Archive BacDiveID:10.13145/bacdive7837.20230509.8.1

Strain identifier

BacDive ID: 7837

Type strain:

Species: Actinoplanes capillaceus

Strain Designation: K95-5561

Strain history: S. ?mura K95-5561.

NCBI tax ID(s): 76756 (species)

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

General

@ref: 12146

BacDive-ID: 7837

DSM-Number: 44859

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

description: Actinoplanes capillaceus K95-5561 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax id: 76756
Matching level: species

strain history

@ref	history
12146	<- JCM <- S. Omura; K95-5561
67770	S. ?mura K95-5561.

doi: 10.13145/bacdive7837.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Micromonosporales
family: Micromonosporaceae
genus: Actinoplanes
species: Actinoplanes capillaceus
full scientific name: Actinoplanes capillaceus Matsumoto et al. 2001

@ref: 12146

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes capillaceus

full scientific name: Actinoplanes capillaceus Matsumoto et al. 2001

strain designation: K95-5561

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 100

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
12146	N-Z-AMINE-MEDIUM (DSMZ Medium 554)	yes	https://mediadive.dsmz.de/medium/554	Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
12146	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
12146	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

culture temp

@ref	growth	type	temperature	range
12146	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	yes	100
69480	yes	100

observation

@ref: 67770
observation: quinones: MK-9(H₄), MK-9(H₆), MK-10(H₄)

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
12146	soil	Saitama Prefecture	Japan	JPN	Asia
67770	Soil	Sayama City, Saitama Pref.	Japan	JPN	Asia

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_53823.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_240;97_16361;98_20282;99_53823&stattab=map
Last taxonomy: Actinoplanes
16S sequence: AB013495
Sequence Identity:
Total samples: 30
soil counts: 12
aquatic counts: 6
animal counts: 9
plant counts: 3

Safety information

risk assessment

@ref: 12146
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 20218
description: Actinoplanes capillaceus gene for 16S rRNA, partial sequence
accession: AB013495
length: 1457
database: ena
NCBI tax ID: 76756

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Actinoplanes capillaceus NBRC 16408	GCA_016862055	contig	ncbi	76756
66792	Actinoplanes capillaceus strain NBRC 16408	76756.3	wgs	patric	76756

GC content

@ref: 67770
GC-content: 71.4
method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	100	no
motile	yes	66.333	no
flagellated	no	88.043	no
gram-positive	yes	87.914	no
anaerobic	no	98.713	no
halophile	no	93.054	no
spore-forming	yes	91.255	no
glucose-util	yes	89.071	no
aerobic	yes	91.051	no
thermophile	no	98.932	yes
glucose-ferment	no	88.438	no

External links

@ref: 12146

culture collection no.: DSM 44859, IFO 16408, JCM 10268, NBRC 16408, NCIMB 14344

straininfo link

@ref: 77274
straininfo: 62220

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	11204762	Actinoplanes capillaceus sp. nov., a new species of the genus Actinoplanes.	Matsumoto A, Takahashi Y, Kudo T, Seino A, Iwai Y, Omura S	Antonie Van Leeuwenhoek	10.1023/a:1026530110874	2000	DNA, Ribosomal/analysis, Fatty Acids/analysis, Flagella/ultrastructure, Genotype, Micromonosporaceae/*classification/isolation & purification/physiology, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/analysis, Sequence Analysis, DNA, Soil Microbiology, Spores/ultrastructure	Genetics
Phylogeny	23114571	Actinoplanes hulinensis sp. nov., a novel actinomycete isolated from soybean root (Glycine max (L.) Merr).	Shen Y, Liu C, Wang X, Zhao J, Jia F, Zhang Y, Wang L, Yang D, Xiang W	Antonie Van Leeuwenhoek	10.1007/s10482-012-9809-9	2012	Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Micromonosporaceae/classification/genetics/isolation & purification/physiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soybeans/microbiology	Genetics
Phylogeny	34499595	Actinoplanes flavus sp. nov., a novel cellulase-producing actinobacterium isolated from coconut palm rhizosphere soil.	Luo X, Sun X, Huang Z, He C, Zhao J, Xiang W, Song J, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.004990	2021	Actinoplanes/classification/isolation & purification, Bacterial Typing Techniques, Base Composition, Cellulase, China, Cocos/microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry	Transcriptome

Reference

@id	authors	catalogue	doi/url	title	journal	pubmed
12146	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44859)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-44859
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
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
77274	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID62220.1	StrainInfo: A central database for resolving microbial strain identifiers