Cite this strain

Halorubrum aidingense (DSM 23496, CGMCC 1.2670, JCM 13560)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5952

Type strain

Strain Designation 31-hong

Culture col. no. DSM 23496 CGMCC 1.2670 JCM 13560 31-hong KCTC 4073

NCBI tax ID(s) 1230454 368623

Special Collections DSMZ JCM KCTC Literature strains

Links

Name and taxonomic classification

Halorubrum aidingense 31-hong is an aerobe, mesophilic, Gram-negative archaeon that was isolated from salt lake.

Gram-negative motile rod-shaped aerobe mesophilic genome sequence 16S sequence Archaea

SI-ID 297205

CGMCC 1.2670, JCM 13560, DSM 23496

Last LPSN update 2024-12-09 10:43:47

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloferacaceae

Genus Halorubrum

Species Halorubrum aidingense

Full scientific name Halorubrum aidingense Cui et al. 2006

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
31797	negative	3.6-6.4 µm	0.9-1 µm	rod-shaped
125439	negative

Pigmentation

31797

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17239	HALOBACTERIA MEDIUM (DSMZ Medium 372)		Medium recipe at MediaDive	Name: HALOBACTERIA MEDIUM (DSMZ Medium 372) Composition: NaCl 200.0 g/l MgSO4 x 7 H2O 20.0 g/l Agar 20.0 g/l Yeast extract 5.0 g/l Casamino acids 5.0 g/l Na3-citrate 3.0 g/l KCl 2.0 g/l Na glutamate 1.0 g/l FeCl2 x 4 H2O 0.036 g/l MnCl2 x 4 H2O 0.00036 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
17239	positive	growth	37	mesophilic
31797	positive	growth	25-52
31797	positive	optimum	40-42	thermophilic
67770	positive	growth	37	mesophilic

Culture pH

@ref	Ability	Type	PH
31797	positive	optimum	7.5
31797	positive	growth	07-09

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31797	NaCl	positive	growth	9.86-24.94 %
31797	NaCl	positive	optimum	15.08 %

Observation

31797

Observationaggregates in chains

Spore formation

@ref	Spore formation
31797
125439

Enzymes

@ref	Value	Activity	Ec
31797	catalase	+	1.11.1.6
31797	cytochrome oxidase	+	1.9.3.1

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31797	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
31797	35581 ChEBI	indole	+

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31797	28757 ChEBI	fructose	+	carbon source
31797	28260 ChEBI	galactose	+	carbon source
31797	17234 ChEBI	glucose	+	carbon source
31797	17306 ChEBI	maltose	+	carbon source
31797	29864 ChEBI	mannitol	+	carbon source
31797	37684 ChEBI	mannose	+	carbon source
31797	17632 ChEBI	nitrate	+	reduction
31797	17992 ChEBI	sucrose	+	carbon source

Oxygen tolerance

31797

Oxygen toleranceaerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Lake (large)
#Condition	#Saline	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17239	salt lake	Xin-Jiang, Aiding Lake	China	CHN	Asia
67770	Aiding salt lake in Xin-Jiang		China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB663402 (>99% sequence identity) for Halorubrum aidingense from Microbeatlas

Aquatic Samples	12
Soil Samples
Animal Samples
Plant Samples
Total Samples	12

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
17239	1	Risk group (German classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)	Method
17239	64.2	thermal denaturation, midpoint method (Tm)
31797	64.2

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Halorubrum aidingense gene for 16S ribosomal RNA, partial sequence, strain: JCM 13560	AB477976	1430	1230454
20218	Halorubrum aidingense gene for 16S rRNA, complete sequence, strain: JCM 13560	AB663402	1470	1230454
17239	Halorubrum aidingense strain 31-hong 16S ribosomal RNA gene, complete sequence	DQ355813	1470	1230454

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Halorubrum aidingense JCM 13560	2554235475	draft	JGI IMG/M	1230454
67770	Halorubrum aidingense JCM 13560	GCA_000336995	contig		1230454
66792	Halorubrum aidingense JCM 13560	1230454.4	wgs	PATRIC	1230454

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Halorubrum aidingense JCM 13560
NCBI: GCA_000336995

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.20	no
125439	motility	BacteriaNetⓘ	yes	64.60	no
125439	gram_stain	BacteriaNetⓘ	negative	92.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	89.40	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halorubrum salsamenti sp. nov., a Novel Halophilic Archaeon Isolated from a Brine of Salt Mine.	Chen S, He J, Zhang J, Xu Y, Huang J, Ke LX	Curr Microbiol	10.1007/s00284-017-1325-8	2017
Phylogeny	Haloparvum sedimenti gen. nov., sp. nov., a member of the family Haloferacaceae.	Chen S, Liu HC, Zhou J, Xiang H	Int J Syst Evol Microbiol	10.1099/ijsem.0.001033	2016
Phylogeny	Halorubrum yunnanense sp. nov., isolated from a subterranean salt mine.	Chen S, Liu HC, Zhao D, Yang J, Zhou J, Xiang H	Int J Syst Evol Microbiol	10.1099/ijsem.0.000605	2015
Phylogeny	Halorubrum kocurii sp. nov., an archaeon isolated from a saline lake.	Gutierrez MC, Castillo AM, Pagaling E, Heaphy S, Kamekura M, Xue Y, Ma Y, Cowan DA, Jones BE, Grant WD, Ventosa A	Int J Syst Evol Microbiol	10.1099/ijs.0.65840-0	2008
Phylogeny	Halorubrum lipolyticum sp. nov. and Halorubrum aidingense sp. nov., isolated from two salt lakes in Xin-Jiang, China.	Cui HL, Tohty D, Zhou PJ, Liu SJ	Int J Syst Evol Microbiol	10.1099/ijs.0.64305-0	2006

Straininfo Link

@ref	Straininfo	Culture collections
75441	297205	CGMCC 1.2670, JCM 13560, DSM 23496

Culture collection no.

Culture collection no.
DSM 23496
CGMCC 1.2670
JCM 13560
31-hong
KCTC 4073

References

#17239	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23496
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#31797	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 #28068 (see below)
#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 .
#75441	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID297205.1 )
#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 .

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Halorubrum aidingense (DSM 23496, CGMCC 1.2670, JCM 13560)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Halophily

Observation

Spore formation

Enzymes

Metabolite production

Metabolite tests

Metabolite utilization

Oxygen tolerance

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Safety information

Risk assessment

Sequence information

GC content

16S sequences

Genome sequences

Genome-based predictions

Predictions

External links

Literature

Straininfo Link

Culture collection no.

References

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