Archive BacDiveID:10.13145/bacdive16478.20230509.8.1

Strain identifier

BacDive ID: 16478

Type strain:

Species: Yinghuangia aomiensis

Strain Designation: M24DS4

Strain history: KACC 14925 <-- NBRC 106164 <-- M. Takagi M24DS4.

NCBI tax ID(s): 676205 (species)

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

General

@ref: 18020

BacDive-ID: 16478

DSM-Number: 42049

keywords: 16S sequence, Bacteria, mesophilic

description: Yinghuangia aomiensis M24DS4 is a mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax id: 676205
Matching level: species

strain history

@ref	history
18020	<- NBRC; NBRC 106164 <- M. Takagi; M24DS4
67770	KACC 14925 <-- NBRC 106164 <-- M. Takagi M24DS4.

doi: 10.13145/bacdive16478.20230509.8.1

Name and taxonomic classification

LPSN

@ref: 20215
description: domain/bacteria
keyword: phylum/actinomycetota
domain: Bacteria
phylum: Actinomycetota
class: Actinomycetes
order: Kitasatosporales
family: Streptomycetaceae
genus: Yinghuangia
species: Yinghuangia aomiensis
full scientific name: Yinghuangia aomiensis (Nagai et al. 2011) Nouioui et al. 2018
synonyms
- @ref: 20215
- synonym: Streptomyces aomiensis

@ref: 18020

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Yinghuangia

species: Yinghuangia aomiensis

full scientific name: Yinghuangia aomiensis (Nagai et al. 2011) Nouioui et al. 2018

strain designation: M24DS4

type strain: yes

Morphology

colony morphology

@ref	colony color	incubation period	medium used
18735	Brown beige (1011)	10-14 days	ISP 2
18735	Beige (1001)	10-14 days	ISP 3
18735	Ivory (1014)	10-14 days	ISP 4
18735	Ivory (1014)	10-14 days	ISP 5
18735	Ivory (1014)	10-14 days	ISP 6
18735	Ivory (1014)	10-14 days	ISP 7

multicellular morphology

@ref	forms multicellular complex	complex name	complex color	medium name
18735	yes	Aerial Mycelium	Silver grey (7001)	ISP 2
18735	yes	Aerial Mycelium	Cream (9001)	ISP 3
18735	yes	Aerial Mycelium	Cream (9001)	ISP 4
18735	yes	Aerial Mycelium	Cream (9001)	ISP 5
18735	yes	Aerial Mycelium	Cream (9001)	ISP 6
18735	no			ISP 7

Culture and growth conditions

culture medium

@ref	name	growth	link	composition
18020	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
18735	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
18735	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:
18735	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
18735	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
18735	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
18735	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
18020	positive	growth	28	mesophilic
18735	positive	optimum	28	mesophilic
67770	positive	growth	28	mesophilic

Physiology and metabolism

observation

@ref: 67770
observation: quinones: MK-9(H₈), MK-9(H₆)

enzymes

@ref	value	activity	ec
68382	alkaline phosphatase	+	3.1.3.1
68382	esterase (C 4)	-
68382	esterase lipase (C 8)	+
68382	lipase (C 14)	-
68382	leucine arylamidase	+	3.4.11.1
68382	valine arylamidase	+
68382	cystine arylamidase	-	3.4.11.3
68382	trypsin	-	3.4.21.4
68382	alpha-chymotrypsin	-	3.4.21.1
68382	acid phosphatase	+	3.1.3.2
68382	naphthol-AS-BI-phosphohydrolase	+
68382	alpha-galactosidase	-	3.2.1.22
68382	beta-galactosidase	+	3.2.1.23
68382	beta-glucuronidase	-	3.2.1.31
68382	alpha-glucosidase	-	3.2.1.20
68382	beta-glucosidase	+	3.2.1.21
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52
68382	alpha-mannosidase	-	3.2.1.24
68382	alpha-fucosidase	-	3.2.1.51

API zym

@ref	Alkaline phosphatase	Esterase	Esterase Lipase	Lipase	Leucine arylamidase	Valine arylamidase	Cystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
18735	+	-	+	-	+	+	-	-	-	+	+	-	+	-	-	+	+	-	-

Isolation, sampling and environmental information

isolation

@ref	sample type	geographic location	country	origin.country	continent
18020	soil	Tokyo, Aomi	Japan	JPN	Asia
67770	Soil	Aomi, Tokyo	Japan	JPN	Asia

isolation source categories

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

taxonmaps

@ref: 69479
File name: preview.99_17406.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_8272;97_9959;98_12244;99_17406&stattab=map
Last taxonomy: Yinghuangia aomiensis
16S sequence: AB522686
Sequence Identity:
Total samples: 1919
soil counts: 1328
aquatic counts: 197
animal counts: 62
plant counts: 332

Safety information

risk assessment

@ref: 18020
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 18020
description: Streptomyces aomiensis gene for 16S rRNA, partial sequence
accession: AB522686
length: 1486
database: ena
NCBI tax ID: 676205

GC content

@ref	GC-content	method
18020	75
67770	75	high performance liquid chromatography (HPLC)

External links

@ref: 18020

culture collection no.: DSM 42049, KACC 14925, NBRC 106164, JCM 17986

straininfo link

@ref: 85513
straininfo: 400109

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	20495021	Streptomyces aomiensis sp. nov., isolated from a soil sample using the membrane-filter method.	Nagai A, Khan ST, Tamura T, Takagi M, Shin-Ya K	Int J Syst Evol Microbiol	10.1099/ijs.0.020719-0	2010	Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Filtration/methods, Molecular Sequence Data, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Streptomyces/classification/genetics/*isolation & purification, Tokyo	Genetics
Phylogeny	24699065	Streptomyces catbensis sp. nov., isolated from soil.	Sakiyama Y, Giang NM, Miyadoh S, Luong DT, Van Hop D, Ando K	Int J Syst Evol Microbiol	10.1099/ijs.0.048264-0	2014	Bacterial Typing Techniques, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vietnam, Vitamin K 2/analogs & derivatives/chemistry	Genetics

Reference

@id	authors	catalogue	doi/url	title
18020	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 42049)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-42049
18735	Wink, J.		http://www.dsmz.de/microorganisms/wink_pdf/DSM42049.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
67770	Curators of the JCM		https://jcm.brc.riken.jp/en/
68382				Automatically annotated from API zym
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
85513	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID400109.1	StrainInfo: A central database for resolving microbial strain identifiers

General

NCBI tax id

strain history

Name and taxonomic classification

LPSN

synonyms

Morphology

colony morphology

multicellular morphology

Culture and growth conditions

culture medium

culture temp

Physiology and metabolism

observation

enzymes

API zym

Isolation, sampling and environmental information

isolation

isolation source categories

taxonmaps

Safety information

risk assessment

Sequence information

16S sequences

GC content

External links

straininfo link

literature

Reference