Archive BacDiveID:10.13145/bacdive11905.20230509.8.1

Strain identifier

BacDive ID: 11905

Type strain:

Species: Methylophaga sulfidovorans

Strain Designation: RB-1

Strain history: CIP <- 1997, J.M.M. de Zwart, Delft Univ., The Netherlands: strain RB-1, Methylopila sulfovorans

NCBI tax ID(s): 45496 (species)

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

General

@ref: 4329

BacDive-ID: 11905

DSM-Number: 11578

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

description: Methylophaga sulfidovorans RB-1 is a mesophilic, motile bacterium of the family Piscirickettsiaceae.

NCBI tax id

NCBI tax id: 45496
Matching level: species

strain history

@ref	history
4329	<- J. Gruwel, TU Delft
67770	IAM 15035 <-- LMD 95.210.
123382	CIP <- 1997, J.M.M. de Zwart, Delft Univ., The Netherlands: strain RB-1, Methylopila sulfovorans

doi: 10.13145/bacdive11905.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Gammaproteobacteria
order: Beggiatoales
family: Piscirickettsiaceae
genus: Methylophaga
species: Methylophaga sulfidovorans
full scientific name: Methylophaga sulfidovorans de Zwart et al. 1998

@ref: 4329

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Thiotrichales

family: Piscirickettsiaceae

genus: Methylophaga

species: Methylophaga sulfidovorans

full scientific name: Methylophaga sulfidovorans de Zwart et al. 1998

strain designation: RB-1

type strain: yes

Morphology

cell morphology

@ref	motility	confidence	gram stain
69480	yes	98.226
69480		99.999	negative

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
4329	MEDIUM FOR MARINE METHYLOTROPHS (DSMZ Medium 750)	yes	https://mediadive.dsmz.de/medium/750	Name: MEDIUM FOR MARINE METHYLOTROPHS (DSMZ Medium 750) Composition: NaCl 25.0 g/l Agar 20.0 g/l Peptone 10.0 g/l Methanol 7.92 g/l Beef extract 7.0 g/l (NH4)2SO4 1.0 g/l K2HPO4 1.0 g/l Distilled water
4329	METHYLOPHAGA SULFIDOVORANS MEDIUM (DSMZ Medium 951)	yes	https://mediadive.dsmz.de/medium/951	Name: METHYLOPHAGA SULFIDOVORANS MEDIUM (DSMZ Medium 951) Composition: Agar 15.0 g/l NaCl 15.0 g/l Methanol 7.92 g/l Na2CO3 2.0 g/l MgSO4 x 7 H2O 1.0 g/l (NH4)2SO4 0.5 g/l CaCl2 x 6 H2O 0.33 g/l KCl 0.2 g/l KH2PO4 0.02 g/l FeCl2 x 4 H2O 0.00149254 g/l FeSO4 x 7 H2O 0.001 g/l Pyridoxine hydrochloride 0.0005 g/l Nicotinic acid 0.0002 g/l MnCl2 x 4 H2O 0.000199005 g/l CoCl2 x 6 H2O 0.000189055 g/l p-Aminobenzoic acid 0.0001 g/l Thiamine 0.0001 g/l ZnCl2 6.96517e-05 g/l Pantothenate 5e-05 g/l Na2MoO4 x 2 H2O 3.58209e-05 g/l NiCl2 x 6 H2O 2.38806e-05 g/l Biotin 2e-05 g/l Riboflavine 1e-05 g/l Vitamin B12 1e-05 g/l H3BO3 5.97015e-06 g/l CuCl2 x 2 H2O 1.99005e-06 g/l HCl Distilled water
41559	MEDIUM 441 - for Methylophaga sulfidovorans	yes		Distilled water make up to (972.000 ml);Sodium chloride (24.000 g);Potassium chloride (0.500 g);Magnesium chloride hexahydrate (3.000 g);Magnesium sulphate heptahydrate (2.000 g);Calcium chloride dihydrate (1.000 g);Methanol (6.000 ml);Trizma hydrochlorid
123382	CIP Medium 441	yes	https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=441

culture temp

@ref	growth	type	temperature	range
4329	positive	growth	25	mesophilic
41559	positive	growth	25	mesophilic
67770	positive	growth	27	mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	no	100
69480	no	99.999

Isolation, sampling and environmental information

isolation

@ref	geographic location	country	origin.country	continent	sample type	isolation date
41559	Delft	Netherlands	NLD	Europe
67770					Microbial mat sediment from the South-West coast of the Netherlands
123382	Delft	Netherlands	NLD	Europe	Environment, Intertidal mud flat	1993

taxonmaps

@ref: 69479
File name: preview.99_41891.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_54;96_118;97_4308;98_5516;99_41891&stattab=map
Last taxonomy: Methylophaga sulfidovorans
16S sequence: X95461
Sequence Identity:
Total samples: 146
soil counts: 9
aquatic counts: 130
animal counts: 7

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
4329	1	Risk group (German classification)
123382	1	Risk group (French classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
20218	Methylophaga sulfidovorans gene for 16S rRNA, partial sequence, strain: NBRC 102423	AB681779	1461	ena	45496
20218	M.sulfidovorans mRNA for 16S ribosomal RNA	X95461	1487	ena	45496

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Methylophaga sulfidovorans strain DSM 11578	45496.5	wgs	patric	45496
66792	Methylophaga sulfidovorans DSM 11578	2622736507	draft	img	45496
67770	Methylophaga sulfidovorans DSM 11578	GCA_900114205	scaffold	ncbi	45496

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	100	no
gram-positive	no	99.06	no
anaerobic	no	97.383	no
halophile	no	76.461	no
spore-forming	no	97.168	no
glucose-util	yes	63.644	no
aerobic	yes	80.962	no
flagellated	yes	59.273	no
thermophile	no	99.28	no
motile	yes	76.156	no
glucose-ferment	no	85.911	no

External links

@ref: 4329

culture collection no.: DSM 11578, LMD 95.210, JCM 21498, CIP 105175, IAM 15035, NBRC 102423

straininfo link

@ref: 81120
straininfo: 100769

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
4329	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11578)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-11578
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
41559	Curators of the CIP		https://brclims.pasteur.fr/brcWeb/souche/detail/1/17165
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)
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)
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
81120	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID100769.1	StrainInfo: A central database for resolving microbial strain identifiers
123382	Curators of the CIP	Collection of Institut Pasteur (CIP 105175)	https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105175