Name: Pseudomonas flexibilis 78-123
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13170

Type strain:

Species: Pseudomonas flexibilis

Strain Designation: 78-123

Culture col. no.: DSM 25351, CGMCC 1.1365, JCM 14085, CCUG 59930, CECT 7766

Strain history: Y.-H. Xin; CGMCC, China; 78-123.

NCBI tax ID(s): 1295129 (strain), 706570 (species)

SI-ID 318381

CGMCC 1.1365, JCM 14085, CECT 7766, DSM 25351, CCUG 59930

Special Collections

Other strains from Pseudomonas flexibilis

Section

When using BacDive for research please cite our paper

Pseudomonas flexibilis 78-123 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sample of a bird's nest.

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

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Pseudomonadales*
	Family	*Pseudomonadaceae*
	Genus	*Pseudomonas*
	Species	**Pseudomonas flexibilis**
	Full Scientific Name (LPSN)	Pseudomonas flexibilis (Hespell 1977) Shin et al. 2016

	Synonym	Serpens tuomuerensis
	Synonym	Serpens flexibilis
	Synonym	Pseudomonas tuomuerensis

Information on morphological and physiological properties Morphology

[Ref.: #28888]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %97.833
[Ref.: #125439]	Gram stain	negative Confidence in %99.5

[Ref.: #28888]	Cell shape	rod-shaped

[Ref.: #28888]	Motility	yes
[Ref.: #125439]	Motility	yes Confidence in %92.8

Information on culture and growth conditions Culture and growth conditions

[Ref.: #18007]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #18007]

Culture medium growth

[Ref.: #18007]

Culture medium link

Medium recipe at MediaDive

[Ref.: #18007]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #18007]	growth	28 °C
[Ref.: #28888]	growth	15-42 °C
[Ref.: #62162]	growth	30 °C
[Ref.: #67770]	growth	28 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28888]	Oxygen tolerance	aerobe
[Ref.: #62162]	Oxygen tolerance	aerobe

[Ref.: #125439]

Ability of spore formation

no Confidence in %98.9

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28888]		NaCl		growth	0-6.5	%

[Ref.: #67770]

Observation

quinones: Q-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28888]	acetate ChEBI	+	carbon source
[Ref.: #28888]	arabinose ChEBI	+	carbon source
[Ref.: #28888]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #28888]	nitrate ChEBI	+	reduction
[Ref.: #28888]	succinate ChEBI	+	carbon source
[Ref.: #28888]	tween 40 ChEBI	+	carbon source
[Ref.: #28888]	tween 80 ChEBI	+	carbon source

	Enzyme	Enzyme activity	EC number
[Ref.: #28888]	catalase	+	1.11.1.6
[Ref.: #28888]	cytochrome oxidase	+	1.9.3.1
[Ref.: #28888]	urease	+	3.5.1.5

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	taurine degradation	100	1 of 1
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	vitamin B6 metabolism	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	85.71	24 of 28
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	flavin biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	gallate degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	sulfate reduction	76.92	10 of 13
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	purine metabolism	67.02	63 of 94
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	lysine metabolism	61.9	26 of 42
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	tryptophan metabolism	60.53	23 of 38
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	pyrimidine metabolism	60	27 of 45
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	polyamine pathway	56.52	13 of 23
[Ref.: #66794]	oxidative phosphorylation	54.95	50 of 91
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	3-phenylpropionate degradation	53.33	8 of 15
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	arginine metabolism	50	12 of 24
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	carnitine metabolism	50	4 of 8
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	vitamin B12 metabolism	44.12	15 of 34
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	41.18	7 of 17
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	hydrogen production	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	degradation of hexoses	33.33	6 of 18
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	33.33	3 of 9
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	ascorbate metabolism	22.73	5 of 22
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #18007]	Sample type/isolated from	sample of a bird's nest
[Ref.: #18007]	Geographic location (country and/or sea, region)	region of Tuomuer Peak of Tianshan Mountain, bank of Qiongtailan River
[Ref.: #18007]	Country	China
[Ref.: #18007]	Country ISO 3 Code	CHN
[Ref.: #18007]	Continent	Asia

[Ref.: #62162]	Sample type/isolated from	Bird's nest,riverside Qiongtailan River
[Ref.: #62162]	Geographic location (country and/or sea, region)	Tianshan Mountain,Tuomuer Peak
[Ref.: #62162]	Country	China
[Ref.: #62162]	Country ISO 3 Code	CHN
[Ref.: #62162]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Bird's nest on the bank of the Qiongtailan River in the region of Tuomuer Peak of Tianshan Mountain
[Ref.: #67770]	Geographic location (country and/or sea, region)	Xin-jiang Uygur Autobomous Region, north-western China
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host

#Birds

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ868767 (>99% sequence identity) for Pseudomonas flexibilis subclade from Microbeatlas

Aquatic Samples	223
Soil Samples	688
Animal Samples	229
Plant Samples	119
Total Samples	1259

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

[Ref.: #18007]

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.: #18007]	Pseudomonas tuomuerensis strain 78-123 16S ribosomal RNA gene, partial sequence	DQ868767	1411	GenBank ENA	706570 tax ID
[Ref.: #124043]	Pseudomonas tuomuerensis strain JCM 14085 16S ribosomal RNA gene, partial sequence.	KP973997	1530	GenBank ENA	706570 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudomonas flexibilis CGMCC 1.1365	GCA_900101515	scaffold	GenBank ENA	706570 tax ID
[Ref.: #67770]	Pseudomonas flexibilis JCM 14085	GCA_000806415	contig	GenBank ENA	706570 tax ID
[Ref.: #67770]	Pseudomonas flexibilis JCM 14085	GCA_001312105	contig	GenBank ENA	1295129 tax ID
[Ref.: #66792]	Pseudomonas tuomuerensis JCM 14085	1295129.3	wgs	PATRIC	1295129 tax ID	*
[Ref.: #66792]	Pseudomonas flexibilis JCM 14085	2728369709	draft	JGI IMG/M	1295129 tax ID	*
[Ref.: #66792]	Pseudomonas flexibilis JCM 14085	2645728058	draft	JGI IMG/M	1295129 tax ID	*

[Ref.: #18007]	GC-content	60.4 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #28888]	GC-content	60.4 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas tuomuerensis JCM 14085 PATRIC: 1295129.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	97.833	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.454	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	89.853	no
[Ref.: #125438]	aerobic	aerobicⓘ	yes	83.472	yes
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.5	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	82.397	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudomonas flexibilis CGMCC 1.1365 NCBI: GCA_900101515
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	92.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	84.2

Availability in culture collections External links

[Ref.: #18007]

Culture collection no.

DSM 25351, CGMCC 1.1365, JCM 14085, CCUG 59930, CECT 7766

[Ref.: #82378]

SI-ID 318381

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Reclassification of Serpens flexibilis Hespell 1977 as Pseudomonas flexibilis comb. nov., with Pseudomonas tuomuerensis Xin et al. 2009 as a later heterotypic synonym.	Shin SK, Hwang CY, Cho YJ, Yi H	Syst Appl Microbiol	10.1016/j.syapm.2015.09.007	2015	*
Phylogeny	Pseudomonas sagittaria sp. nov., a siderophore-producing bacterium isolated from oil-contaminated soil.	Lin SY, Hameed A, Liu YC, Hsu YH, Lai WA, Chen WM, Shen FT, Young CC	Int J Syst Evol Microbiol	10.1099/ijs.0.045567-0	2012	*
Phylogeny	Pseudomonas linyingensis sp. nov.: a novel bacterium isolated from wheat soil subjected to long-term herbicides application.	He WH, Wang YN, Du X, Zhou Y, Jia B, Bian J, Liu SJ, Chen GC	Curr Microbiol	10.1007/s00284-012-0187-3	2012	*
Phylogeny	Pseudomonas tuomuerensis sp. nov., isolated from a bird's nest.	Xin YH, Zhang DC, Liu HC, Zhou HL, Zhou YG	Int J Syst Evol Microbiol	10.1099/ijs.0.000547-0	2009	*

References

#18007

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25351

#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 )

#28888

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 #25328 (see below)

#62162 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 59930

#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 )

#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 .

#82378

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-ID318381.1 )

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#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 .

#25328

IJSEM 139 2009 ( DOI 10.1099/ijs.0.000547-0 , PubMed 19126738 )

* These data were automatically processed and therefore are not curated

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Pseudomonas tuomuerensis JCM 14085

Pseudomonas flexibilis CGMCC 1.1365

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