Archive BacDiveID:10.13145/bacdive3251.20230509.8.1

Strain identifier

BacDive ID: 3251

Type strain:

Species: Archangium gephyra

Strain Designation: M18

Strain history: <- ATCC <- H.D. McCurdy, M18

NCBI tax ID(s): 48 (species)

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

General

@ref: 1009

BacDive-ID: 3251

DSM-Number: 2261

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

description: Archangium gephyra M18 is a mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

NCBI tax id: 48
Matching level: species

strain history

@ref: 1009
history: <- ATCC <- H.D. McCurdy, M18

doi: 10.13145/bacdive3251.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Deltaproteobacteria
order: Myxococcales
family: Archangiaceae
genus: Archangium
species: Archangium gephyra
full scientific name: Archangium gephyra Jahn 1924 (Approved Lists 1980)

@ref: 1009

domain: Bacteria

phylum: Proteobacteria

class: Deltaproteobacteria

order: Myxococcales

family: Archangiaceae

genus: Archangium

species: Archangium gephyra

full scientific name: Archangium gephyra Jahn 1924 emend. Lang et al. 2015

strain designation: M18

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.919

multimedia

@ref: 1009
multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_2261.jpg
caption: myxospores formed in fruiting bodies on agar medium 9
intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
1009	CY/H MEDIUM FOR MYXOBACTERIA (DSMZ Medium 1542)	yes	https://mediadive.dsmz.de/medium/1542	Name: CY/H LIQUID MEDIUM FOR MYXOBACTERIA (DSMZ Medium 1542) Composition: HEPES 11.9 g/l Starch 4.0 g/l Yeast extract 1.5 g/l Casitone 1.5 g/l CaCl2 x 2 H2O 1.0 g/l D-Glucose 1.0 g/l Soy flour 1.0 g/l MgSO4 x 7 H2O 0.5 g/l Fe(III)-EDTA 0.008 g/l Vitamin B12 0.0005 g/l Distilled water
1009	VY/2 AGAR (DSMZ Medium 9)	yes	https://mediadive.dsmz.de/medium/9	Name: VY/2 AGAR (DSMZ Medium 9) Composition: Agar 15.0 g/l Baker's yeast 5.0 g/l CaCl2 x 2 H2O 1.36 g/l Vitamin B12 0.0005 g/l Distilled water
1009	SP - MEDIUM (DSMZ Medium 222)	yes	https://mediadive.dsmz.de/medium/222	Name: SP - MEDIUM (DSMZ Medium 222) Composition: Agar 15.0 g/l Starch 5.0 g/l Casitone 2.5 g/l Galactose 1.0 g/l Sucrose 1.0 g/l Raffinose 1.0 g/l MgSO4 x 7 H2O 0.5 g/l K2HPO4 0.25 g/l Distilled water

culture temp

@ref: 1009
growth: positive
type: growth
temperature: 30
range: mesophilic

Physiology and metabolism

spore formation

@ref: 69480
spore formation: no
confidence: 97.621

Isolation, sampling and environmental information

isolation

@ref: 1009
sample type: soil
country: Canada
origin.country: CAN
continent: North America

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

taxonmaps

@ref: 69479
File name: preview.99_7498.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_211;96_740;97_958;98_3213;99_7498&stattab=map
Last taxonomy: Archangium
16S sequence: AB218222
Sequence Identity:
Total samples: 2918
soil counts: 2270
aquatic counts: 200
animal counts: 126
plant counts: 322

Safety information

risk assessment

@ref: 1009
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Archangium gephyra 16S ribosomal RNA gene, complete sequence	M94273	1483	ena	48
20218	Archangium gephyra strain DSM 2261 16S ribosomal RNA gene, partial sequence	GU207872	1482	ena	48
20218	Archangium gephyra gene for 16S rRNA, partial sequence, strain: NBRC 100087	AB218222	1461	ena	48
20218	Archangium gephyra gene for 16S-23S rRNA internal transcribed spacer regions, partial sequence, strain: NBRC 100087, A type	AB218256	670	ena	48
20218	Archangium gephyra gene for 16S-23S rRNA internal transcribed spacer regions, partial sequence, strain: NBRC 100087, B type	AB218257	625	ena	48
1009	Archangium gephyra strain DSM 2261 16S ribosomal RNA gene, partial sequence	DQ768106	1491	ena	48

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Archangium gephyra DSM 2261	GCA_001027285	complete	ncbi	48
66792	Archangium gephyra DSM 2261	GCA_003387095	scaffold	ncbi	48
66792	Archangium gephyra strain DSM 2261	48.18	complete	patric	48
66792	Archangium gephyra strain DSM 2261	48.8	wgs	patric	48
66792	Archangium gephyra DSM 2261	2654587630	complete	img	48
66792	Archangium gephyra DSM 2261	2619619032	draft	img	48

GC content

@ref: 1009
GC-content: 68.3

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	72	no
motile	no	60.284	no
flagellated	no	86.454	no
gram-positive	no	96.353	no
anaerobic	no	97.829	no
aerobic	yes	76.808	no
halophile	no	87.246	no
spore-forming	no	75.294	no
thermophile	no	98.467	yes
glucose-util	yes	82.28	no
glucose-ferment	no	89.799	no

External links

@ref: 1009

culture collection no.: DSM 2261, ATCC 25201, NBRC 100087

straininfo link

@ref: 72764
straininfo: 38410

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	26286530	Reclassification of Angiococcus disciformis, Cystobacter minus and Cystobacter violaceus as Archangium disciforme comb. nov., Archangium minus comb. nov. and Archangium violaceum comb. nov., unification of the families Archangiaceae and Cystobacteraceae, and emended descriptions of the families Myxococcaceae and Archangiaceae.	Lang E, Schumann P, Tindall BJ, Mohr KI, Sproer C	Int J Syst Evol Microbiol	10.1099/ijsem.0.000533	2015	Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Myxococcales/classification, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA	Transcriptome
Phylogeny	28141508	Vitiosangium cumulatum gen. nov., sp. nov. and Vitiosangium subalbum sp. nov., soil myxobacteria, and emended descriptions of the genera Archangium and Angiococcus, and of the family Cystobacteraceae.	Awal RP, Garcia R, Gemperlein K, Wink J, Kunwar B, Parajuli N, Muller R	Int J Syst Evol Microbiol	10.1099/ijsem.0.001829	2017	Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/chemistry, Myxococcales/classification/genetics/isolation & purification, Nepal, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology	Transcriptome
Phylogeny	28379546	Unravelling the Complete Genome of Archangium gephyra DSM 2261T and Evolutionary Insights into Myxobacterial Chitinases.	Sharma G, Subramanian S	Genome Biol Evol	10.1093/gbe/evx066	2017	Bacterial Typing Techniques, Chitinases/genetics, Evolution, Molecular, Genome, Bacterial, Myxococcales/classification/enzymology/genetics, Phylogeny, Sequence Analysis, DNA/*methods	Genetics

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
1009	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2261)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-2261
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
20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.		10.1016/j.syapm.2013.11.002	StrainInfo introduces electronic passports for microorganisms.	Syst Appl Microbiol. 37: 42-50 2014	24321274
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)
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
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)
72764	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID38410.1	StrainInfo: A central database for resolving microbial strain identifiers