Name: Chryseolinea serpens RYG
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24794

Type strain:

Species: Chryseolinea serpens

Strain Designation: RYG

Culture col. no.: DSM 24574, ATCC BAA-2075

Strain history: <- P. Dunfield, Univ. Calgary, Canada; RYG

NCBI tax ID(s): 947013 (species)

SI-ID 407123

DSM 24574

Section

Chryseolinea serpens RYG is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment at the bottom of a small ephemeral brook in a forest.

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	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Cytophagia*
	Order	*Cytophagales*
	Family	*Fulvivirgaceae*
	Genus	*Chryseolinea*
	Species	**Chryseolinea serpens**
	Full Scientific Name (LPSN)	Chryseolinea serpens Kim et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #30592]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.964

[Ref.: #30592]	Cell length	3.75 µm

[Ref.: #30592]	Cell width	0.5 µm

[Ref.: #30592]	Cell shape	rod-shaped

[Ref.: #30592]	Motility	yes

[Ref.: #30592]	Flagellum arrangement	gliding

[Ref.: #30592]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21244]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #21244]

Culture medium growth

[Ref.: #21244]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21244]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21244]			growth	25 °C
[Ref.: #30592]			growth	13-37 °C

[Ref.: #21244]

Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #30592]			growth	5.6-7.7

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30592]

Oxygen tolerance

aerobe

[Ref.: #30592]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.48

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30592]		NaCl		growth	0-1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30592]	4-hydroxy-L-proline ChEBI	+	carbon source
[Ref.: #30592]	acetate ChEBI	+	carbon source
[Ref.: #30592]	asparagine ChEBI	+	carbon source
[Ref.: #30592]	aspartate ChEBI	+	carbon source
[Ref.: #30592]	cellobiose ChEBI	+	carbon source
[Ref.: #30592]	dextrin ChEBI	+	carbon source
[Ref.: #30592]	fructose ChEBI	+	carbon source
[Ref.: #30592]	galactose ChEBI	+	carbon source
[Ref.: #30592]	gluconate ChEBI	+	carbon source
[Ref.: #30592]	glucose ChEBI	+	carbon source
[Ref.: #30592]	glucuronamide ChEBI	+	carbon source
[Ref.: #30592]	glutamate ChEBI	+	carbon source
[Ref.: #30592]	glycerol ChEBI	+	carbon source
[Ref.: #30592]	glycogen ChEBI	+	carbon source
[Ref.: #30592]	lactate ChEBI	+	carbon source
[Ref.: #30592]	lactose ChEBI	+	carbon source
[Ref.: #30592]	maltose ChEBI	+	carbon source
[Ref.: #30592]	mannose ChEBI	+	carbon source
[Ref.: #30592]	melibiose ChEBI	+	carbon source
[Ref.: #30592]	methyl D-glucoside ChEBI	+	carbon source
[Ref.: #30592]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #30592]	proline ChEBI	+	carbon source
[Ref.: #30592]	raffinose ChEBI	+	carbon source
[Ref.: #30592]	sucrose ChEBI	+	carbon source
[Ref.: #30592]	threonine ChEBI	+	carbon source
[Ref.: #30592]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #30592]	acid phosphatase	+	3.1.3.2
[Ref.: #30592]	alkaline phosphatase	+	3.1.3.1
[Ref.: #30592]	catalase	+	1.11.1.6
[Ref.: #30592]	cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	gallate degradation	100	5 of 5
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	molybdenum cofactor biosynthesis	100	9 of 9
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	phenylalanine metabolism	92.31	12 of 13
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	NAD metabolism	88.89	16 of 18
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	lipid metabolism	87.1	27 of 31
[Ref.: #66794]	flavin biosynthesis	86.67	13 of 15
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	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]	selenocysteine biosynthesis	83.33	5 of 6
[Ref.: #66794]	glutamate and glutamine metabolism	82.14	23 of 28
[Ref.: #66794]	tryptophan metabolism	81.58	31 of 38
[Ref.: #66794]	purine metabolism	80.85	76 of 94
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	histidine metabolism	79.31	23 of 29
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	lysine metabolism	78.57	33 of 42
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	degradation of hexoses	77.78	14 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	isoprenoid biosynthesis	76.92	20 of 26
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	glycolysis	76.47	13 of 17
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	methionine metabolism	73.08	19 of 26
[Ref.: #66794]	metabolism of disaccharids	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	degradation of pentoses	71.43	20 of 28
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	arginine metabolism	70.83	17 of 24
[Ref.: #66794]	ascorbate metabolism	68.18	15 of 22
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	4-hydroxymandelate degradation	66.67	6 of 9
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	degradation of sugar acids	60	15 of 25
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	daunorubicin biosynthesis	55.56	5 of 9
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	urea cycle	53.85	7 of 13
[Ref.: #66794]	polyamine pathway	52.17	12 of 23
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	myo-inositol biosynthesis	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	oxidative phosphorylation	46.15	42 of 91
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	carotenoid biosynthesis	45.45	10 of 22
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	aclacinomycin biosynthesis	42.86	3 of 7
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	30.77	4 of 13
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[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.: #21244]	Sample type/isolated from	sediment at the bottom of a small ephemeral brook in a forest
[Ref.: #21244]	Geographic location (country and/or sea, region)	near Marburg
[Ref.: #21244]	Country	Germany
[Ref.: #21244]	Country ISO 3 Code	DEU
[Ref.: #21244]	Continent	Europe
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Sediment
#Environmental	#Terrestrial	#Forest

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FR774778 (>99% sequence identity) for Chryseolinea serpens subclade from Microbeatlas

Aquatic Samples	772
Soil Samples	17220
Animal Samples	518
Plant Samples	2669
Total Samples	21179

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

[Ref.: #21244]

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.: #21244]	Chryseolinea serpens partial 16S rRNA gene, type strain RYGT	FR774778	1472	ENA	947013 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chryseolinea serpens DSM 24574	GCA_900129725	scaffold	GenBank	947013 tax ID	*
[Ref.: #66792]	Chryseolinea serpens strain DSM 24574	947013.3	wgs	PATRIC	947013 tax ID	*
[Ref.: #66792]	Chryseolinea serpens DSM 24574	2617270831	draft	JGI IMG/M	947013 tax ID	*

[Ref.: #21244]	GC-content	49.9 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #30592]	GC-content	49.9 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: Chryseolinea serpens DSM 24574 NCBI: GCA_900129725.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Chryseolinea serpens DSM 24574 NCBI: GCA_900129725.1
[Ref.: #69480]	motile	no	91.232	no
[Ref.: #69480]	flagellated	no	96.665	yes
[Ref.: #69480]	gram-positive	no	97.587	yes
[Ref.: #69480]	anaerobic	no	99.376	yes
[Ref.: #69480]	aerobic	yes	90.817	no
[Ref.: #69480]	halophile	no	93.111	yes
[Ref.: #69480]	spore-forming	no	92.318	no
[Ref.: #69480]	thermophile	no	98.922	yes
[Ref.: #69480]	glucose-util	yes	85.237	yes
[Ref.: #69480]	glucose-ferment	no	88.68	no

Availability in culture collections External links

[Ref.: #21244]

Culture collection no.

DSM 24574, ATCC BAA-2075

[Ref.: #88616]

SI-ID 407123

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chryseolinea soli sp. nov., isolated from soil.	Lee SA, Kim Y, Sang MK, Song J, Kwon SW, Weon HY	J Microbiol	10.1007/s12275-019-8562-4	2019	*
Phylogeny	Chryseolinea flava sp. nov., a new species of Chryseolinea isolated from soil.	Wang JJ, Chen Q, Li YZ	Int J Syst Evol Microbiol	10.1099/ijsem.0.003022	2018	*
Phylogeny	Chryseolinea serpens gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from soil.	Kim JJ, Alkawally M, Brady AL, Rijpstra WIC, Sinninghe Damste JS, Dunfield PF	Int J Syst Evol Microbiol	10.1099/ijs.0.039404-0	2012	*
Phylogeny	Parachryseolinea silvisoli gen. nov., sp. nov., isolated from forest soil, and reclassification of Chryseolinea flava as Pseudochryseolinea flava gen. nov., comb. nov.	Wang C, Lv Y, Li A, Yao Q, Zhu H	Int J Syst Evol Microbiol	10.1099/ijsem.0.005523	2022	*

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 )

#21244

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 24574

#30592

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 #26923 (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) .

#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 .

#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 )

#88616

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-ID407123.1 )

#26923

IJSEM 654 2013 ( DOI 10.1099/ijs.0.039404-0 , PubMed 22544793 )

* These data were automatically processed and therefore are not curated

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Chryseolinea serpens DSM 24574

Chryseolinea serpens DSM 24574

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