Salinimicrobium catena (DSM 23553, CGMCC 1.6101, JCM 14015)

Name: Salinimicrobium catena (DSM 23553, CGMCC 1.6101, JCM 14015)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5733

Type strain

Strain Designation HY1

Culture col. no. DSM 23553 CGMCC 1.6101 JCM 14015 HY1 CIP 109554

NCBI tax ID(s) 390640

Special Collections DSMZ JCM CIP Literature strains

History <- JCM; JCM 14015 <- S. Liu S. Liu HY1.

Links

Salinimicrobium catena HY1 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from sediment from oilfield.

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

Name and taxonomic classification

SI-ID 297329

CGMCC 1.6101,JCM 14015,CIP 109554,DSM 23553

@ref 20215

Last LPSN update 2025-12-16 09:48:08

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Salinimicrobium

Species Salinimicrobium catena

Full scientific name Salinimicrobium catena (Ying et al. 2007) Lim et al. 2008

Synonyms (1)

Salegentibacter catena

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31923	negative	2-6 µm	0.5-0.8 µm	rod-shaped
125438					93
125438	negative				98.5
125439	negative				99.8

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17282	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)	Range
17282	positive	growth	28	mesophilic
31923	positive	growth	15-42
31923	positive	optimum	33	mesophilic
67770	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
31923	positive	optimum	7.85
31923	positive	growth	6.5-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

31923

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
31923
125438		93.5
125439		99

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31923	NaCl	positive	growth	0.1-10 %
31923	NaCl	positive	optimum	2.5 %

Observation

67770

Observationquinones: MK-6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31923	4853 ChEBI	esculin	+	hydrolysis
31923	17234 ChEBI	glucose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31923	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
31923	acid phosphatase	+	3.1.3.2
31923	alkaline phosphatase	+	3.1.3.1
31923	catalase	+	1.11.1.6
31923	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	biotin biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	starch degradation	100	10 of 10
66794	palmitate biosynthesis	100	22 of 22
66794	denitrification	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	vitamin K metabolism	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	ppGpp biosynthesis	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	lipid A biosynthesis	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	gluconeogenesis	87.5	7 of 8
66794	tetrahydrofolate metabolism	85.71	12 of 14
66794	threonine metabolism	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	lipoate biosynthesis	80	4 of 5
66794	glycogen metabolism	80	4 of 5
66794	photosynthesis	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	lipid metabolism	77.42	24 of 31
66794	phenylalanine metabolism	76.92	10 of 13
66794	glycogen biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	tryptophan metabolism	73.68	28 of 38
66794	alanine metabolism	72.41	21 of 29
66794	glutamate and glutamine metabolism	71.43	20 of 28
66794	propanol degradation	71.43	5 of 7
66794	propionate fermentation	70	7 of 10
66794	histidine metabolism	68.97	20 of 29
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	pyrimidine metabolism	66.67	30 of 45
66794	cyanate degradation	66.67	2 of 3
66794	flavin biosynthesis	66.67	10 of 15
66794	octane oxidation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	purine metabolism	64.89	61 of 94
66794	glycolysis	64.71	11 of 17
66794	heme metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	citric acid cycle	64.29	9 of 14
66794	lysine metabolism	64.29	27 of 42
66794	proline metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	leucine metabolism	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	arachidonate biosynthesis	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	methionine metabolism	57.69	15 of 26
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	reductive acetyl coenzyme A pathway	57.14	4 of 7
66794	mevalonate metabolism	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	metabolism of disaccharids	54.55	6 of 11
66794	urea cycle	53.85	7 of 13
66794	ethanol fermentation	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	pantothenate biosynthesis	50	3 of 6
66794	quinate degradation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	isoleucine metabolism	50	4 of 8
66794	tyrosine metabolism	50	7 of 14
66794	isoprenoid biosynthesis	50	13 of 26
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	valine metabolism	44.44	4 of 9
66794	oxidative phosphorylation	43.96	40 of 91
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	coenzyme M biosynthesis	40	4 of 10
66794	3-chlorocatechol degradation	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	degradation of hexoses	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	d-xylose degradation	36.36	4 of 11
66794	pentose phosphate pathway	36.36	4 of 11
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	molybdenum cofactor biosynthesis	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	vitamin B1 metabolism	30.77	4 of 13
66794	sulfate reduction	30.77	4 of 13
66794	Entner Doudoroff pathway	30	3 of 10
66794	degradation of pentoses	28.57	8 of 28
66794	arachidonic acid metabolism	27.78	5 of 18
66794	carotenoid biosynthesis	27.27	6 of 22
66794	polyamine pathway	26.09	6 of 23
66794	lactate fermentation	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	catecholamine biosynthesis	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Industrial	#Oil reservoir
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17282	sediment from oilfield	Xijiang, South China Sea	China	CHN	Asia
67770	Sediment of Xijiang oilfield in the South China Sea

Taxonmaps

69479

Global distribution of 16S sequence DQ640642 (>99% sequence identity) for Salinimicrobium catena subclade from Microbeatlas

Aquatic Samples	285
Soil Samples	100
Animal Samples	16
Plant Samples	9
Total Samples	410

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17282	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	IMG-taxon 2622736500 annotated assembly for Salinimicrobium catena DSM 23553	scaffold	GCA_900107495	390640.7	2622736500	390640	65.59
67770	IMG-taxon 2617270763 annotated assembly for Salinimicrobium catena CGMCC 1.6101	scaffold	GCA_900102915	390640.6	2617270763	390640	65.39

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17282	Salinimicrobium catena strain HY1 16S ribosomal RNA gene, partial sequence	DQ640642	1487		390640

GC content

@ref	GC-content (mol%)	Method
17282	44.4	thermal denaturation, midpoint method (Tm)
31923	44.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Salinimicrobium catena CGMCC 1.6101
NCBI: GCA_900102915

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.00	no
125439	motility	BacteriaNetⓘ	no	71.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	60.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Salinimicrobium catena strain CGMCC 1.6101
PATRIC: 390640.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.50	yes
125438	anaerobic	anaerobicⓘ	no	95.61	yes
125438	spore-forming	spore-formingⓘ	no	93.50	yes
125438	aerobic	aerobicⓘ	yes	82.19	no
125438	thermophilic	thermophileⓘ	no	97.85	yes
125438	flagellated	motile2+ⓘ	no	93.00	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Salinimicrobium gaetbulicola sp. nov., isolated from tidal flat sediment.	Lee SY, Park S, Oh TK, Yoon JH	Int J Syst Evol Microbiol	10.1099/ijs.0.033399-0	2011
Phylogeny	Reclassification of Salegentibacter catena Ying et al. 2007 as Salinimicrobium catena gen. nov., comb. nov. and description of Salinimicrobium xinjiangense sp. nov., a halophilic bacterium isolated from Xinjiang province in China.	Lim JM, Jeon CO, Lee SS, Park DJ, Xu LH, Jiang CL, Kim CJ	Int J Syst Evol Microbiol	10.1099/ijs.0.65297-0	2008
Phylogeny	Salegentibacter catena sp. nov., isolated from sediment of the South China Sea, and emended description of the genus Salegentibacter.	Ying JY, Liu ZP, Wang BJ, Dai X, Yang SS, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64658-0	2007

References

#17282	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23553
#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 )
#28180	IJSEM 219 2007 ( DOI 10.1099/ijs.0.64658-0 , PubMed 17267953 )
#31923	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 #28180
#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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Salinimicrobium catena (DSM 23553, CGMCC 1.6101, JCM 14015)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

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_900107495

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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