Kordiimonas lacus (DSM 23258, CGMCC 1.9109, JCM 16261)

Name: Kordiimonas lacus (DSM 23258, CGMCC 1.9109, JCM 16261)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17859

Type strain

Strain Designation S3-22

Culture col. no. DSM 23258 CGMCC 1.9109 JCM 16261 S3-22

NCBI tax ID(s) 637679

Special Collections DSMZ JCM Literature strains

History DSMZ <- Y.-Y. Huo, Zhejiang Univ., Zijingang Campus, P.R. China; S3-22 <- X.-W. Xu, Second Inst. Oceanography, State Oceanic Admin., Hangzhou, China JCM <-- X.-W. Xu S3-22.

Links

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

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

Name and taxonomic classification

SI-ID 399869

JCM 16261,DSM 23258

@ref 20215

Last LPSN update 2026-05-29 08:29:06

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Kordiimonadales

Family Temperatibacteraceae

Genus Kordiimonas

Species Kordiimonas lacus

Full scientific name Kordiimonas lacus Xu et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29662	negative	4.5 µm	0.65 µm	rod-shaped
125438	negative				96.6
125439	negative				97.744

Pigmentation

29662

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16763	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
16763	positive	growth	37
29662	positive	growth	10-43
29662	positive	optimum	33.5
67770	positive	growth	35

Culture pH

@ref	Ability	Type	PH	PH range
29662	positive	optimum	7
29662	positive	growth	06-09	alkaliphile

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125439		99.865

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29662	NaCl	positive	growth	0.5-10 %
29662	NaCl	positive	optimum	2.5 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29662	30089 ChEBI	acetate	+	carbon source
29662	16449 ChEBI	alanine	+	carbon source
29662	29016 ChEBI	arginine	+	carbon source
29662	22653 ChEBI	asparagine	+	carbon source
29662	35391 ChEBI	aspartate	+	carbon source
29662	17057 ChEBI	cellobiose	+	carbon source
29662	4853 ChEBI	esculin	+	hydrolysis
29662	24265 ChEBI	gluconate	+	carbon source
29662	17234 ChEBI	glucose	+	carbon source
29662	29987 ChEBI	glutamate	+	carbon source
29662	17754 ChEBI	glycerol	+	carbon source
29662	27570 ChEBI	histidine	+	carbon source
29662	24996 ChEBI	lactate	+	carbon source
29662	25115 ChEBI	malate	+	carbon source
29662	17306 ChEBI	maltose	+	carbon source
29662	17268 ChEBI	myo-inositol	+	carbon source
29662	18257 ChEBI	ornithine	+	carbon source
29662	17814 ChEBI	salicin	+	carbon source
29662	17822 ChEBI	serine	+	carbon source
29662	27082 ChEBI	trehalose	+	carbon source
29662	53424 ChEBI	tween 20	+	carbon source
29662	53423 ChEBI	tween 40	+	carbon source
29662	53425 ChEBI	tween 60	+	carbon source
29662	53426 ChEBI	tween 80	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29662	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
29662	acid phosphatase	+	3.1.3.2
29662	alkaline phosphatase	+	3.1.3.1
29662	catalase	+	1.11.1.6
29662	cytochrome oxidase	+	1.9.3.1
29662	gelatinase	+

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	#Container (Reservoir)
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
16763	sediment from a ballast water tank	Zhejiang province	China	CHN	Asia
67770	Sediment sample collected from a ballast water tank

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16763	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM155005v1 assembly for Kordiimonas lacus S3-22	scaffold	GCA_001550055	637679.3	2690315885	637679	77.17
66792	IMG-taxon 2617270924 annotated assembly for Kordiimonas lacus CGMCC 1.9109	contig	GCA_900101935	637679.5	2617270924	637679	77.03

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16763	Kordiimonas lacus strain S3-22 16S ribosomal RNA gene, partial sequence	FJ847942	1419		637679

GC content

@ref	GC-content (mol%)	Method
16763	54.9	high performance liquid chromatography (HPLC)
29662	54.9
16763	57.2	sequence analysis
67770	54.6-55.2	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: ASM155005v1 assembly for Kordiimonas lacus S3-22
NCBI: GCA_001550055

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	69.31	no
125439	gram_stain	BacteriaNetⓘ	negative	97.74	no
125439	spore_formation	BacteriaNetⓘ	no	99.87	no
125439	motility	BacteriaNetⓘ	yes	64.03	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Kordiimonas lacus strain CGMCC 1.9109
PATRIC: 637679.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.60	no
125438	anaerobic	anaerobicⓘ	no	90.87	no
125438	aerobic	aerobicⓘ	yes	79.83	no
125438	spore-forming	spore-formingⓘ	no	88.49	no
125438	thermophilic	thermophileⓘ	no	96.95	yes
125438	flagellated	motile2+ⓘ	yes	76.69	no

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 )
#26050	IJSEM 422 2011 ( DOI 10.1099/ijs.0.018200-0 , PubMed 20348321 )
#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
#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 .
#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 )

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Kordiimonas lacus (DSM 23258, CGMCC 1.9109, JCM 16261)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001550055

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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