Name: Litoribacter ruber ACCC 05414
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133622

Type strain:

Species: Litoribacter ruber

Culture col. no.: ACCC 05414, KCTC 22899, YIM CH208

NCBI tax ID(s): 702568 (species)

SI-ID 374148

KCTC 22899

Section

Litoribacter ruber ACCC 05414 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from soda lake.

Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Cytophagaceae*
	Genus	*Litoribacter*
	Species	**Litoribacter ruber**
	Full Scientific Name (LPSN)	Litoribacter ruber Tian et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29810]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.995

[Ref.: #29810]	Cell length	1.2-1.5 µm

[Ref.: #29810]	Cell width	0.3-0.5 µm

[Ref.: #29810]	Cell shape	rod-shaped

[Ref.: #29810]	Motility	no

[Ref.: #29810]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

	Temperatures	Kind of temperature		Temperature
[Ref.: #29810]			growth	20-37 °C
[Ref.: #29810]			optimum	28 °C

[Ref.: #29810]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #29810]			optimum	8.5
[Ref.: #29810]			growth	7.5-10.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29810]

Oxygen tolerance

aerobe

[Ref.: #29810]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.657

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29810]		NaCl		growth	0-9	%
[Ref.: #29810]		NaCl		optimum	0.5-2.5	%

[Ref.: #29810]

Observation

aggregates in chains

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29810]	acetate ChEBI	+	carbon source
[Ref.: #29810]	citrate ChEBI	+	carbon source
[Ref.: #29810]	fructose ChEBI	+	carbon source
[Ref.: #29810]	galactose ChEBI	+	carbon source
[Ref.: #29810]	glucose ChEBI	+	carbon source
[Ref.: #29810]	glycerol ChEBI	+	carbon source
[Ref.: #29810]	lactose ChEBI	+	carbon source
[Ref.: #29810]	malate ChEBI	+	carbon source
[Ref.: #29810]	mannitol ChEBI	+	carbon source
[Ref.: #29810]	mannose ChEBI	+	carbon source
[Ref.: #29810]	raffinose ChEBI	+	carbon source
[Ref.: #29810]	ribose ChEBI	+	carbon source
[Ref.: #29810]	sorbitol ChEBI	+	carbon source
[Ref.: #29810]	sucrose ChEBI	+	carbon source
[Ref.: #29810]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #29810]		catalase	+	1.11.1.6
[Ref.: #29810]		cytochrome oxidase	+	1.9.3.1

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #29810]	Sample type/isolated from	soda lake
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Lake (large)
#Condition	#Alkaline	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence GU254164 (>99% sequence identity) for Litoribacter from Microbeatlas

Aquatic Samples	79
Soil Samples	85
Animal Samples	103
Plant Samples	13
Total Samples	280

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #29810]	Litoribacter ruber strain YIM CH208 16S ribosomal RNA gene, partial sequence	GU254164	1450	GenBank	702568 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Litoribacter ruber KCTC 22899	GCA_018500185	contig	GenBank	702568 tax ID	*
[Ref.: #66792]	Litoribacter ruber strain KCTC 22899	702568.3	wgs	PATRIC	702568 tax ID	*

[Ref.: #29810]

GC-content

45.1 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Litoribacter ruber strain KCTC 22899 PATRIC: 702568.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Litoribacter ruber strain KCTC 22899 PATRIC: 702568.3
[Ref.: #69480]	gram-positive	no	98.123	yes
[Ref.: #69480]	anaerobic	no	97.274	yes
[Ref.: #69480]	halophile	no	63.377	no
[Ref.: #69480]	spore-forming	no	95.649	yes
[Ref.: #69480]	glucose-util	yes	90.169	no
[Ref.: #69480]	thermophile	no	96.96	yes
[Ref.: #69480]	flagellated	no	97.175	yes
[Ref.: #69480]	motile	no	91.509	yes
[Ref.: #69480]	aerobic	yes	88.453	yes
[Ref.: #69480]	glucose-ferment	no	90.78	no

Availability in culture collections External links

[Ref.: #29810]

Culture collection no.

ACCC 05414, KCTC 22899, YIM CH208

[Ref.: #91528]

SI-ID 374148

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Litoribacter ruber gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from a soda lake sediment.	Tian SP, Wang YX, Hu B, Zhang XX, Xiao W, Chen Y, Lai YH, Wen ML, Cui XL	Int J Syst Evol Microbiol	10.1099/ijs.0.021626-0	2010	*
Phylogeny	Litoribacter populi sp. nov., isolated from the soil of a Populus euphratica forest.	Wang N, Sayim G, Hou M, Sun J, Ahmat M, Tang Q, Yang H, Wang W, Zhang Z, Osman G	Arch Microbiol	10.1007/s00203-021-02488-z	2021	*
Phylogeny	Mongoliicoccus alkaliphilus sp. nov. and Litoribacter alkaliphilus sp. nov., isolated from salt pans.	Subhash Y, Tushar L, Sasikala C, Ramana CV	Int J Syst Evol Microbiol	10.1099/ijs.0.049924-0	2013	*
Phylogeny	Anditalea andensis gen. nov., sp. nov., an alkaliphilic, halotolerant bacterium isolated from extreme alkali-saline soil.	Shi W, Takano T, Liu S	Antonie Van Leeuwenhoek	10.1007/s10482-012-9770-7	2012	*
Phylogeny	Mongoliicoccus roseus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake.	Liu YP, Wang YX, Li YX, Feng FY, Liu HR, Wang J	Int J Syst Evol Microbiol	10.1099/ijs.0.035766-0	2011	*

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 )

#29810

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 #26187 (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) .

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#91528

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-ID374148.1 )

#26187

IJSEM 2996 2010 ( DOI 10.1099/ijs.0.021626-0 , PubMed 20118287 )

* These data were automatically processed and therefore are not curated

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Litoribacter ruber strain KCTC 22899

Litoribacter ruber strain KCTC 22899

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