Archive BacDiveID:10.13145/bacdive24208.20230509.8.1

Strain identifier

BacDive ID: 24208

Type strain:

Species: Actinoplanes lutulentus

Strain Designation: NEAU-GRX6

Strain history: CGMCC 4.7090 <-- R. Gao et al.; Northeast Agric. Univ., China; NEAU-GRX6.

NCBI tax ID(s): 1287878 (species)

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

General

@ref: 20247

BacDive-ID: 24208

DSM-Number: 45883

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

description: Actinoplanes lutulentus NEAU-GRX6 is a spore-forming, mesophilic, Gram-positive bacterium that was isolated from mucky soil.

NCBI tax id

NCBI tax id: 1287878
Matching level: species

strain history

@ref	history
20247	<- C. Liu, Northeast Agricultural Univ., Harbin, China; NEAU-GRX6 <- R. Gao, Northeast Agricultural Univ., Harbin, China
67770	CGMCC 4.7090 <-- R. Gao et al.; Northeast Agric. Univ., China; NEAU-GRX6.

doi: 10.13145/bacdive24208.20230509.8.1

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 lutulentus
full scientific name: Actinoplanes lutulentus Gao et al. 2014

@ref: 20247

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micromonosporaceae

genus: Actinoplanes

species: Actinoplanes lutulentus

full scientific name: Actinoplanes lutulentus Gao et al. 2014

strain designation: NEAU-GRX6

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: positive
confidence: 100

multimedia

@ref: 20247
multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45883.jpg
caption: Medium 554 28°C
intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
20247	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
20247	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	yes	https://mediadive.dsmz.de/medium/535	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20247	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
20247	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
20247	positive	growth	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

spore formation

@ref	spore formation	confidence
69481	yes	98
69480	yes	100

observation

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

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent	latitude	longitude
20247	mucky soil	Heilongjiang Province, Harbin, Jinlong Mountain (45° 30' N 127° 06' E)	China	CHN	Asia	45.5	127.1
67770	Mucky soil from a stream of Jinlong Mountain	Harbin, Heilongjiang Province, north China	China	CHN	Asia

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_53360.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_94;96_240;97_1422;98_8994;99_53360&stattab=map
Last taxonomy: Actinoplanes lutulentus
16S sequence: KC134255
Sequence Identity:
Total samples: 122
soil counts: 77
aquatic counts: 9
animal counts: 32
plant counts: 4

Safety information

risk assessment

@ref: 20247
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 20247
description: Actinoplanes lutulentus strain NEAU-GRX6 from China 16S ribosomal RNA gene, partial sequence
accession: KC134255
length: 1508
database: ena
NCBI tax ID: 1287878

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Actinoplanes lutulentus DSM 45883	GCA_014191235	contig	ncbi	1287878
66792	Actinoplanes lutulentus strain CGMCC 4.7090	1287878.3	wgs	patric	1287878
66792	Actinoplanes lutulentus strain DSM 45883	1287878.5	wgs	patric	1287878
66792	Actinoplanes lutulentus DSM 45883	2824186164	draft	img	1287878
66792	Actinoplanes lutulentus CGMCC 4.7090	2718217682	draft	img	1287878
67770	Actinoplanes lutulentus CGMCC 4.7090	GCA_003259845	scaffold	ncbi	1287878

GC content

@ref: 20247
GC-content: 67
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	yes	98	no
motile	yes	68.594	no
gram-positive	yes	89.607	no
anaerobic	no	98.774	no
aerobic	yes	92.271	no
halophile	no	96.256	no
spore-forming	yes	90.902	no
glucose-util	yes	90.871	no
flagellated	no	87.411	no
thermophile	no	99.469	yes
glucose-ferment	no	88.953	no

External links

@ref: 20247

culture collection no.: DSM 45883, CGMCC 4.7090, JCM 30776

straininfo link

@ref: 88154
straininfo: 398769

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	24566827	Actinoplanes lutulentus sp. nov., isolated from mucky soil in China.	Gao R, Liu C, Zhao J, Jia F, Li C, Xing J, Wang X, Xiang W	Int J Syst Evol Microbiol	10.1099/ijs.0.057802-0	2014	Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Micromonosporaceae/classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistry	Genetics
Phylogeny	34324105	Actinoplanes aureus sp. nov., a novel protease-producing actinobacterium isolated from soil.	Song J, Sun X, Luo X, He C, Huang Z, Zhao J, He B, Du X, Wang X, Xiang W	Antonie Van Leeuwenhoek	10.1007/s10482-021-01617-4	2021	Actinoplanes/classification/isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptide Hydrolases/metabolism, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives	Transcriptome

Reference

@id	authors	title	doi/url	catalogue
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ	10.1099/ijsem.0.004332
20247	Curators of the DSMZ		https://www.dsmz.de/collection/catalogue/details/culture/DSM-45883	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45883)
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)	https://diaspora-project.de/progress.html#genomes
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.	MicrobeAtlas 1.0 beta	https://microbeatlas.org/
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)	https://diaspora-project.de/progress.html#genomes
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch	Predictions based on the model GenomeNet Sporulation v. 1	10.21203/rs.3.rs-2527258/v1
88154	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.	StrainInfo: A central database for resolving microbial strain identifiers	10.60712/SI-ID398769.1