Name: Hymenobacter psychrotolerans Tibet-IIU11
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 3804

Type strain:

Species: Hymenobacter psychrotolerans

Strain Designation: Tibet-IIU11

Culture col. no.: DSM 18569, CGMCC 1.6365

Strain history: <- G. Zhang, School of Life Sci., Lanzhou Univ., China; Tibet-IIU11

NCBI tax ID(s): 1121959 (strain), 344998 (species)

SI-ID 312287

CGMCC 1.6365, DSM 18569

Section

Hymenobacter psychrotolerans Tibet-IIU11 is an aerobe, Gram-negative, rod-shaped bacterium that was isolated from permafrost sediment sample.

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	*Hymenobacteraceae*
	Genus	*Hymenobacter*
	Species	**Hymenobacter psychrotolerans**
	Full Scientific Name (LPSN)	Hymenobacter psychrotolerans Zhang et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32500]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #32500]	Cell length	1.25 µm

[Ref.: #32500]	Cell width	0.5 µm

[Ref.: #32500]	Cell shape	rod-shaped

[Ref.: #32500]	Motility	no

[Ref.: #32500]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7529]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7529]

Culture medium growth

[Ref.: #7529]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7529]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7529]	growth	20-25 °C
[Ref.: #32500]	growth	04-28 °C
[Ref.: #32500]	optimum	18 °C

[Ref.: #32500]

Temperature range

psychrophilic

	pH	Kind of pH		pH
[Ref.: #32500]			optimum	7
[Ref.: #32500]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32500]

Oxygen tolerance

aerobe

[Ref.: #32500]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.998

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32500]		NaCl		growth	0-1.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32500]	glucose ChEBI	+	carbon source
[Ref.: #32500]	mannose ChEBI	+	carbon source
[Ref.: #32500]	nitrate ChEBI	+	reduction
[Ref.: #32500]	propionate ChEBI	+	carbon source
[Ref.: #32500]	sucrose ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #32500]	acid phosphatase	+	3.1.3.2
[Ref.: #32500]	alkaline phosphatase	+	3.1.3.1
[Ref.: #32500]	catalase	+	1.11.1.6
[Ref.: #32500]	cytochrome oxidase	+	1.9.3.1

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

[Ref.: #7529]	Sample type/isolated from	permafrost sediment sample
[Ref.: #7529]	Geographic location (country and/or sea, region)	Qinghai–Tibet Plateau, Beilu river basin (34° 50' N 92° 56' E, 4676 m above sea level)
[Ref.: #7529]	Country	China
[Ref.: #7529]	Country ISO 3 Code	CHN
[Ref.: #7529]	Continent	Asia
[Ref.: #7529]	Geographic location	34.8333°/92.9333°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Permafrost

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7529]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #7529]	Hymenobacter psychrotolerans strain Tibet-IIU11 16S ribosomal RNA gene, partial sequence	DQ177475	1484	ENA	1121959 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Hymenobacter psychrotolerans DSM 18569	GCA_900142395	contig	GenBank	1121959 tax ID	*
[Ref.: #66792]	Hymenobacter psychrotolerans DSM 18569	1121959.3	wgs	PATRIC	1121959 tax ID	*
[Ref.: #66792]	Hymenobacter psychrotolerans DSM 18569	2585428192	draft	JGI IMG/M	1121959 tax ID	*

[Ref.: #7529]	GC-content	60.0 mol%
[Ref.: #32500]	GC-content	60 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: Hymenobacter psychrotolerans DSM 18569 PATRIC: 1121959.3
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Hymenobacter psychrotolerans DSM 18569 PATRIC: 1121959.3
[Ref.: #69480]	motile	no	92.078	yes
[Ref.: #69480]	flagellated	no	97.372	yes
[Ref.: #69480]	gram-positive	no	97.441	no
[Ref.: #69480]	anaerobic	no	99.173	no
[Ref.: #69480]	halophile	no	92.795	yes
[Ref.: #69480]	spore-forming	no	94.186	yes
[Ref.: #69480]	thermophile	no	93.267	no
[Ref.: #69480]	glucose-util	yes	82.962	yes
[Ref.: #69480]	aerobic	yes	90.819	yes
[Ref.: #69480]	glucose-ferment	no	90.758	no

Availability in culture collections External links

[Ref.: #7529]

Culture collection no.

DSM 18569, CGMCC 1.6365

[Ref.: #73316]

SI-ID 312287

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Hymenobacter guriensis sp. nov., and Hymenobacter duratus sp. nov., Radiation-Resistant Species Isolated from Soil in South Korea.	Damdintogtokh T, Cha IT, Kim MK	Curr Microbiol	10.1007/s00284-021-02517-6	2021	*
Phylogeny	Hymenobacter profundi sp. nov., isolated from deep-sea water.	Sun J, Xing M, Wang W, Dai F, Liu J, Hao J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002621	2018	*
Phylogeny	Hymenobacter defluvii sp. nov., isolated from wastewater of an acidic water neutralization facility.	Kang JW, Choi S, Choe HN, Seong CN	Int J Syst Evol Microbiol	10.1099/ijsem.0.002497	2017	*
Phylogeny	Hymenobacter glacieicola sp. nov., isolated from glacier ice.	Liu K, Liu Y, Wang N, Gu Z, Shen L, Xu B, Zhou Y, Liu H, Jiao N	Int J Syst Evol Microbiol	10.1099/ijsem.0.001266	2016	*
Phylogeny	Hymenobacter kanuolensis sp. nov., a novel radiation-resistant bacterium.	Su S, Chen M, Teng C, Jiang S, Zhang C, Lin M, Zhang W	Int J Syst Evol Microbiol	10.1099/ijs.0.051680-0	2014	*
Phylogeny	Hymenobacter psychrotolerans sp. nov., isolated from the Qinghai--Tibet Plateau permafrost region.	Zhang G, Niu F, Busse HJ, Ma X, Liu W, Dong M, Feng H, An L, Cheng G	Int J Syst Evol Microbiol	10.1099/ijs.0.65588-0	2008	*

References

#7529

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18569

#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 )

#32500

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 #28720 (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) .

#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 )

#73316

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-ID312287.1 )

#28720

IJSEM 1215 2008 ( DOI 10.1099/ijs.0.65588-0 , PubMed 18450716 )

* These data were automatically processed and therefore are not curated

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Hymenobacter psychrotolerans DSM 18569

Hymenobacter psychrotolerans DSM 18569

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