Cite this strain

Halosimplex rubrum (CGMCC 1.10591, JCM 17268, R27)

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

BacDive ID 134076

Type strain

Strain Designation R27

Culture col. no. CGMCC 1.10591 JCM 17268 R27

NCBI tax ID(s) 869889

Special Collections JCM Literature strains

Links

Name and taxonomic classification

Halosimplex rubrum R27 is an aerobe, Gram-negative, motile archaeon that was isolated from salted brown alga.

Gram-negative motile aerobe genome sequence 16S sequence Archaea

Culture Collection Numbers

CGMCC 1.10591 JCM 17268 R27

Last LPSN update 2024-12-09 10:49:20

Domain Archaea

Phylum Methanobacteriota

Class Halobacteria

Order Halobacteriales

Family Haloarculaceae

Genus Halosimplex

Species Halosimplex rubrum

Full scientific name Halosimplex rubrum Han and Cui 2014

Morphology

Cell morphology

@ref	Gram stain	Motility
31179	negative

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
31179	positive	growth	25-45
31179	positive	optimum	42
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
31179	positive	optimum	7
31179	positive	growth	5.5-9.5

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31179	NaCl	positive	growth	0.9-3.4 %
31179	NaCl	positive	optimum	3.1 %

Spore formation

@ref	Spore formation	Confidence
125439		93.3

Metabolite production

@ref	Chebi-ID	Metabolite	Production
31179	16136 ChEBI	hydrogen sulfide

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31179	35391 ChEBI	aspartate	+	carbon source
31179	28260 ChEBI	galactose	+	carbon source
31179	17234 ChEBI	glucose	+	carbon source
31179	29987 ChEBI	glutamate	+	carbon source
31179	24996 ChEBI	lactate	+	carbon source
31179	29864 ChEBI	mannitol	+	carbon source
31179	37684 ChEBI	mannose	+	carbon source
31179	18257 ChEBI	ornithine	+	carbon source
31179	30911 ChEBI	sorbitol	+	carbon source
31179	17992 ChEBI	sucrose	+	carbon source

Oxygen tolerance

31179

Oxygen toleranceaerobe

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Algae	#Brown Algae
#Condition	#Saline	-

Isolation

@ref	Sample type
31179	salted brown alga
67770	Salted brown alga Laminaria produced at Dalian

Taxonmaps

69479

Global distribution of 16S sequence HM159603 (>99% sequence identity) for Halosimplex from Microbeatlas

Aquatic Samples	2
Soil Samples
Animal Samples
Plant Samples
Total Samples	2

Safety information

Sequence information

GC content

@ref	GC-content (mol%)
31179	64
67770	64

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Halosimplex rubrum strain R27 16S ribosomal RNA gene, partial sequence	HM159603	1473		869889
67770	Halosimplex rubrum strain R27 16S ribosomal RNA (rrnB) gene, partial sequence	KF434757	1473		869889

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Halosimplex rubrum R27	GCA_013415885	complete		869889

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Halosimplex rubrum R27
NCBI: GCA_013415885

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.30	no
125439	motility	BacteriaNetⓘ	yes	58.60	no
125439	gram_stain	BacteriaNetⓘ	negative	87.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate anaerobe	81.40	no

Predictions from Diaspora project based on:
Halosimplex rubrum R27
NCBI: GCA_013415885.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	72.97	yes
125438	anaerobic	anaerobicⓘ	no	81.93	yes
125438	aerobic	aerobicⓘ	yes	78.68	yes
125438	spore-forming	spore-formingⓘ	no	83.23	no
125438	thermophilic	thermophileⓘ	no	79.02	no
125438	flagellated	motile2+ⓘ	no	86.53	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Halosimplex pelagicum sp. nov. and Halosimplex rubrum sp. nov., isolated from salted brown alga Laminaria, and emended description of the genus Halosimplex.	Han D, Cui HL	Int J Syst Evol Microbiol	10.1099/ijs.0.056887-0	2013

Culture collection no.

Culture collection no.
CGMCC 1.10591
JCM 17268
R27

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 )
#31179	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 #27506 (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 .
#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 .

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