Silvimonas iriomotensis (DSM 24036, CGMCC 1.8859, KCTC 22513)

Name: Silvimonas iriomotensis (DSM 24036, CGMCC 1.8859, KCTC 22513)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 10503

Type strain

Strain Designation ir6-1

Culture col. no. DSM 24036 CGMCC 1.8859 KCTC 22513 NBRC 103188 ir6-1

NCBI tax ID(s) 449662

Special Collections DSMZ KCTC Literature strains

History <- NBRC <- Y. Muramatsu; ir6-1

Links

Silvimonas iriomotensis ir6-1 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from soil of bamboo rhizosphere.

Gram-negative motile rod-shaped facultative anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401383

KCTC 22513,NBRC 103188,DSM 24036

@ref 20215

Last LPSN update 2026-02-09 11:20:16

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Neisseriales

Family Chromobacteriaceae

Genus Silvimonas

Species Silvimonas iriomotensis

Full scientific name Silvimonas iriomotensis Muramatsu et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29329	negative	1.25 µm	0.4 µm	rod-shaped
125438	negative				98.494
125439	negative				98.6

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17483	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)		Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
17483	positive	growth	28
29329	positive	growth	05-40
29329	positive	optimum	30

Culture pH

@ref	Ability	Type	PH	PH range
29329	positive	optimum	4
29329	positive	growth	04-09	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29329	facultative anaerobe
125439	obligate aerobe	98.8

Spore formation

@ref	Spore formation	Confidence
125439		97.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29329	NaCl	positive	growth	0-3 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29329	22653 ChEBI	asparagine	+	carbon source
29329	35391 ChEBI	aspartate	+	carbon source
29329	4853 ChEBI	esculin	+	hydrolysis
29329	17632 ChEBI	nitrate	+	reduction
29329	17748 ChEBI	thymidine	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
29329	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
29329	catalase	+	1.11.1.6
29329	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17483	soil of bamboo rhizosphere	Taketomi, Iriomote Island	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB326110 (>99% sequence identity) for Silvimonas iriomotensis from Microbeatlas

Aquatic Samples	1
Soil Samples	11
Animal Samples
Plant Samples	1
Total Samples	13

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17483	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	ASM1464553v1 assembly for Silvimonas iriomotensis CGMCC 1.8859	contig	GCA_014645535	449662.3	2994869973	449662	75.02

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17483	Silvimonas iriomotensis gene for 16S ribosomal RNA, partial sequence	AB326110	1459		449662

GC content

29329

GC-content (mol%)59.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Silvimonas iriomotensis CGMCC 1.8859
NCBI: GCA_014645535

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.50	no
125439	motility	BacteriaNetⓘ	yes	74.60	no
125439	gram_stain	BacteriaNetⓘ	negative	98.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Silvimonas iriomotensis strain CGMCC 1.8859
PATRIC: 449662.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	yes
125438	anaerobic	anaerobicⓘ	no	96.52	no
125438	spore-forming	spore-formingⓘ	no	85.27	no
125438	aerobic	aerobicⓘ	yes	54.92	no
125438	thermophilic	thermophileⓘ	no	98.21	yes
125438	flagellated	motile2+ⓘ	yes	74.10	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amantichitinum ursilacus gen. nov., sp. nov., a chitin-degrading bacterium isolated from soil.	Moss KS, Hartmann SC, Muller I, Fritz C, Krugener S, Zibek S, Hirth T, Rupp S	Int J Syst Evol Microbiol	10.1099/ijs.0.034447-0	2012
Phylogeny	Silvimonas iriomotensis sp. nov. and Silvimonas amylolytica sp. nov., new members of the class Betaproteobacteria isolated from the subtropical zone in Japan.	Muramatsu Y, Suzuki KI, Nakagawa Y	Int J Syst Evol Microbiol	10.1099/ijs.0.011007-0	2009

References

#17483	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24036
#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 )
#25741	IJSEM 174 2010 ( DOI 10.1099/ijs.0.011007-0 , PubMed 19648333 )
#29329	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 #25741
#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) .
#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 )

Rate our new design

Content

About us

Silvimonas iriomotensis (DSM 24036, CGMCC 1.8859, KCTC 22513)

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

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014645535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media