Name: Salinimicrobium catena HY1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5733

Type strain:

Species: Salinimicrobium catena

Strain Designation: HY1

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

Strain history: S. Liu HY1.

NCBI tax ID(s): 390640 (species)

SI-ID 297329

CGMCC 1.6101, JCM 14015, CIP 109554, DSM 23553

Section

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

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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Salinimicrobium*
	Species	**Salinimicrobium catena**
	Full Scientific Name (LPSN)	Salinimicrobium catena (Ying et al. 2007) Lim et al. 2008

Synonym

Salegentibacter catena

Information on morphological and physiological properties Morphology

[Ref.: #31923]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.977

[Ref.: #31923]	Cell length	2-6 µm

[Ref.: #31923]	Cell width	0.5-0.8 µm

[Ref.: #31923]	Cell shape	rod-shaped

[Ref.: #31923]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17282]

Culture medium

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

[Ref.: #17282]

Culture medium growth

[Ref.: #17282]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17282]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #17282]	growth	28 °C
[Ref.: #31923]	growth	15-42 °C
[Ref.: #31923]	optimum	33 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #17282]	Temperature range	mesophilic
[Ref.: #31923]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #31923]			optimum	7.85
[Ref.: #31923]			growth	6.5-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31923]

Oxygen tolerance

aerobe

[Ref.: #31923]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.999

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31923]		NaCl		growth	0.1-10	%
[Ref.: #31923]		NaCl		optimum	2.5	%

[Ref.: #67770]

Observation

quinones: MK-6

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31923]		esculin ChEBI	+	hydrolysis
[Ref.: #31923]		glucose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #31923]		hydrogen sulfide ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #31923]	acid phosphatase	+	3.1.3.2
[Ref.: #31923]	alkaline phosphatase	+	3.1.3.1
[Ref.: #31923]	catalase	+	1.11.1.6
[Ref.: #31923]	gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	lipid metabolism	77.42	24 of 31
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	non-pathway related	65.79	25 of 38
[Ref.: #66794]	purine metabolism	64.89	61 of 94
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	leucine 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]	gallate degradation	60	3 of 5
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	57.14	4 of 7
[Ref.: #66794]	mevalonate metabolism	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	phenylpropanoid biosynthesis	46.15	6 of 13
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	valine metabolism	44.44	4 of 9
[Ref.: #66794]	oxidative phosphorylation	43.96	40 of 91
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	carnitine metabolism	37.5	3 of 8
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	pentose phosphate pathway	36.36	4 of 11
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	33.33	3 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	vitamin B1 metabolism	30.77	4 of 13
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	Entner Doudoroff pathway	30	3 of 10
[Ref.: #66794]	degradation of pentoses	28.57	8 of 28
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	polyamine pathway	26.09	6 of 23
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	catecholamine biosynthesis	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]	nitrate assimilation	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.: #17282]	Sample type/isolated from	sediment from oilfield
[Ref.: #17282]	Geographic location (country and/or sea, region)	Xijiang, South China Sea
[Ref.: #17282]	Country	China
[Ref.: #17282]	Country ISO 3 Code	CHN
[Ref.: #17282]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Sediment of Xijiang oilfield in the South China Sea
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	#Oil reservoir
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #17282]

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.: #17282]	Salinimicrobium catena strain HY1 16S ribosomal RNA gene, partial sequence	DQ640642	1487	ENA	390640 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Salinimicrobium catena CGMCC 1.6101	GCA_900102915	scaffold	GenBank	390640 tax ID
[Ref.: #67770]	Salinimicrobium catena DSM 23553	GCA_900107495	scaffold	GenBank	390640 tax ID
[Ref.: #66792]	Salinimicrobium catena strain CGMCC 1.6101	390640.6	wgs	PATRIC	390640 tax ID	*
[Ref.: #66792]	Salinimicrobium catena strain DSM 23553	390640.7	wgs	PATRIC	390640 tax ID	*
[Ref.: #66792]	Salinimicrobium catena CGMCC 1.6101	2617270763	draft	JGI IMG/M	390640 tax ID	*
[Ref.: #66792]	Salinimicrobium catena DSM 23553	2622736500	draft	JGI IMG/M	390640 tax ID	*

[Ref.: #17282]	GC-content	44.4 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #31923]	GC-content	44.4 mol%

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: Salinimicrobium catena CGMCC 1.6101 NCBI: GCA_900102915.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Salinimicrobium catena strain CGMCC 1.6101 PATRIC: 390640.6
[Ref.: #69480]	gram-positive	no	98.351	yes
[Ref.: #69480]	anaerobic	no	97.833	no
[Ref.: #69480]	halophile	yes	54.243	no
[Ref.: #69480]	spore-forming	no	94.908	yes
[Ref.: #69480]	glucose-util	yes	85.463	yes
[Ref.: #69480]	aerobic	yes	82.396	yes
[Ref.: #69480]	motile	no	89.829	yes
[Ref.: #69480]	flagellated	no	95.076	yes
[Ref.: #69480]	thermophile	no	98.228	no
[Ref.: #69480]	glucose-ferment	no	90.238	no

Availability in culture collections External links

[Ref.: #17282]

Culture collection no.

DSM 23553, CGMCC 1.6101, JCM 14015, CIP 109554

[Ref.: #75213]

SI-ID 297329

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 )

#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 (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 )

#75213

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-ID297329.1 )

#28180

IJSEM 219 2007 ( DOI 10.1099/ijs.0.64658-0 , PubMed 17267953 )

* These data were automatically processed and therefore are not curated

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Salinimicrobium catena CGMCC 1.6101

Salinimicrobium catena strain CGMCC 1.6101

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