Dyadobacter tibetensis (JCM 18589, CGMCC 1.12215, Y620-1)

Name: Dyadobacter tibetensis (JCM 18589, CGMCC 1.12215, Y620-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 134005

Type strain

Strain Designation Y620-1

Culture col. no. JCM 18589 CGMCC 1.12215 Y620-1

NCBI tax ID(s) 1211851

Special Collections JCM Literature strains

History L. Shen Y620-1.

Links

Dyadobacter tibetensis Y620-1 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from glacier.

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

Name and taxonomic classification

SI-ID 132108

JCM 18589

@ref 20215

Last LPSN update 2026-02-09 11:32:05

Domain Bacteria

Phylum Bacteroidota

Class Cytophagia

Order Cytophagales

Family Spirosomataceae

Genus Dyadobacter

Species Dyadobacter tibetensis

Full scientific name Dyadobacter tibetensis Shen et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31036	negative	1.5 µm	0.5 µm	rod-shaped
125438					90.006
125438	negative				98.865
125439	negative				99.8

Pigmentation

31036

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
31036	positive	growth	04-35
31036	positive	optimum	30
67770	positive	growth	25

Physiology and metabolism

Oxygen tolerance

31036

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99.3

Observation

@ref	Observation
31036	aggregates in clumps
67770	quinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31036	22599 ChEBI	arabinose	+	carbon source
31036	17234 ChEBI	glucose	+	carbon source
31036	29864 ChEBI	mannitol	+	carbon source
31036	37684 ChEBI	mannose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31036	acid phosphatase	+	3.1.3.2
31036	alkaline phosphatase	+	3.1.3.1
31036	alpha-galactosidase	+	3.2.1.22
31036	catalase	+	1.11.1.6

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Glacier

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
31036	glacier
67770	Ice core section drilled 59 m-deep in Yuzhufeng Glacier	Tibetan Plateau	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence JQ824420 (>99% sequence identity) for Dyadobacter tibetensis from Microbeatlas

Aquatic Samples	347
Soil Samples	149
Animal Samples	781
Plant Samples	46
Total Samples	1323

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Dyadobacter tibetensis Y620-1 assembly for Dyadobacter tibetensis Y620-1	contig	GCA_000566685	1434325.3	2585427797	1434325	67.86

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
31036	Dyadobacter tibetensis strain Y620-1 16S ribosomal RNA gene, partial sequence	JQ824420	1353		1434325

GC content

@ref	GC-content (mol%)	Method
31036	44.4
67770	44.1-44.7	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: Dyadobacter tibetensis Y620-1
NCBI: GCA_000566685

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.30	no
125439	motility	BacteriaNetⓘ	no	58.60	no
125439	gram_stain	BacteriaNetⓘ	negative	99.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	86.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dyadobacter tibetensis Y620-1
PATRIC: 1434325.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.87	yes
125438	anaerobic	anaerobicⓘ	no	98.41	yes
125438	spore-forming	spore-formingⓘ	no	88.36	no
125438	aerobic	aerobicⓘ	yes	87.48	no
125438	thermophilic	thermophileⓘ	no	97.13	yes
125438	flagellated	motile2+ⓘ	no	90.01	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genomic Insights of Dyadobacter tibetensis Y620-1 Isolated from Ice Core Reveal Genomic Features for Succession in Glacier Environment.	Shen L, Liu Y, Wang N, Adhikari NP	Microorganisms	10.3390/microorganisms7070211	2019
Genetics	Draft genome sequence of Dyadobacter tibetensis type strain (Y620-1) isolated from glacial ice.	Liu Y, Hu A, Shen L, Yao T, Jiao N, Wang N, Xu B	Stand Genomic Sci	10.4056/sigs.5649756	2014
Phylogeny	Dyadobacter tibetensis sp. nov., isolated from glacial ice core.	Shen L, Liu Y, Yao T, Wang N, Xu B, Jiao N, Liu H, Zhou Y, Liu X, Wang Y	Int J Syst Evol Microbiol	10.1099/ijs.0.050328-0	2013

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 )
#27366	IJSEM 3636 2013 ( DOI 10.1099/ijs.0.050328-0 , PubMed 23606482 )
#31036	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 #27366
#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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Dyadobacter tibetensis (JCM 18589, CGMCC 1.12215, Y620-1)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000566685

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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