Name: Sinomicrobium oceani DSM 25598
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24051

Type strain:

Species: Sinomicrobium oceani

Culture col. no.: DSM 25598, CGMCC 1.12145, KCTC 23994, SCSIO 03483

Strain history: <- X.-P. Tian, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China; SCSIO 03483

NCBI tax ID(s): 1150368 (species)

SI-ID 399374

DSM 25598

Section

Sinomicrobium oceani DSM 25598 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from deep-sea sediment.

Gram-negative
motile
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	*Sinomicrobium*
	Species	**Sinomicrobium oceani**
	Full Scientific Name (LPSN)	Sinomicrobium oceani Xu et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30680]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.979

[Ref.: #30680]	Cell length	4.3 µm

[Ref.: #30680]	Cell width	0.6 µm

[Ref.: #30680]	Cell shape	rod-shaped

[Ref.: #30680]	Motility	yes

[Ref.: #30680]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21245]

Culture medium

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

[Ref.: #21245]

Culture medium growth

[Ref.: #21245]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21245]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21245]	growth	28 °C
[Ref.: #30680]	growth	10-45 °C
[Ref.: #30680]	optimum	32.5 °C

[Ref.: #21245]	Temperature range	mesophilic
[Ref.: #30680]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30680]			optimum	7
[Ref.: #30680]			growth	06-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30680]

Oxygen tolerance

aerobe

[Ref.: #30680]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.99

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30680]		NaCl		growth	0-10	%
[Ref.: #30680]		NaCl		optimum	2	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30680]	fructose ChEBI	+	carbon source
[Ref.: #30680]	glucose ChEBI	+	carbon source
[Ref.: #30680]	glycerol ChEBI	+	carbon source
[Ref.: #30680]	lactose ChEBI	+	carbon source
[Ref.: #30680]	mannose ChEBI	+	carbon source
[Ref.: #30680]	nitrate ChEBI	+	reduction
[Ref.: #30680]	rhamnose ChEBI	+	carbon source
[Ref.: #30680]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30680]		catalase	+	1.11.1.6
[Ref.: #30680]		gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	pentose phosphate pathway	100	11 of 11
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	aerobactin biosynthesis	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	alanine metabolism	75.86	22 of 29
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	degradation of sugar alcohols	75	12 of 16
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	pyrimidine metabolism	73.33	33 of 45
[Ref.: #66794]	proline metabolism	72.73	8 of 11
[Ref.: #66794]	degradation of hexoses	72.22	13 of 18
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[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]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of sugar acids	56	14 of 25
[Ref.: #66794]	ascorbate metabolism	54.55	12 of 22
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	carotenoid biosynthesis	50	11 of 22
[Ref.: #66794]	3-phenylpropionate degradation	46.67	7 of 15
[Ref.: #66794]	oxidative phosphorylation	42.86	39 of 91
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	toluene degradation	25	1 of 4
[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.: #21245]	Sample type/isolated from	deep-sea sediment
[Ref.: #21245]	Geographic location (country and/or sea, region)	South China Sea, Nansha Islands sea area (6° 0.733' N 113° 28.842' E) at a depth of 2548 m
[Ref.: #21245]	Country	China
[Ref.: #21245]	Country ISO 3 Code	CHN
[Ref.: #21245]	Continent	Asia
[Ref.: #21245]	Geographic location	6.0122°/113.4810°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence JQ352762 (>99% sequence identity) for Sinomicrobium from Microbeatlas

Aquatic Samples	649
Soil Samples	159
Animal Samples	575
Plant Samples	28
Total Samples	1411

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

[Ref.: #21245]

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.: #21245]	Sinomicrobium oceani strain SCSIO 03483 16S ribosomal RNA gene, partial sequence	JQ352762	1371	ENA	1150368 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sinomicrobium oceani CGMCC 1.12145	GCA_900119185	scaffold	GenBank	1150368 tax ID	*
[Ref.: #66792]	Sinomicrobium oceani strain CGMCC 1.12145	1150368.4	wgs	PATRIC	1150368 tax ID	*
[Ref.: #66792]	Sinomicrobium oceani CGMCC 1.12145	2596583572	draft	JGI IMG/M	1150368 tax ID	*

[Ref.: #21245]	GC-content	38.4 mol%	high performance liquid chromatography (HPLC)
[Ref.: #30680]	GC-content	38.4 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: Sinomicrobium oceani CGMCC 1.12145 NCBI: GCA_900119185.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sinomicrobium oceani CGMCC 1.12145 NCBI: GCA_900119185.1
[Ref.: #69480]	motile	no	85.118	yes
[Ref.: #69480]	flagellated	no	96.273	no
[Ref.: #69480]	gram-positive	no	97.699	no
[Ref.: #69480]	anaerobic	no	99.345	yes
[Ref.: #69480]	aerobic	yes	86.844	yes
[Ref.: #69480]	halophile	no	75.472	no
[Ref.: #69480]	spore-forming	no	96.624	yes
[Ref.: #69480]	glucose-ferment	no	83.425	no
[Ref.: #69480]	thermophile	no	98.609	no
[Ref.: #69480]	glucose-util	yes	92.055	yes

Availability in culture collections External links

[Ref.: #21245]

Culture collection no.

DSM 25598, CGMCC 1.12145, KCTC 23994, SCSIO 03483

[Ref.: #88022]

SI-ID 399374

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pustulibacterium marinum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the Bashi Channel.	Wang G, Zhou D, Dai S, Tian X, Li J, Chen W, Xiang W, Li X	Int J Syst Evol Microbiol	10.1099/ijs.0.048413-0	2013	*
Phylogeny	Sinomicrobium oceani gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment.	Xu Y, Tian XP, Liu YJ, Li J, Kim CJ, Yin H, Li WJ, Zhang S	Int J Syst Evol Microbiol	10.1099/ijs.0.041889-0	2012	*
Phylogeny	Sinomicrobium weinanense sp. nov., a halophilic bacterium isolated from saline-alkali soil.	Wu P, Ren H, Zhu Q, Mei Y, Liang Y, Chen Z	Int J Syst Evol Microbiol	10.1099/ijsem.0.005282	2022	*
Phylogeny	Sinomicrobium pectinilyticum sp. nov., a pectinase-producing bacterium isolated from alkaline and saline soil, and emended description of the genus Sinomicrobium.	Cheng B, Li C, Lai Q, Du M, Shao Z, Xu P, Yang C	Int J Syst Evol Microbiol	10.1099/ijs.0.061671-0	2014	*

References

#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 )

#21245

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25598

#30680

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 #27011 (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 )

#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 )

#88022

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-ID399374.1 )

#27011

IJSEM 1045 2013 ( DOI 10.1099/ijs.0.041889-0 , PubMed 22707529 )

* These data were automatically processed and therefore are not curated

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Sinomicrobium oceani CGMCC 1.12145

Sinomicrobium oceani CGMCC 1.12145

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