976-0	2012	*
Phylogeny	Kordiimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat.	Math RK, Jeong SH, Jin HM, Park MS, Kim JM, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijs.0.038943-0	2012	*
Phylogeny	Kordiimonas lacus sp. nov., isolated from a ballast water tank, and emended description of the genus Kordiimonas.	Xu XW, Huo YY, Bai XD, Wang CS, Oren A, Li SY, Wu M	Int J Syst Evol Microbiol	10.1099/ijs.0.018200-0	2010	*

References

#16763

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23258

#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 )

#29662

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 #26050 (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 )

#86850

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-ID399869.1 )

#26050

IJSEM 422 2011 ( DOI 10.1099/ijs.0.018200-0 , PubMed 20348321 )

* These data were automatically processed and therefore are not curated

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Kordiimonas lacus strain CGMCC 1.9109

Kordiimonas lacus strain CGMCC 1.9109

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