Name: Armatimonas rosea YO-36
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17836

Type strain:

Species: Armatimonas rosea

Strain Designation: YO-36

Culture col. no.: DSM 23562, NBRC 105658

Strain history: <- H. Tamaki, Natl. Inst. Advanced Industrial Sci. and Technol., Tsukuba, Japan; YO-36 <- Y. Tanaka, University of Yamanashi, Kofu, Japan

NCBI tax ID(s): 685828 (species)

SI-ID 407100

DSM 23562

Section

Armatimonas rosea YO-36 is a mesophilic, Gram-negative bacterium that was isolated from rhizoplane of reed Phragmites australis inhabiting a mesophilic freshwater lake.

Gram-negative
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Armatimonadota*
	Class	*Armatimonadia*
	Order	*Armatimonadales*
	Family	*Armatimonadaceae*
	Genus	*Armatimonas*
	Species	**Armatimonas rosea**
	Full Scientific Name (LPSN)	Armatimonas rosea Tamaki et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.933

[Ref.: #17284]

Incubation period

3-7 days

[Ref.: #69306]	Pigment production	no
[Ref.: #69306]	Pigment name	Melanin
[Ref.: #69306]	Pigment production	no
[Ref.: #69306]	Pigment name	soluble pigment

Information on culture and growth conditions Culture and growth conditions

[Ref.: #17284]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #17284]

Culture medium growth

[Ref.: #17284]

Culture medium link

Medium recipe at MediaDive

[Ref.: #17284]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #17284]			growth	30 °C

[Ref.: #17284]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.932

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	esculin ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	nitrate ChEBI	-	reduction	* from API Coryne
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne, API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne, API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68379]	beta-galactosidase	+	3.2.1.23	* from API Coryne
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68379]	beta-glucosidase	-	3.2.1.21	* from API Coryne, API zym
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #68379]	gelatinase	+		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API Coryne, API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
	Only first 10 entries are displayed. Click here to see all.

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #69306]	3799	-	-	-	+	-	+	-	-	-	-	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #69306]	5983	not determinedn.d.	+	+/-	+/-	+/-	+	+/-	+/-	-	-	+/-	-	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #17284]	Sample type/isolated from	rhizoplane of reed Phragmites australis inhabiting a mesophilic freshwater lake
[Ref.: #17284]	Host species	Phragmites australis
[Ref.: #17284]	Geographic location (country and/or sea, region)	Yamanashi Prefecture
[Ref.: #17284]	Country	Japan
[Ref.: #17284]	Country ISO 3 Code	JPN
[Ref.: #17284]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizoplane

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB529679 (>99% sequence identity) for Armatimonas rosea subclade from Microbeatlas

Aquatic Samples	11
Soil Samples
Animal Samples	3
Plant Samples
Total Samples	14

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #17284]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #17284]	Armatimonas rosea gene for 16S ribosomal RNA, partial sequence	AB529679	1438	ENA	685828 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Armatimonas rosea DSM 23562	GCA_014202505	scaffold	GenBank	685828 tax ID	*
[Ref.: #66792]	Armatimonas rosea strain DSM 23562	685828.3	wgs	PATRIC	685828 tax ID	*
[Ref.: #66792]	Armatimonas rosea DSM 23562	2861551589	draft	JGI IMG/M	685828 tax ID	*

[Ref.: #17284]

GC-content

62.4 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Armatimonas rosea DSM 23562 NCBI: GCA_014202505.1
[Ref.: #69481]	spore-forming	no	86	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Armatimonas rosea DSM 23562 NCBI: GCA_014202505.1
[Ref.: #69480]	flagellated	no	98.009	no
[Ref.: #69480]	gram-positive	no	86.219	no
[Ref.: #69480]	anaerobic	no	98.281	no
[Ref.: #69480]	aerobic	yes	88.164	no
[Ref.: #69480]	halophile	no	94.079	no
[Ref.: #69480]	spore-forming	no	89.597	no
[Ref.: #69480]	glucose-util	yes	78.818	no
[Ref.: #69480]	thermophile	no	93.74	yes
[Ref.: #69480]	motile	no	92.439	no
[Ref.: #69480]	glucose-ferment	no	86.43	no

Availability in culture collections External links

[Ref.: #17284]

Culture collection no.

DSM 23562, NBRC 105658

[Ref.: #86827]

SI-ID 407100

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Capsulimonas corticalis gen. nov., sp. nov., an aerobic capsulated bacterium, of a novel bacterial order, Capsulimonadales ord. nov., of the class Armatimonadia of the phylum Armatimonadetes.	Li J, Kudo C, Tonouchi A	Int J Syst Evol Microbiol	10.1099/ijsem.0.003135	2018	*
Phylogeny	Armatimonas rosea gen. nov., sp. nov., of a novel bacterial phylum, Armatimonadetes phyl. nov., formally called the candidate phylum OP10.	Tamaki H, Tanaka Y, Matsuzawa H, Muramatsu M, Meng XY, Hanada S, Mori K, Kamagata Y	Int J Syst Evol Microbiol	10.1099/ijs.0.025643-0	2010	*

References

#17284

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23562

#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. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#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) .

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#69306

Wink, J.: Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig .

#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 .

#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) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86827

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 . ( DOI 10.60712/SI-ID407100.1 )

* These data were automatically processed and therefore are not curated

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Armatimonas rosea DSM 23562

Armatimonas rosea DSM 23562

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