Psychroflexus sediminis (DSM 19803, CCTCC AA 207030, KCTC 22166)

Name: Psychroflexus sediminis (DSM 19803, CCTCC AA 207030, KCTC 22166)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23019

Type strain

Strain Designation YIM-C238

Culture col. no. DSM 19803 CCTCC AA 207030 KCTC 22166 YIM-C238

NCBI tax ID(s) 470826

Special Collections DSMZ KCTC Literature strains

Links

Psychroflexus sediminis YIM-C238 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from sediment sample, Dachaidamu salt lake in the Qaidam Basin.

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

Name and taxonomic classification

SI-ID 402816

KCTC 22166,DSM 19803

@ref 20215

Last LPSN update 2025-12-16 09:52:33

Domain Pseudomonadati

Phylum Bacteroidota

Class Flavobacteriia

Order Flavobacteriales

Family Flavobacteriaceae

Genus Psychroflexus

Species Psychroflexus sediminis

Full scientific name Psychroflexus sediminis Chen et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
28988	negative	3.0-6.0 µm	0.4-1.0 µm	rod-shaped
125438					91.75
125438	negative				98.558
125439	negative				99

Pigmentation

28988

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19085	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
19085	positive	growth	25	mesophilic
28988	positive	growth	10-40
28988	positive	optimum	27.5	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
28988	positive	optimum	7.5
28988	positive	growth	06-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
28988	aerobe
125439	obligate aerobe	95.6

Spore formation

@ref	Spore formation	Confidence
28988
125438		91.833
125439		97.4

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28988	NaCl	positive	growth	0.5-6 %
28988	NaCl	positive	optimum	2.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28988	35391 ChEBI	aspartate	+	carbon source
28988	23652 ChEBI	dextrin	+	carbon source
28988	4853 ChEBI	esculin	+	hydrolysis
28988	28757 ChEBI	fructose	+	carbon source
28988	28087 ChEBI	glycogen	+	carbon source
28988	17306 ChEBI	maltose	+	carbon source
28988	29864 ChEBI	mannitol	+	carbon source
28988	37657 ChEBI	methyl D-glucoside	+	carbon source
28988	17632 ChEBI	nitrate	+	reduction
28988	17822 ChEBI	serine	+	carbon source
28988	30031 ChEBI	succinate	+	carbon source
28988	17992 ChEBI	sucrose	+	carbon source
28988	27082 ChEBI	trehalose	+	carbon source
28988	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
28988	acid phosphatase	+	3.1.3.2
28988	alkaline phosphatase	+	3.1.3.1
28988	catalase	+	1.11.1.6
28988	cytochrome oxidase	+	1.9.3.1
28988	gelatinase	+

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	starch degradation	100	10 of 10
66794	biotin biosynthesis	100	4 of 4
66794	sulfopterin metabolism	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	vitamin K metabolism	100	5 of 5
66794	palmitate biosynthesis	100	22 of 22
66794	methylglyoxal degradation	100	5 of 5
66794	folate polyglutamylation	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	suberin monomers biosynthesis	100	2 of 2
66794	octane oxidation	100	3 of 3
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	threonine metabolism	90	9 of 10
66794	NAD metabolism	88.89	16 of 18
66794	aspartate and asparagine metabolism	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	photosynthesis	85.71	12 of 14
66794	leucine metabolism	84.62	11 of 13
66794	peptidoglycan biosynthesis	80	12 of 15
66794	cellulose degradation	80	4 of 5
66794	glutamate and glutamine metabolism	78.57	22 of 28
66794	d-mannose degradation	77.78	7 of 9
66794	valine metabolism	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	lipid A biosynthesis	77.78	7 of 9
66794	acetate fermentation	75	3 of 4
66794	butanoate fermentation	75	3 of 4
66794	CMP-KDO biosynthesis	75	3 of 4
66794	isoleucine metabolism	75	6 of 8
66794	glycogen biosynthesis	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	tetrahydrofolate metabolism	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	purine metabolism	70.21	66 of 94
66794	Entner Doudoroff pathway	70	7 of 10
66794	propionate fermentation	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	alanine metabolism	68.97	20 of 29
66794	pyrimidine metabolism	68.89	31 of 45
66794	tryptophan metabolism	68.42	26 of 38
66794	lipid metabolism	67.74	21 of 31
66794	serine metabolism	66.67	6 of 9
66794	cysteine metabolism	66.67	12 of 18
66794	acetoin degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	citric acid cycle	64.29	9 of 14
66794	tyrosine metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	proline metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
66794	lysine metabolism	61.9	26 of 42
66794	glycogen metabolism	60	3 of 5
66794	ubiquinone biosynthesis	57.14	4 of 7
66794	histidine metabolism	55.17	16 of 29
66794	pentose phosphate pathway	54.55	6 of 11
66794	cyclohexanol degradation	50	2 of 4
66794	quinate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	ethanol fermentation	50	1 of 2
66794	carotenoid biosynthesis	50	11 of 22
66794	phenylmercury acetate degradation	50	1 of 2
66794	heme metabolism	50	7 of 14
66794	kanosamine biosynthesis II	50	1 of 2
66794	selenocysteine biosynthesis	50	3 of 6
66794	catecholamine biosynthesis	50	2 of 4
66794	isoprenoid biosynthesis	46.15	12 of 26
66794	urea cycle	46.15	6 of 13
66794	methionine metabolism	46.15	12 of 26
66794	vitamin B1 metabolism	46.15	6 of 13
66794	phenylpropanoid biosynthesis	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	arginine metabolism	41.67	10 of 24
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	oxidative phosphorylation	38.46	35 of 91
66794	carnitine metabolism	37.5	3 of 8
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	metabolism of disaccharids	36.36	4 of 11
66794	degradation of pentoses	35.71	10 of 28
66794	sphingosine metabolism	33.33	2 of 6
66794	IAA biosynthesis	33.33	1 of 3
66794	glycolate and glyoxylate degradation	33.33	2 of 6
66794	cyanate degradation	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	enterobactin biosynthesis	33.33	1 of 3
66794	sulfate reduction	30.77	4 of 13
66794	glycine metabolism	30	3 of 10
66794	coenzyme M biosynthesis	30	3 of 10
66794	4-hydroxyphenylacetate degradation	30	3 of 10
66794	mevalonate metabolism	28.57	2 of 7
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	d-xylose degradation	27.27	3 of 11
66794	3-phenylpropionate degradation	26.67	4 of 15
66794	polyamine pathway	26.09	6 of 23
66794	lactate fermentation	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	degradation of sugar acids	24	6 of 25
66794	4-hydroxymandelate degradation	22.22	2 of 9
66794	molybdenum cofactor biosynthesis	22.22	2 of 9
66794	nitrate assimilation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
19085	sediment sample, Dachaidamu salt lake in the Qaidam Basin	Qinghai Province,	China	CHN	Asia

Taxonmaps

69479

Global distribution of 16S sequence EU135715 (>99% sequence identity) for Psychroflexus sediminis subclade from Microbeatlas

Aquatic Samples	21
Soil Samples
Animal Samples
Plant Samples
Total Samples	21

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
19085	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	IMG-taxon 2622736510 annotated assembly for Psychroflexus sediminis DSM 19803	scaffold	GCA_900099815	470826.3	2622736510	470826	66.31

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19085	Psychroflexus sediminis strain YIM C238 16S ribosomal RNA gene, partial sequence	EU135715	1475		470826

GC content

28988

GC-content (mol%)35.8

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Psychroflexus sediminis DSM 19803
NCBI: GCA_900099815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.40	no
125439	motility	BacteriaNetⓘ	no	80.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.60	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Psychroflexus sediminis DSM 19803
NCBI: GCA_900099815.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.56	no
125438	anaerobic	anaerobicⓘ	no	96.00	yes
125438	aerobic	aerobicⓘ	yes	84.89	no
125438	spore-forming	spore-formingⓘ	no	91.83	yes
125438	thermophilic	thermophileⓘ	no	98.33	yes
125438	flagellated	motile2+ⓘ	no	91.75	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Psychroflexus aurantiacus sp. nov., isolated from soil in the Yellow River Delta wetlands.	Wu SG, Wang JJ, Wang JN, Chen Q, Sheng DH, Li YZ	Int J Syst Evol Microbiol	10.1099/ijsem.0.004527	2020
Phylogeny	Psychroflexus sediminis sp. nov., a mesophilic bacterium isolated from salt lake sediment in China.	Chen YG, Cui XL, Wang YX, Tang SK, Zhang YQ, Li WJ, Liu JH, Peng Q, Xu LH	Int J Syst Evol Microbiol	10.1099/ijs.0.003269-0	2009

References

#19085	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19803
#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 )
#25421	IJSEM 569 2009 ( DOI 10.1099/ijs.0.003269-0 , PubMed 19244443 )
#28988	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 #25421
#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) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#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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Psychroflexus sediminis (DSM 19803, CCTCC AA 207030, KCTC 22166)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_900099815

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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