Archive BacDiveID:10.13145/bacdive23100.20240916.9.1

Strain identifier

BacDive ID: 23100

Type strain:

Species: Methylotenera versatilis

Strain Designation: 301

Strain history: A. Vorobev 301 <-- M. Kalyuzhnaya.

NCBI tax ID(s): 1055487 (species)

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

General

@ref: 19131

BacDive-ID: 23100

DSM-Number: 24635

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, motile, ovoid-shaped

description: Methylotenera versatilis 301 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from freshwater sediment.

NCBI tax id

NCBI tax id: 1055487
Matching level: species

strain history

@ref	history
19131	<- A. Vorobev, Univ. of Washington, Seattle, USA; strain 301 <- M. Kalyuzhnaya
67770	A. Vorobev 301 <-- M. Kalyuzhnaya.

doi: 10.13145/bacdive23100.20240916.9.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Betaproteobacteria
order: Nitrosomonadales
family: Methylophilaceae
genus: Methylotenera
species: Methylotenera versatilis
full scientific name: Methylotenera versatilis Kalyuzhnaya et al. 2012

@ref: 19131

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Methylophilales

family: Methylophilaceae

genus: Methylotenera

species: Methylotenera versatilis

full scientific name: Methylotenera versatilis Kalyuzhnaya et al. 2012

strain designation: 301

type strain: yes

Morphology

cell morphology

@ref	gram stain	cell length	cell width	cell shape	motility	confidence
30081	negative	0.8-1.2 µm	0.3-0.7 µm	ovoid-shaped	yes
69480	negative					98

colony morphology

@ref: 19131
incubation period: 1-2 days

pigmentation

@ref: 30081
production: no

Culture and growth conditions

culture medium

@ref: 19131
name: HYPHOMICROBIUM MEDIUM (DSMZ Medium 1355)
growth: yes
link: https://mediadive.dsmz.de/medium/1355
composition: Name: HYPHOMICROBIUM MEDIUM (DSMZ Medium 1355) Composition: Agar 12.0 g/l K2HPO4 2.5 g/l NaH2PO4 2.25 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l EDTA 0.01 g/l ZnSO4 x 7 H2O 0.0044 g/l CaCl2 x 2 H2O 0.001466 g/l MnCl2 x 4 H2O 0.001012 g/l FeSO4 x 7 H2O 0.000998 g/l CoCl2 x 6 H2O 0.000322 g/l CuSO4 x 5 H2O 0.000314 g/l (NH4)6Mo7O24 x 4 H2O 0.00022 g/l Methylamine Distilled water

culture temp

@ref	growth	type	temperature
19131	positive	growth	25
30081	positive	optimum	18-21
67770	positive	growth	25

culture pH

@ref	ability	type	pH
30081	positive	growth	4.2-8.0
30081	positive	optimum	5.8-6.5

Physiology and metabolism

oxygen tolerance

@ref: 30081
oxygen tolerance: facultative anaerobe

spore formation

@ref	spore formation	confidence
30081	no
69480	no	92.23

observation

@ref: 30081
observation: aggregates in clumps

metabolite utilization

@ref	Chebi-ID	metabolite	utilization activity	kind of utilization tested
30081	16236	ethanol	+	carbon source
30081	28757	fructose	+	carbon source
30081	15361	pyruvate	+	carbon source
30081	17632	nitrate	+	reduction

enzymes

@ref: 30081
value: urease
activity: +
ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
19131	freshwater sediment	Lake Washington	USA	USA	North America
67770	Sediment of Lake Washington	Seattle, WA	USA	USA	North America

isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Sediment
#Environmental	#Aquatic	#Freshwater

taxonmaps

@ref: 69479
File name: preview.99_1183.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_174;96_690;97_805;98_933;99_1183&stattab=map
Last taxonomy: Methylotenera versatilis subclade
16S sequence: NR_074693
Sequence Identity:
Total samples: 2559
soil counts: 549
aquatic counts: 1731
animal counts: 80
plant counts: 199

Safety information

risk assessment

@ref: 19131
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 67770
description: Methylotenera versatilis strain 301 16S ribosomal RNA, partial sequence
accession: NR_074693
length: 1526
database: nuccore
NCBI tax ID: 1055487

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Methylotenera versatilis 301	GCA_000093025	complete	ncbi	666681
66792	Methylotenera versatilis 301	666681.3	complete	patric	666681
66792	Methylotenera versatilis 301, JCM 17579	646564551	complete	img	666681

GC content

@ref	GC-content	method
19131	42.6	sequence analysis
30081	42.6
67770	42.6	genome sequence analysis

Genome-based predictions

predictions

@ref	trait	model	description	prediction	confidence	training_data
69480	gram-positive	gram-positive	Positive reaction to Gram-staining	no	98	no
69480	anaerobic	anaerobic	Ability to grow under anoxygenic conditions (including facultative anaerobes)	no	92.426	yes
69480	aerobic	aerobic	Ability to grow under oxygenic conditions (including facultative aerobes)	yes	70.389	no
69480	spore-forming	spore-forming	Ability to form endo- or exospores	no	92.23	yes
69480	thermophilic	thermophile	Ability to grow at temperatures above or equal to 45°C	no	95.395	no
69480	flagellated	motile2+	Ability to perform flagellated movement	yes	68.29	no

External links

@ref: 19131

culture collection no.: DSM 24635, JCM 17579, VKM B-2679

straininfo link

@ref: 87338
straininfo: 400810

literature

topic: Phylogeny
Pubmed-ID: 21335496
title: Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera.
authors: Kalyuzhnaya MG, Beck DAC, Vorobev A, Smalley N, Kunkel DD, Lidstrom ME, Chistoserdova L
journal: Int J Syst Evol Microbiol
DOI: 10.1099/ijs.0.029165-0
year: 2011
mesh: Bacterial Typing Techniques, Base Composition, Carbon/*metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, *Fresh Water, Geologic Sediments/*microbiology, Methylophilaceae/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Washington
topic2: Genetics

Reference

@id	authors	catalogue	doi/url	title	ID_cross_reference	pubmed
19131	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24635)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-24635
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
30081	Barberan A, Caceres Velazquez H, Jones S, Fierer N.		10.1128/mSphere.00237-17	Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information	26438	28776041
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)
87338	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID400810.1	StrainInfo: A central database for resolving microbial strain identifiers