Sandarakinorhabdus fusca (DSM 105347, CGMCC 1.12714, JCM 19740)

Name: Sandarakinorhabdus fusca (DSM 105347, CGMCC 1.12714, JCM 19740)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 132959

Type strain

Strain Designation D40P

Culture col. no. DSM 105347 CGMCC 1.12714 JCM 19740 D40P

NCBI tax ID(s) 1439888

Special Collections DSMZ JCM

Links

Sandarakinorhabdus fusca D40P is a mesophilic prokaryote that was isolated from permafrost soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404984

JCM 19740,DSM 105347

@ref 20215

Last LPSN update 2025-12-16 10:01:39

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingosinicellaceae

Genus Sandarakinorhabdus

Species Sandarakinorhabdus fusca

Full scientific name Sandarakinorhabdus fusca (Jia et al. 2015) Wang et al. 2025

Synonyms (1)

Polymorphobacter fuscus

Morphology

Cell morphology

@ref	Gram stain	Confidence
125439	negative	98.3
125438	negative	95.795

Multimedia

@ref:	24747
multimedia content:	DSM_105347.jpg
multimedia.multimedia content:	https://www.dsmz.de/microorganisms/photos/DSM_105347.jpg
intellectual property rights:	© Leibniz-Institut DSMZ
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
24747	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
24747	positive	growth	28	mesophilic
67770	positive	growth	25	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.1

Spore formation

@ref	Spore formation	Confidence
125439		97.4

Observation

67770

Observationquinones: Q-10, Q-9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Permafrost
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
24747	permafrost soil	Kunlun Pass Basin, Qinghai-Tibet Plateau	China	CHN	Asia	35.6667	94.05 35.6667/94.05
67770	Permafrost soil of Kunlun Mountains Gap	Qinghai-Tibet Plateau	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence KF737330 (>99% sequence identity) for Polymorphobacter from Microbeatlas

Aquatic Samples	12147
Soil Samples	2630
Animal Samples	1756
Plant Samples	315
Total Samples	16848

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
24747	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM1192782v1 assembly for Sandarakinorhabdus fusca DSM 105347	contig	GCA_011927825	1439888.6	2830037985	1439888	79.02
66792	ASM937207v1 assembly for Sandarakinorhabdus fusca D40P	scaffold	GCA_009372075	1439888.3	8048213643	1439888	76.04
66792	ASM960767v1 assembly for Sandarakinorhabdus fusca D40P	scaffold	GCA_009607675	1439888.4	8118739537	1439888	76.04

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
24747	Polymorphobacter fuscus strain D40P 16S ribosomal RNA gene, partial sequence	KF737330	1452		1439888

GC content

@ref	GC-content (mol%)	Method
67770	67.4	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Polymorphobacter fuscus D40P
NCBI: GCA_009372075

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.40	no
125439	motility	BacteriaNetⓘ	yes	74.00	no
125439	gram_stain	BacteriaNetⓘ	negative	98.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Polymorphobacter fuscus D40P
NCBI: GCA_009372075.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	95.80	no
125438	anaerobic	anaerobicⓘ	no	94.56	no
125438	aerobic	aerobicⓘ	yes	85.39	no
125438	spore-forming	spore-formingⓘ	no	89.95	no
125438	thermophilic	thermophileⓘ	no	95.48	yes
125438	flagellated	motile2+ⓘ	yes	61.07	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Polymorphobacter fuscus sp. nov., isolated from permafrost soil, and emended description of the genus Polymorphobacter.	Jia L, Feng X, Zheng Z, Han L, Hou X, Lu Z, Lv J	Int J Syst Evol Microbiol	10.1099/ijsem.0.000514	2015

References

#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 )
#24747	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105347
#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 .
#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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Sandarakinorhabdus fusca (DSM 105347, CGMCC 1.12714, JCM 19740)

Name and taxonomic classification

Morphology

Cell morphology

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_011927825

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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