Cellulomonas oligotrophica (DSM 24482, JCM 17534, Kc5)

Name: Cellulomonas oligotrophica (DSM 24482, JCM 17534, Kc5)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2376

Type strain

Strain Designation Kc5

Culture col. no. DSM 24482 JCM 17534 Kc5 NBRC 109435

NCBI tax ID(s) 931536

Special Collections DSMZ JCM Literature strains

History <- K. Hatayama, Sagami Chemical Research Institute, Kanagawa, Japan; Kc5 <- K. Esaki K. Hatayama Kc5.

Links

Cellulomonas oligotrophica Kc5 is an aerobe, Gram-positive, motile bacterium that was isolated from soil at an urban area.

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

Name and taxonomic classification

SI-ID 399478

JCM 17534,NBRC:109435,DSM 24482

@ref 20215

Last LPSN update 2026-02-09 11:18:16

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Micrococcales

Family Cellulomonadaceae

Genus Cellulomonas

Species Cellulomonas oligotrophica

Full scientific name Cellulomonas oligotrophica Hatayama et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
30542	positive	6 µm	2 µm	rod-shaped
125438	positive					90.349

Pigmentation

30542

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17686	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)
17686	positive	growth	28
30542	positive	growth	25
30542	positive	optimum	15-37
67770	positive	growth	25

Culture pH

@ref	Ability	Type	PH	PH range
30542	positive	optimum	9
30542	positive	growth	06-11	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
30542	aerobe
125439	obligate anaerobe	99.1

Spore formation

30542

Spore formationno

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30542	NaCl	positive	growth	0-6 %
30542	NaCl	positive	optimum	3 %

Observation

67770

Observationquinones: MK-9(H₄), MK-9(H₂)

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30542	30089 ChEBI	acetate	+	carbon source
30542	22599 ChEBI	arabinose	+	carbon source
30542	17057 ChEBI	cellobiose	+	carbon source
30542	28757 ChEBI	fructose	+	carbon source
30542	28260 ChEBI	galactose	+	carbon source
30542	17234 ChEBI	glucose	+	carbon source
30542	17754 ChEBI	glycerol	+	carbon source
30542	28087 ChEBI	glycogen	+	carbon source
30542	17306 ChEBI	maltose	+	carbon source
30542	29864 ChEBI	mannitol	+	carbon source
30542	37684 ChEBI	mannose	+	carbon source
30542	28053 ChEBI	melibiose	+	carbon source
30542	17632 ChEBI	nitrate	+	reduction
30542	17814 ChEBI	salicin	+	carbon source
30542	30911 ChEBI	sorbitol	+	carbon source
30542	17992 ChEBI	sucrose	+	carbon source
30542	27082 ChEBI	trehalose	+	carbon source
30542	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30542	catalase	+	1.11.1.6
30542	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17686	soil at an urban area	Kanagawa, Kawasaki	Japan	JPN	Asia
67770	Moist soil from an urban area	Kawasaki, Kanagawa Pref.	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB602499 (>99% sequence identity) for Cellulomonas oligotrophica from Microbeatlas

Aquatic Samples	14
Soil Samples	15
Animal Samples	4
Plant Samples
Total Samples	33

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17686	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
67770	ASM1340987v1 assembly for Cellulomonas oligotrophica DSM 24482	contig	GCA_013409875	931536.4	2844845222	931536	78.39
66792	ASM1686273v1 assembly for Cellulomonas oligotrophica NBRC 109435	contig	GCA_016862735	931536.5	8110511158	931536	72.97
124043	ASM3954083v1 assembly for Cellulomonas oligotrophica JCM 17534	contig	GCA_039540835			931536	66.71
67770	ASM638648v1 assembly for Cellulomonas oligotrophica JCM 17534	scaffold	GCA_006386485	931536.3	8118129834	931536	16.43

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17686	Cellulomonas oligotrophica gene for 16S ribosomal RNA, partial sequence	AB602499	1443		931536

GC content

@ref	GC-content (mol%)	Method
17686	75.8	high performance liquid chromatography (HPLC)
30542	75.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Cellulomonas oligotrophica JCM 17534
NCBI: GCA_006386485

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	76.80	no
125439	motility	BacteriaNetⓘ	yes	64.10	no
125439	gram_stain	BacteriaNetⓘ	negative	85.40	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Cellulomonas oligotrophica strain DSM 24482
PATRIC: 931536.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	90.35	no
125438	anaerobic	anaerobicⓘ	no	96.31	yes
125438	aerobic	aerobicⓘ	yes	73.60	yes
125438	spore-forming	spore-formingⓘ	no	58.98	yes
125438	thermophilic	thermophileⓘ	no	94.70	no
125438	flagellated	motile2+ⓘ	no	67.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Cellulomonas shaoxiangyii sp. nov., isolated from faeces of Tibetan antelope (Pantholops hodgsonii) on the Qinghai-Tibet Plateau.	Tian Z, Lu S, Jin D, Yang J, Pu J, Lai XH, Ren ZH, Wu XM, Li J, Wang S, Xu J	Int J Syst Evol Microbiol	10.1099/ijsem.0.003939	2020
Phylogeny	Cellulomonas telluris sp. nov., an endoglucanase-producing actinobacterium isolated from Badain Jaran desert sand.	Shi YL, Sun Y, Ruan ZY, Su J, Yu LY, Zhang YQ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003806	2020
Phylogeny	Cellulomonas soli sp. nov. and Cellulomonas oligotrophica sp. nov., isolated from soil.	Hatayama K, Esaki K, Ide T	Int J Syst Evol Microbiol	10.1099/ijs.0.038364-0	2012

References

#17686	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24482
#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 )
#26873	IJSEM 60 2013 ( DOI 10.1099/ijs.0.038364-0 , PubMed 22328604 )
#30542	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 #26873
#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) .
#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 .
#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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Cellulomonas oligotrophica (DSM 24482, JCM 17534, Kc5)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

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_013409875

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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