Name: Haliangium ochraceum SMP-2
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5869

Type strain:

Species: Haliangium ochraceum

Strain Designation: SMP-2

Culture col. no.: DSM 14365, JCM 11303, AJ 13395, CIP 107738

Strain history: R. Fudou SMP-2.

NCBI tax ID(s): 502025 (strain), 80816 (species)

SI-ID 100667

DSM 14365, JCM 11303, CIP 107738

Special Collections

Section

Haliangium ochraceum SMP-2 is a Gram-negative bacterium that was isolated from coastal sands.

Gram-negative
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	*Deltaproteobacteria*
	Order	*Myxococcales*
	Family	*Kofleriaceae*
	Genus	*Haliangium*
	Species	**Haliangium ochraceum**
	Full Scientific Name (LPSN)	Haliangium ochraceum Fudou et al. 2002

Information on morphological and physiological properties Morphology

Multimedia content

[Ref.: #66793]

Caption:

electron microscopic image

[Ref.: #66793]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5321]

Culture medium

VY/4-SWS AGAR (DSMZ Medium 958)

[Ref.: #5321]

Culture medium growth

[Ref.: #5321]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5321]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #5321]			growth	30 °C
[Ref.: #67770]			growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #5321]	Name of produced compound	haliangicin
[Ref.: #5321]	Name of produced compound	haliamide

[Ref.: #67770]

Observation

quinones: MK-8

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	enterobactin biosynthesis	100	3 of 3
[Ref.: #66794]	glycine betaine biosynthesis	100	5 of 5
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	factor 420 biosynthesis	100	5 of 5
[Ref.: #66794]	Entner Doudoroff pathway	100	10 of 10
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ethanol fermentation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	leucine metabolism	92.31	12 of 13
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	83.33	10 of 12
[Ref.: #66794]	alanine metabolism	82.76	24 of 29
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	tyrosine metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	cyclohexanol degradation	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	benzoyl-CoA degradation	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	arachidonic acid metabolism	66.67	12 of 18
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	tryptophan metabolism	65.79	25 of 38
[Ref.: #66794]	polyamine pathway	65.22	15 of 23
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	urea cycle	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	oxidative phosphorylation	60.44	55 of 91
[Ref.: #66794]	carotenoid biosynthesis	59.09	13 of 22
[Ref.: #66794]	androgen and estrogen metabolism	56.25	9 of 16
[Ref.: #66794]	lipid A biosynthesis	55.56	5 of 9
[Ref.: #66794]	lipid metabolism	54.84	17 of 31
[Ref.: #66794]	d-xylose degradation	54.55	6 of 11
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	4-hydroxyphenylacetate degradation	50	5 of 10
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	vitamin E metabolism	50	2 of 4
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	47.06	8 of 17
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	isoprenoid biosynthesis	42.31	11 of 26
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	degradation of pentoses	39.29	11 of 28
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	phenylpropanoid biosynthesis	38.46	5 of 13
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	cholesterol biosynthesis	36.36	4 of 11
[Ref.: #66794]	allantoin degradation	33.33	3 of 9
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	methane metabolism	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	chlorophyll metabolism	22.22	4 of 18
[Ref.: #66794]	vitamin B12 metabolism	20.59	7 of 34
		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.: #5321]	Sample type/isolated from	coastal sands
[Ref.: #5321]	Geographic location (country and/or sea, region)	Kanagawa
[Ref.: #5321]	Country	Japan
[Ref.: #5321]	Country ISO 3 Code	JPN
[Ref.: #5321]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Dry Laminariales seaweed sample collected from a sandy beach (Aburatsubo-wan) of the Miura Peninsula
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental

#Terrestrial

#Sandy

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB016470 (>99% sequence identity) for Haliangium ochraceum subclade from Microbeatlas

Aquatic Samples	560
Soil Samples	336
Animal Samples	18
Plant Samples	67
Total Samples	981

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

[Ref.: #5321]

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.: #67770]	Haliangium ochraceum gene for 16S rRNA, partial sequence	AB016470	1507	GenBank ENA	502025 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Haliangium ochraceum DSM 14365	GCA_000024805	complete	GenBank ENA	502025 tax ID	*
[Ref.: #66792]	Haliangium ochraceum DSM 14365	502025.10	complete	PATRIC	502025 tax ID	*
[Ref.: #66792]	Haliangium ochraceum SMP-2, DSM 14365	646311933	complete	JGI IMG/M	502025 tax ID	*

[Ref.: #5321]	GC-content	67 mol%
[Ref.: #67770]	GC-content	67 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Haliangium ochraceum DSM 14365 DSM 14365 NCBI: GCA_000024805.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	78	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Haliangium ochraceum DSM 14365 DSM 14365 NCBI: GCA_000024805.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	83.821	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	82.541	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	73.193	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	68.599	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	86.55	no
[Ref.: #69480]	flagellated	motile2+ⓘ	no	54.974	no

Availability in culture collections External links

[Ref.: #5321]

Culture collection no.

DSM 14365, JCM 11303, AJ 13395, CIP 107738

[Ref.: #75349]

SI-ID 100667

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites.	Amiri Moghaddam J, Crusemann M, Alanjary M, Harms H, Davila-Cespedes A, Blom J, Poehlein A, Ziemert N, Konig GM, Schaberle TF	Sci Rep	10.1038/s41598-018-34954-y	2018	*
Biotechnology	Heterologous Production of the Marine Myxobacterial Antibiotic Haliangicin and Its Unnatural Analogues Generated by Engineering of the Biochemical Pathway.	Sun Y, Feng Z, Tomura T, Suzuki A, Miyano S, Tsuge T, Mori H, Suh JW, Iizuka T, Fudou R, Ojika M	Sci Rep	10.1038/srep22091	2016	*
Metabolism	Isolation and Biosynthetic Analysis of Haliamide, a New PKS-NRPS Hybrid Metabolite from the Marine Myxobacterium Haliangium ochraceum.	Sun Y, Tomura T, Sato J, Iizuka T, Fudou R, Ojika M	Molecules	10.3390/molecules21010059	2016	*
Phylogeny	A novel family VII esterase with industrial potential from compost metagenomic library.	Kang CH, Oh KH, Lee MH, Oh TK, Kim BH, Yoon J	Microb Cell Fact	10.1186/1475-2859-10-41	2011	*
Genetics	Investigation of cytochromes P450 in myxobacteria: excavation of cytochromes P450 from the genome of Sorangium cellulosum So ce56.	Khatri Y, Hannemann F, Perlova O, Muller R, Bernhardt R	FEBS Lett	10.1016/j.febslet.2011.04.035	2011	*
Genetics	Complete genome sequence of Haliangium ochraceum type strain (SMP-2).	Ivanova N, Daum C, Lang E, Abt B, Kopitz M, Saunders E, Lapidus A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Copeland A, Cheng JF, Chen F, Bruce D, Goodwin L, Pitluck S, Mavromatis K, Pati A, Mikhailova N, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Detter JC, Brettin T, Rohde M, Goker M, Bristow J, Markowitz V, Eisen JA, Hugenholtz P, Kyrpides NC, Klenk HP	Stand Genomic Sci	10.4056/sigs.69.1277	2010	*
Cultivation	Characteristics and living patterns of marine myxobacterial isolates.	Zhang YQ, Li YZ, Wang B, Wu ZH, Zhang CY, Gong X, Qiu ZJ, Zhang Y	Appl Environ Microbiol	10.1128/AEM.71.6.3331-3336.2005	2005	*
Phylogeny	Haliangium ochraceum gen. nov., sp. nov. and Haliangium tepidum sp. nov.: novel moderately halophilic myxobacteria isolated from coastal saline environments.	Fudou R, Jojima Y, Iizuka T, Yamanaka S	J Gen Appl Microbiol	10.2323/jgam.48.109	2002	*

References

#5321

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 14365

#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 )

#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) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#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 )

#75349

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-ID100667.1 )

* These data were automatically processed and therefore are not curated

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Haliangium ochraceum DSM 14365 DSM 14365

Haliangium ochraceum DSM 14365 DSM 14365

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