Archive BacDiveID:10.13145/bacdive5869.20230509.8.1

Strain identifier

BacDive ID: 5869

Type strain:

Species: Haliangium ochraceum

Strain Designation: SMP-2

Strain history: R. Fudou SMP-2.

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

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 5321

BacDive-ID: 5869

DSM-Number: 14365

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

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

NCBI tax id

NCBI tax id	Matching level
502025	strain
80816	species

strain history

@ref	history
5321	<- R. Fudou; SMP-2 <- T. Iizuka
67770	R. Fudou SMP-2.

doi: 10.13145/bacdive5869.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Myxococcales
family: Kofleriaceae
genus: Haliangium
species: Haliangium ochraceum
full scientific name: Haliangium ochraceum Fudou et al. 2002

@ref: 5321

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Myxococcales

family: Kofleriaceae

genus: Haliangium

species: Haliangium ochraceum

full scientific name: Haliangium ochraceum Fudou et al. 2002

strain designation: SMP-2

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.867

multimedia

@ref: 66793
multimedia content: EM_DSM_14365_1.jpg
caption: electron microscopic image
intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 5321
name: VY/4-SWS AGAR (DSMZ Medium 958)
growth: yes
link: https://mediadive.dsmz.de/medium/958
composition: Name: VY/4-SWS AGAR (DSMZ Medium 958) Composition: NaCl 20.0 g/l Agar 15.0 g/l MgSO4 x 7 H2O 8.0 g/l Yeast cell paste 2.5 g/l CaCl2 x 2 H2O 1.0 g/l KCl 0.5 g/l NaHCO3 0.16 g/l KBr 0.08 g/l SrCl2 x 6 H2O 0.03 g/l Sodium beta-glycerophosphate 0.01 g/l Ferric citrate 0.01 g/l Cyanocobalamine 0.0005 g/l EDTA 0.0005 g/l FeSO4 x 7 H2O 0.0002 g/l H3BO3 3e-05 g/l CoCl2 x 6 H2O 2e-05 g/l ZnSO4 x 7 H2O 1e-05 g/l Na2MoO4 x 2 H2O 3e-06 g/l MnCl2 x 4 H2O 3e-06 g/l NiCl2 x 6 H2O 2e-06 g/l CuCl2 x 2 H2O 1e-06 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
5321	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

spore formation

@ref: 69480
spore formation: no
confidence: 99.209

compound production

@ref	compound
5321	haliangicin
5321	haliamide

observation

@ref: 67770
observation: quinones: MK-8

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
5321	coastal sands	Kanagawa	Japan	JPN	Asia
67770	Dry Laminariales seaweed sample collected from a sandy beach (Aburatsubo-wan) of the Miura Peninsula		Japan	JPN	Asia

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Sandy

taxonmaps

@ref: 69479
File name: preview.99_3211.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15848;96_1670;97_2000;98_2460;99_3211&stattab=map
Last taxonomy: Haliangium ochraceum subclade
16S sequence: AB016470
Sequence Identity:
Total samples: 981
soil counts: 336
aquatic counts: 560
animal counts: 18
plant counts: 67

Safety information

risk assessment

@ref: 5321
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 67770
description: Haliangium ochraceum gene for 16S rRNA, partial sequence
accession: AB016470
length: 1507
database: ena
NCBI tax ID: 502025

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Haliangium ochraceum DSM 14365	GCA_000024805	complete	ncbi	502025
66792	Haliangium ochraceum DSM 14365	502025.10	complete	patric	502025
66792	Haliangium ochraceum SMP-2, DSM 14365	646311933	complete	img	502025

GC content

@ref	GC-content	method
5321	67
67770	67	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	78	no
motile	no	84.719	no
flagellated	no	93.139	no
gram-positive	no	94.383	no
anaerobic	no	97.287	no
aerobic	yes	79.996	no
halophile	no	65.807	no
spore-forming	no	78.263	no
thermophile	no	98.847	yes
glucose-util	yes	84.35	no
glucose-ferment	no	88.817	no

External links

@ref: 5321

culture collection no.: DSM 14365, JCM 11303, AJ 13395, CIP 107738

straininfo link

@ref: 75349
straininfo: 100667

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	12469307	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	Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, Geologic Sediments/microbiology, Molecular Sequence Data, Myxococcales/classification/genetics/isolation & purification/metabolism, Phylogeny, Polymerase Chain Reaction, Quinones/metabolism, RNA, Ribosomal, 16S/chemistry/genetics, Sodium Chloride/metabolism	Metabolism
Cultivation	15933036	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	Culture Media, Microscopy, Phase-Contrast, Morphogenesis, Myxococcales/drug effects/growth & development/isolation & purification/physiology, Seawater/microbiology, Sodium Chloride/pharmacology	Enzymology
Genetics	21304682	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
Genetics	21521637	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	Cytochrome P-450 Enzyme System/genetics/metabolism, Genome, Bacterial, Genomics, Myxococcales/enzymology/genetics/physiology, Spores, Bacterial/enzymology/genetics	Enzymology
Phylogeny	21619698	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	Amino Acid Sequence, Esterases/classification/genetics/metabolism, Hydrogen-Ion Concentration, Hydrolysis, Industrial Microbiology, Metagenomics, Molecular Sequence Data, Phylogeny, Sequence Alignment, *Soil Microbiology, Substrate Specificity, Temperature, Triglycerides/metabolism	Genetics
Metabolism	26751435	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	Antineoplastic Agents/isolation & purification/metabolism/pharmacology, Aquatic Organisms, Bacterial Proteins/chemistry/genetics/metabolism, Cell Survival/drug effects, Deltaproteobacteria/chemistry/genetics/metabolism, Gene Expression, HeLa Cells, Humans, Inhibitory Concentration 50, Metabolome, Multigene Family, Peptides/isolation & purification/metabolism/pharmacology, Polyketides/isolation & purification/*metabolism/pharmacology, Protein Structure, Tertiary, Sulfotransferases/chemistry/genetics/metabolism, Thiolester Hydrolases/chemistry/genetics/metabolism	Phylogeny
Biotechnology	26915413	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	Antifungal Agents, Fatty Acids, Unsaturated/biosynthesis/genetics, Myxococcales/metabolism, Transgenes	Metabolism
Phylogeny	30413766	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	Bacterial Proteins/genetics, Computational Biology, Genome, Bacterial, Metabolome, Multigene Family, Myxococcales/classification/genetics/metabolism, Phylogeny, Seawater/*microbiology	Genetics

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
5321	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14365)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-14365
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793	Mukherjee et al.		10.1038/nbt.3886	GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life	35: 676-683 2017	28604660
66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg		10.1093/nar/gkaa1025	BRENDA, the ELIXIR core data resource in 2021: new developments and updates	Nucleic Acids Res. 49: D498-D508 2020	33211880
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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.		https://microbeatlas.org/	MicrobeAtlas 1.0 beta
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75349	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID100667.1	StrainInfo: A central database for resolving microbial strain identifiers