Arthrobacter humicola (DSM 25587, JCM 15921, NBRC 102056)

Name: Arthrobacter humicola (DSM 25587, JCM 15921, NBRC 102056)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 7617

Type strain

Strain Designation KV-653

Culture col. no. DSM 25587 JCM 15921 NBRC 102056 NRRL B-24479 KV-653

NCBI tax ID(s) 409291

Special Collections DSMZ JCM Literature strains

History DSMZ <- NRRL; NRRL B-24479 JCM <-- NRRL B-24479 <-- S. ?mura KV-653.

Links

Arthrobacter humicola KV-653 is an aerobe, Gram-positive, motile bacterium that was isolated from paddy soil.

Gram-positive motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 396638

NBRC 102056,JCM 15921,DSM 25587

@ref 20215

Last LPSN update 2026-05-29 08:26:41

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Micrococcaceae

Genus Arthrobacter

Species Arthrobacter humicola

Full scientific name Arthrobacter humicola Kageyama et al. 2008

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Motility
32047	positive	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18053	TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)		Medium recipe at MediaDive	Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
18053	positive	growth	28
32047	positive	growth	04-34
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
32047	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
32047	aerobe
125439	obligate aerobe	97.831

Spore formation

@ref	Spore formation	Confidence
125439		95.774

Halophily

@ref	Salt	Growth	Tested relation	Concentration
32047	NaCl	positive	growth	<3 %

Observation

67770

Observationquinones: MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
32047	17234 ChEBI	glucose	+	carbon source
32047	29864 ChEBI	mannitol	+	carbon source
32047	28053 ChEBI	melibiose	+	carbon source
32047	16634 ChEBI	raffinose	+	carbon source
32047	26546 ChEBI	rhamnose	+	carbon source
32047	17992 ChEBI	sucrose	+	carbon source
32047	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
32047	acid phosphatase	+	3.1.3.2
32047	alpha-galactosidase	+	3.2.1.22
32047	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Condition	#Anoxic (anaerobic)	-
#Condition	#Humid	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
18053	paddy soil		Japan	JPN	Asia
67770	Paddy soil	Saitama Pref.	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB279890 (>99% sequence identity) for Arthrobacter from Microbeatlas

Aquatic Samples	364
Soil Samples	2849
Animal Samples	580
Plant Samples	2017
Total Samples	5810

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18053	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3953144v1 assembly for Arthrobacter humicola JCM 15921	scaffold	GCA_039531445	409291	57.08

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18053	Arthrobacter humicola gene for 16S rRNA, partial sequence	AB279890	1463		409291

GC content

@ref	GC-content (mol%)	Method
18053	67
67770	67	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3953144v1 assembly for Arthrobacter humicola JCM 15921
NCBI: GCA_039531445

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.83	no
125439	gram_stain	BacteriaNetⓘ	negative	53.55	no
125439	motility	BacteriaNetⓘ	yes	58.38	no
125439	spore_formation	BacteriaNetⓘ	no	95.77	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Micrococcoides hystricis gen. nov., sp. nov., a novel member of the family Micrococcaceae, phylum Actinobacteria.	Toth A, Baka E, Bata-Vidacs I, Luzics S, Kosztik J, Toth E, Keki Z, Schumann P, Tancsics A, Nagy I, Sos E, Kukolya J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002018	2017
Phylogeny	Arthrobacter oryzae sp. nov. and Arthrobacter humicola sp. nov.	Kageyama A, Morisaki K, Omura S, Takahashi Y	Int J Syst Evol Microbiol	10.1099/ijs.0.64875-0	2008

References

#18053	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25587
#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 )
#28297	IJSEM 53 2008 ( DOI 10.1099/ijs.0.64875-0 , PubMed 18175682 )
#32047	Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28297
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Arthrobacter humicola (DSM 25587, JCM 15921, NBRC 102056)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039531445

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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