Archive BacDiveID:10.13145/bacdive7232.20230509.8.1

Strain identifier

BacDive ID: 7232

Type strain:

Species: Methylobacillus glycogenes

Strain Designation: T-11

Strain history: T. Urakami TK 0113 <-- ATCC 29475 <-- J. R. Yordy T-11 <-- T. Weaver.

NCBI tax ID(s): 1236959 (strain), 406 (species)

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

General

@ref: 2282

BacDive-ID: 7232

DSM-Number: 5685

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

description: Methylobacillus glycogenes T-11 is a mesophilic bacterium that was isolated from decaying tomato.

NCBI tax id

NCBI tax id	Matching level
1236959	strain
406	species

strain history

@ref	history
2282	<- NCIMB <- ATCC <- Yordy <- Weaver
67770	T. Urakami TK 0113 <-- ATCC 29475 <-- J. R. Yordy T-11 <-- T. Weaver.

doi: 10.13145/bacdive7232.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/pseudomonadota
domain: Bacteria
phylum: Pseudomonadota
class: Betaproteobacteria
order: Nitrosomonadales
family: Methylophilaceae
genus: Methylobacillus
species: Methylobacillus glycogenes
full scientific name: Methylobacillus glycogenes Yordy and Weaver 1977 (Approved Lists 1980)

@ref: 2282

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Methylophilales

family: Methylophilaceae

genus: Methylobacillus

species: Methylobacillus glycogenes

full scientific name: Methylobacillus glycogenes Yordy and Weaver 1977 emend. Urakami and Komagata 1986

strain designation: T-11

type strain: yes

Culture and growth conditions

culture medium

@ref: 2282
name: COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606)
growth: yes
link: https://mediadive.dsmz.de/medium/606
composition: Name: COLBY AND ZATHMAN MEDIUM (DSMZ Medium 606) Composition: Agar 15.0 g/l Methanol 1.584 g/l K2HPO4 1.2 g/l KH2PO4 0.62 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l NaCl 0.1 g/l CaCl2 x 6 H2O 0.05 g/l FeCl3 x 6 H2O 0.001 g/l ZnSO4 x 7 H2O 7e-05 g/l Na2MoO4 x 2 H2O 1e-05 g/l H3BO3 1e-05 g/l MnSO4 x 5 H2O 1e-05 g/l CuSO4 x 5 H2O 5e-06 g/l CoCl2 x 6 H2O 5e-06 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
2282	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

observation

@ref: 67770
observation: quinones: Q-8

Isolation, sampling and environmental information

isolation

@ref	sample type
2282	decaying tomato
67770	Decaying tomato

isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Decomposing plant
#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Fruit (Seed)

taxonmaps

@ref: 69479
File name: preview.99_3987.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_174;96_1029;97_2441;98_3019;99_3987&stattab=map
Last taxonomy: Methylobacillus
16S sequence: FR733701
Sequence Identity:
Total samples: 5097
soil counts: 589
aquatic counts: 1076
animal counts: 2643
plant counts: 789

Safety information

risk assessment

@ref: 2282
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 2282
description: Methylobacillus glycogenes partial 16S rRNA gene, type strain DSM5685T
accession: FR733701
length: 1532
database: ena
NCBI tax ID: 406

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Methylobacillus glycogenes JCM 2850	1236959.3	wgs	patric	1236959
66792	Methylobacillus glycogenes JCM 2850	2585427884	draft	img	1236959
67770	Methylobacillus glycogenes JCM 2850	GCA_000617925	contig	ncbi	1236959

GC content

@ref	GC-content	method
67770	53.2	thermal denaturation, midpoint method (Tm)
67770	54.1

Genome-based predictions

predictions

trait	prediction	confidence	training_data
motile	yes	86.105	no
gram-positive	no	98.123	no
anaerobic	no	98.225	no
aerobic	yes	92.225	no
halophile	no	93.811	no
spore-forming	no	92.615	no
thermophile	no	98.726	yes
glucose-util	yes	63.344	no
flagellated	yes	53.871	no
glucose-ferment	no	90.23	no

External links

@ref: 2282

culture collection no.: DSM 5685, ATCC 29475, DSM 46232, IMET 10774, NCIMB 11375, JCM 2850, LMG 6082, VKM B-2060

straininfo link

@ref: 76684
straininfo: 3558

literature

topic	Pubmed-ID	title	authors	journal	year	mesh	topic2
Phylogeny	2463459	[Analysis of DNA-DNA homologies in obligate methylotrophic bacteria].	Doronina NV, Govorukhina NI, Lysenko AM, Trotsenko IuA	Mikrobiologiia	1988	Bacteria/genetics, Base Sequence, DNA, Bacterial/genetics, Nucleic Acid Hybridization, RNA, Bacterial/genetics, *Sequence Homology, Nucleic Acid
Phylogeny	11315676	[Methylovorus mays--novel species of aerobic, obligatory methylotrophic bacteria associated with plants].	Doronina NV, Kudinova LV, Trotsenko IuA	Mikrobiologiia	2000	Methanol/metabolism, Methylobacterium/classification/*isolation & purification/physiology, Plants/microbiology	Metabolism

Reference

@id	authors	catalogue	doi/url	title
2282	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5685)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-5685
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)
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
76684	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID3558.1	StrainInfo: A central database for resolving microbial strain identifiers