Archive BacDiveID:10.13145/bacdive13495.20230509.8.1

Strain identifier

BacDive ID: 13495

Type strain:

Species: Thermobispora bispora

Strain Designation: R51

Strain history: IFO 14880 <-- S. Miyadoh; Meiji Seika Kaisha, Ltd., Japan <-- ATCC 19993 <-- A. Henssen R₅₁.

NCBI tax ID(s): 469371 (strain), 2006 (species)

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

General

@ref: 11317

BacDive-ID: 13495

DSM-Number: 43833

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, thermophilic, Gram-positive

description: Thermobispora bispora R51 is a spore-forming, thermophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from decaying manure.

NCBI tax id

NCBI tax id	Matching level
2006	species
469371	strain

strain history

@ref	history
11317	<- G. Vobis <- A. Henssen, R51
67770	IFO 14880 <-- S. Miyadoh; Meiji Seika Kaisha, Ltd., Japan <-- ATCC 19993 <-- A. Henssen R₅₁.

doi: 10.13145/bacdive13495.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Streptosporangiales
family: Streptosporangiaceae
genus: Thermobispora
species: Thermobispora bispora
full scientific name: Thermobispora bispora (Henssen 1957) Wang et al. 1996
synonyms
@ref synonym
20215 Microbispora bispora
20215 Thermopolyspora bispora

@ref	synonym
20215	Microbispora bispora
20215	Thermopolyspora bispora

@ref: 11317

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptosporangiaceae

genus: Thermobispora

species: Thermobispora bispora

full scientific name: Thermobispora bispora (Henssen 1957) Wang et al. 1996 emend. Nouioui et al. 2018

strain designation: R51

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 100

colony morphology

@ref	colony color	incubation period	medium used
19961	Beige (1001)	10-14 days	ISP 2
19961	Dahlia yellow (1033)	10-14 days	ISP 3
19961	Beige (1001)	10-14 days	ISP 4
19961	Beige (1001)	10-14 days	ISP 5
19961	Beige (1001)	10-14 days	ISP 6
19961	Beige (1001)	10-14 days	ISP 7

multicellular morphology

@ref	forms multicellular complex	medium name	complex name	complex color
19961	no	ISP 2
19961	yes	ISP 3	Aerial Mycelium	White
19961	no	ISP 4
19961	no	ISP 5
19961	no	ISP 6
19961	no	ISP 7

multimedia

@ref	multimedia content	caption	intellectual property rights
11317	https://www.dsmz.de/microorganisms/photos/DSM_43833.jpg	Medium 553 45°C	© Leibniz-Institut DSMZ
66793	EM_DSM_43833_1.jpg	electron microscopic image	© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
11317	GPHF-MEDIUM (DSMZ Medium 553)	yes	https://mediadive.dsmz.de/medium/553	Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
19961	ISP 2	yes		Name: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
19961	ISP 3	yes		Name: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
19961	ISP 4	yes		Name: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
19961	ISP 5	yes		Name: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
19961	ISP 6	yes		Name: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
19961	ISP 7	yes		Name: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@ref	growth	type	temperature	range	confidence
19961	positive	optimum	45	thermophilic
11317	positive	growth	45	thermophilic
67770	positive	growth	50	thermophilic
69480				thermophilic	91.097

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	yes	100
69480	yes	100

halophily

@ref: 19961
salt: NaCl
growth: positive
tested relation: growth
concentration: 0 %

observation

@ref: 67770
observation: quinones: MK-9, MK-9(H₂)

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
11317	decaying manure
67770	Decaying manure	Berlin	Germany	DEU	Europe

isolation source categories

Cat1: #Host Body Product
Cat2: #Gastrointestinal tract
Cat3: #Feces (Stool)

Safety information

risk assessment

@ref	biosafety level	biosafety level comment
19961	1	German classification
11317	1	Risk group (German classification)

Sequence information

16S sequences

@ref	description	accession	length	database	NCBI tax ID
67770	Thermobispora bispora strain DSM 43833 16S ribosomal RNA, partial sequence	NR_027583	1469	nuccore	2006
67770	Thermobispora bispora strain DSM 43833 16S ribosomal RNA, partial sequence	NR_074680	1525	nuccore	2006
67770	Microbispora bispora strain ATCC19993 16S ribosomal RNA gene sequence	U58523	1469	ena	469371

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Thermobispora bispora DSM 43833	GCA_000092645	complete	ncbi	469371
66792	Thermobispora bispora DSM 43833	469371.5	complete	patric	469371
66792	Thermobispora bispora R51, DSM 43833	646564581	complete	img	469371

GC content

@ref	GC-content	method
11317	70.0
67770	72.43	genome sequence analysis
67770	71	thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
motile	no	93.922	no
flagellated	no	98.601	no
gram-positive	yes	87.943	no
anaerobic	no	96.208	no
aerobic	yes	81.28	no
halophile	no	90.974	yes
spore-forming	yes	81.769	no
glucose-util	yes	84.375	no
thermophile	yes	77.209	no
glucose-ferment	no	94.484	no

External links

@ref: 11317

culture collection no.: DSM 43833, ATCC 19993, CBS 139.67, IFO 14880, NBRC 14880, JCM 10125, IMSNU 21333, KCTC 9307

straininfo link

@ref: 82687
straininfo: 37211

literature

topic: Phylogeny
Pubmed-ID: 8863419
title: A proposal to transfer Microbispora bispora (Lechevalier 1965) to a new genus, Thermobispora gen. nov., as Thermobispora bispora comb. nov.
authors: Wang Y, Zhang Z, Ruan J
journal: Int J Syst Bacteriol
DOI: 10.1099/00207713-46-4-933
year: 1996
mesh: Actinomycetales/*classification, Base Sequence, DNA, Ribosomal/chemistry, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics
topic2: Genetics

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
11317	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43833)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-43833
19961	Wink, J.		http://www.dsmz.de/microorganisms/wink_pdf/DSM43833.pdf	Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
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
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
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
82687	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID37211.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

cell morphology

colony morphology

multicellular morphology

multimedia

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

spore formation

halophily

observation

Isolation, sampling and environmental information

isolation

isolation source categories

Safety information

risk assessment

Sequence information

16S sequences

Genome sequences

GC content

Genome-based predictions

predictions

External links

straininfo link

literature

Reference