Archive BacDiveID:10.13145/bacdive7881.20230509.8.1

Strain identifier

BacDive ID: 7881

Type strain:

Species: Longispora albida

Strain Designation: K97-0003

Strain history: S. ?mura K97-0003.

NCBI tax ID(s): 1122182 (strain), 203523 (species)

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

General

@ref: 12088

BacDive-ID: 7881

DSM-Number: 44784

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

description: Longispora albida K97-0003 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax id	Matching level
203523	species
1122182	strain

strain history

@ref	history
12088	<- NRRL <- S. Omura; K97-0003
67770	S. ?mura K97-0003.

doi: 10.13145/bacdive7881.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Micromonosporales
family: Micromonosporaceae
genus: Longispora
species: Longispora albida
full scientific name: Longispora albida Matsumoto et al. 2003

@ref: 12088

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Longispora

species: Longispora albida

full scientific name: Longispora albida Matsumoto et al. 2003 emend. Piao et al. 2017

strain designation: K97-0003

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 100

multimedia

@ref	multimedia content	caption	intellectual property rights
66793	EM_DSM_44784_1.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_44784_2.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_44784_3.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_44784_4.jpg	electron microscopic image	© HZI/Manfred Rohde
66793	EM_DSM_44784_5.jpg	electron microscopic image	© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
12088	ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)	yes	https://mediadive.dsmz.de/medium/84	Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
12088	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	yes	https://mediadive.dsmz.de/medium/65	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water

culture temp

@ref	growth	type	temperature	range
12088	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	yes	94
69480	yes	97.602

observation

@ref: 67770
observation: quinones: MK-10(H₄), MK-10(H₆)

metabolite production

@ref: 67770
metabolite: actinohivin
production: yes

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
12088	soil	Tokyo	Japan	JPN	Asia
67770	Soil	Suginami, Tokyo	Japan	JPN	Asia

isolation source categories

Cat1: #Environmental
Cat2: #Terrestrial
Cat3: #Soil

Safety information

risk assessment

@ref: 12088
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 12088
description: Longispora albida gene for 16S rRNA, partial sequence
accession: AB089241
length: 1476
database: ena
NCBI tax ID: 203523

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Longispora albida DSM 44784	1122182.3	wgs	patric	1122182
66792	Longispora albida DSM 44784	2515154011	draft	img	1122182
67770	Longispora albida DSM 44784	GCA_000379825	scaffold	ncbi	1122182

GC content

@ref	GC-content	method
12088	70
67770	70	high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	94	no
motile	no	94.31	no
flagellated	no	97.772	no
gram-positive	yes	88.031	no
anaerobic	no	99.193	no
aerobic	yes	91.172	no
halophile	no	94.032	no
spore-forming	yes	86.815	no
thermophile	no	98.086	yes
glucose-util	yes	87.1	no
glucose-ferment	no	92.17	no

External links

@ref: 12088

culture collection no.: DSM 44784, JCM 11711, NRRL B-24201, BCRC 16381, CGMCC 4.5504, NBRC 100759

straininfo link

@ref: 77317
straininfo: 100323

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	13130047	Longispora albida gen. nov., sp. nov., a novel genus of the family Micromonosporaceae.	Matsumoto A, Takahashi Y, Shinose M, Seino A, Iwai Y, Omura S	Int J Syst Evol Microbiol	10.1099/ijs.0.02595-0	2003	Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Japan, Micromonosporaceae/*classification/genetics/isolation & purification/metabolism, Microscopy, Electron, Scanning, Molecular Sequence Data, Peptidoglycan/chemistry, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology	Genetics
Phylogeny	20207801	Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash.	Lee DW, Lee SD	Int J Syst Evol Microbiol	10.1099/ijs.0.020313-0	2010	Bacterial Typing Techniques, Carbohydrates/analysis, DNA, Bacterial/genetics, Lipids/analysis, Micromonosporaceae/classification/genetics/isolation & purification, Molecular Sequence Data, Phylogeny, Pigments, Biological/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2/analysis, Volcanic Eruptions	Genetics
Phylogeny	28920833	Longispora urticae sp. nov., isolated from rhizosphere soil of Urtica urens L., and emended descriptions of the species Longisporaalbida and Longisporafulva.	Piao C, Jin L, Zhao J, Liu C, Zhao Y, Wang X, Xiang W	Int J Syst Evol Microbiol	10.1099/ijsem.0.002288	2017	Actinobacteria/genetics, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Micromonosporaceae/classification/genetics/isolation & purification, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, Soil Microbiology, Urticaceae/*microbiology, Vitamin K 2/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
12088	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44784)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-44784
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
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
77317	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID100323.1	StrainInfo: A central database for resolving microbial strain identifiers