Archive BacDiveID:10.13145/bacdive17850.20230509.8.1

Strain identifier

BacDive ID: 17850

Type strain:

Species: Rubritalea marina

Strain Designation: Pol012

Strain history: <- M. Scheuermayer, Univ. Würzburg; Pol012

NCBI tax ID(s): 1123070 (strain), 361055 (species)

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

General

@ref: 7158

BacDive-ID: 17850

DSM-Number: 17716

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Rubritalea marina Pol012 is a mesophilic bacterium that was isolated from marine sponge Axinella polypoides.

NCBI tax id

NCBI tax id	Matching level
361055	species
1123070	strain

strain history

@ref: 7158
history: <- M. Scheuermayer, Univ. Würzburg; Pol012

doi: 10.13145/bacdive17850.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/verrucomicrobiota
domain: Bacteria
phylum: Verrucomicrobiota
class: Verrucomicrobiia
order: Verrucomicrobiales
family: Rubritaleaceae
genus: Rubritalea
species: Rubritalea marina
full scientific name: Rubritalea marina Scheuermayer et al. 2006

@ref: 7158

domain: Bacteria

phylum: Verrucomicrobia

class: Verrucomicrobiae

order: Verrucomicrobiales

family: Rubritaleaceae

genus: Rubritalea

species: Rubritalea marina

full scientific name: Rubritalea marina Scheuermayer et al. 2006

strain designation: Pol012

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	no	95.751
69480		99.757	negative

multimedia

@ref	multimedia content	caption	intellectual property rights
66793	EM_DSM_17716_1.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_17716_2.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_17716_3.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_17716_4.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_17716_5.jpg	electron microscopic image	© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref: 7158
name: RUBRITALEA MEDIUM (DSMZ Medium 1137)
growth: yes
link: https://mediadive.dsmz.de/medium/1137
composition: Name: RUBRITALEA MEDIUM (DSMZ Medium 1137) Composition: NaCl 68.6693 g/l MgCl2 x 6 H2O 31.0635 g/l Na2SO4 11.4563 g/l CaCl2 x 2 H2O 4.24125 g/l NaHCO3 2.808 g/l KCl 1.94025 g/l Glucose 1.5 g/l Yeast extract 1.5 g/l Peptone 1.5 g/l MgSO4 x 7 H2O 0.594 g/l KBr 0.28275 g/l Nitrilotriacetic acid 0.2 g/l H3BO3 0.078 g/l ZnSO4 x 7 H2O 0.001095 g/l FeSO4 x 7 H2O 0.0005 g/l Na-EDTA 0.00025 g/l (NH4)6Mo7O24 x 4 H2O 0.000185 g/l MnSO4 x H2O 0.000154 g/l CuSO4 x 5 H2O 3.92e-05 g/l Co(NO3)2 x 6 H2O 2.48e-05 g/l Na2B4O7 x 10 H2O 1.77e-05 g/l Tris-HCl Distilled water

culture temp

@ref: 7158
growth: positive
type: growth
temperature: 30
range: mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.99

Isolation, sampling and environmental information

isolation

@ref: 7158
sample type: marine sponge Axinella polypoides
host species: Axinella polypoides
geographic location: Mediterranean Sea, Banyuls-sur-Mer (42° 29' N 03° 08' E)
country: France
origin.country: FRA
continent: Europe
latitude: 42.4833
longitude: 3.1333

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Porifera (Sponges)

taxonmaps

@ref: 69479
File name: preview.99_32014.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1051;96_15550;97_19040;98_23752;99_32014&stattab=map
Last taxonomy: Rubritalea marina subclade
16S sequence: DQ302104
Sequence Identity:
Total samples: 273
soil counts: 3
aquatic counts: 266
animal counts: 3
plant counts: 1

Safety information

risk assessment

@ref: 7158
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 7158
description: Rubritalea marina strain Pol012 16S ribosomal RNA gene, partial sequence
accession: DQ302104
length: 1429
database: ena
NCBI tax ID: 361055

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Rubritalea marina DSM 17716	GCA_000378105	scaffold	ncbi	1123070
66792	Rubritalea marina DSM 17716	1123070.3	wgs	patric	1123070
66792	Rubritalea marina DSM 17716	2518645606	draft	img	1123070

GC content

@ref: 7158
GC-content: 50.9

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
motile	no	93.297	no
flagellated	no	96.554	no
gram-positive	no	97.791	no
anaerobic	no	98.79	no
aerobic	yes	83.014	no
halophile	yes	53.089	no
spore-forming	no	97.37	no
glucose-util	yes	75.827	no
thermophile	no	98.577	yes
glucose-ferment	no	84.139	no

External links

@ref: 7158

culture collection no.: DSM 17716, CIP 108984

straininfo link

@ref: 86841
straininfo: 404559

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	16957108	Rubritalea marina gen. nov., sp. nov., a marine representative of the phylum 'Verrucomicrobia', isolated from a sponge (Porifera).	Scheuermayer M, Gulder TAM, Bringmann G, Hentschel U	Int J Syst Evol Microbiol	10.1099/ijs.0.64360-0	2006	Animals, Bacteria/isolation & purification, Base Composition, DNA, Bacterial/analysis, Mediterranean Sea, Molecular Sequence Data, Porifera/microbiology, RNA, Ribosomal, 16S/analysis/genetics, Seawater, Water Microbiology	Genetics
Phylogeny	17625207	Rubritalea squalenifaciens sp. nov., a squalene-producing marine bacterium belonging to subdivision 1 of the phylum 'Verrucomicrobia'.	Kasai H, Katsuta A, Sekiguchi H, Matsuda S, Adachi K, Shindo K, Yoon J, Yokota A, Shizuri Y	Int J Syst Evol Microbiol	10.1099/ijs.0.65010-0	2007	Alanine/analysis, Animals, Bacteria/chemistry/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Glutamic Acid/analysis, Japan, Locomotion, Microscopy, Electron, Scanning, Microscopy, Electron, Transmission, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, Pigments, Biological/biosynthesis, Porifera/microbiology, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Squalene/metabolism	Genetics
Phylogeny	29509135	Rubritalea profundi sp. nov., isolated from deep-seawater and emended description of the genus Rubritalea in the phylum Verrucomicrobia.	Song J, Lim Y, Joung Y, Cho JC, Kogure K	Int J Syst Evol Microbiol	10.1099/ijsem.0.002686	2018

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
7158	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17716)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-17716
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
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)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
86841	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID404559.1	StrainInfo: A central database for resolving microbial strain identifiers