Armatimonas rosea (DSM 23562, NBRC 105658, YO-36)

Name: Armatimonas rosea (DSM 23562, NBRC 105658, YO-36)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17836

Type strain

Strain Designation YO-36

Culture col. no. DSM 23562 NBRC 105658 YO-36

NCBI tax ID(s) 685828

Special Collections DSMZ Wink compendium

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

Links

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

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407100

NBRC 105658,DSM 23562

@ref 20215

Last LPSN update 2026-05-29 08:29:06

Domain Bacteria

Phylum Armatimonadota

Class Armatimonadia

Order Armatimonadales

Family Armatimonadaceae

Genus Armatimonas

Species Armatimonas rosea

Full scientific name Armatimonas rosea Tamaki et al. 2011

Morphology

Colony morphology

17284

Incubation period3-7 days

Pigmentation

@ref	Production	Name
69306		melanin pigment
69306		soluble pigment

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17284	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
17284	positive	growth	30

Physiology and metabolism

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
68379	4853 ChEBI	esculin	-	hydrolysis	from API Coryne
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
68379	17632 ChEBI	nitrate	-	reduction	from API Coryne
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne

Enzymes

@ref	Value	Activity	Ec
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68379	beta-galactosidase	+	3.2.1.23	from API Coryne
68382	beta-glucosidase	-	3.2.1.21	from API zym
68379	beta-glucosidase	-	3.2.1.21	from API Coryne
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne

API coryne

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
69306	-	-	-	+	-	+	-	-	-	-	+	not determinedn.d.	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
69306	not determinedn.d.	+	+/-	+/-	+/-	+	+/-	+/-	-	-	+/-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Freshwater
#Environmental	#Aquatic	#Lake (large)
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizoplane

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
17284	rhizoplane of reed Phragmites australis inhabiting a mesophilic freshwater lake	Phragmites australis	Yamanashi Prefecture	Japan	JPN	Asia

Taxonmaps

69479

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

Aquatic Samples	11
Soil Samples	0
Animal Samples	3
Plant Samples	0
Total Samples	14

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17284	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1420250v1 assembly for Armatimonas rosea DSM 23562	scaffold	GCA_014202505	685828.4	2861551589	685828	73.81
66792	Armatimonas rosea strain DSM 23562	contig		685828.3		685828	72.03

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17284	Armatimonas rosea gene for 16S ribosomal RNA, partial sequence	AB529679	1438		685828

GC content

17284

GC-content (mol%)62.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1420250v1 assembly for Armatimonas rosea DSM 23562
NCBI: GCA_014202505

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	68.29	no
125439	gram_stain	BacteriaNetⓘ	negative	71.57	no
125439	spore_formation	BacteriaNetⓘ	no	89.14	no
125439	motility	BacteriaNetⓘ	yes	51.25	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Armatimonas rosea DSM 23562
NCBI: GCA_014202505.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	79.00	no
125438	anaerobic	anaerobicⓘ	no	85.00	no
125438	aerobic	aerobicⓘ	yes	76.91	no
125438	spore-forming	spore-formingⓘ	no	68.85	no
125438	thermophilic	thermophileⓘ	no	90.24	yes
125438	flagellated	motile2+ⓘ	no	78.76	no

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 .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Armatimonas rosea (DSM 23562, NBRC 105658, YO-36)

Name and taxonomic classification

Morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Metabolite utilization

Enzymes

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014202505

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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