Name: Robiginitalea myxolifaciens YM6-073
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5638

Type strain:

Species: Robiginitalea myxolifaciens

Strain Designation: YM6-073

Culture col. no.: DSM 21019, KCTC 22216, MBIC 06409

Strain history: <- H kasai, MBI, Japan <- Y Matsuo, Japan

NCBI tax ID(s): 400055 (species)

SI-ID 401150

DSM 21019

Section

Robiginitalea myxolifaciens YM6-073 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine sediment.

Gram-negative
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	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Flavobacteriaceae*
	Genus	*Robiginitalea*
	Species	**Robiginitalea myxolifaciens**
	Full Scientific Name (LPSN)	Robiginitalea myxolifaciens Manh et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32509]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.991

[Ref.: #32509]	Cell length	0.9-3.5 µm

[Ref.: #32509]	Cell width	0.3-0.65 µm

[Ref.: #32509]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #32509]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %90.059

[Ref.: #32509]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15512]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #15512]

Culture medium growth

[Ref.: #15512]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15512]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15512]	growth	28 °C
[Ref.: #32509]	growth	15-42 °C
[Ref.: #32509]	optimum	30 °C
[Ref.: #67771]	growth	30 °C

[Ref.: #15512]	Temperature range	mesophilic
[Ref.: #32509]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #32509]			optimum	7.6-8.5
[Ref.: #32509]			growth	6.5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32509]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

[Ref.: #32509]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

[Ref.: #15512]

Name of produced compound

myxol

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32509]		NaCl		growth	03-07	%
[Ref.: #32509]		NaCl		optimum	03-04	%

[Ref.: #32509]	Observation	aggregates in chains
[Ref.: #67771]	Observation	quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32509]	cellobiose ChEBI	+	carbon source
[Ref.: #32509]	fructose ChEBI	+	carbon source
[Ref.: #32509]	galactose ChEBI	+	carbon source
[Ref.: #32509]	glucose ChEBI	+	carbon source
[Ref.: #32509]	glycerol ChEBI	+	carbon source
[Ref.: #32509]	lactose ChEBI	+	carbon source
[Ref.: #32509]	maltose ChEBI	+	carbon source
[Ref.: #32509]	mannose ChEBI	+	carbon source
[Ref.: #32509]	melibiose ChEBI	+	carbon source
[Ref.: #32509]	raffinose ChEBI	+	carbon source
[Ref.: #32509]	sorbitol ChEBI	+	carbon source
[Ref.: #32509]	sucrose ChEBI	+	carbon source
[Ref.: #32509]	trehalose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32509]		catalase	+	1.11.1.6
[Ref.: #32509]		cytochrome oxidase	+	1.9.3.1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	quinate degradation	100	2 of 2
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	kanosamine biosynthesis II	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	92.86	13 of 14
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	purine metabolism	77.66	73 of 94
[Ref.: #66794]	leucine metabolism	76.92	10 of 13
[Ref.: #66794]	pyrimidine metabolism	75.56	34 of 45
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	tryptophan metabolism	68.42	26 of 38
[Ref.: #66794]	carotenoid biosynthesis	68.18	15 of 22
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	lysine metabolism	64.29	27 of 42
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	citric acid cycle	64.29	9 of 14
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	lipid metabolism	61.29	19 of 31
[Ref.: #66794]	non-pathway related	60.53	23 of 38
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	propionate fermentation	60	6 of 10
[Ref.: #66794]	Entner Doudoroff pathway	60	6 of 10
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	isoprenoid biosynthesis	50	13 of 26
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	degradation of pentoses	46.43	13 of 28
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	4-hydroxymandelate degradation	44.44	4 of 9
[Ref.: #66794]	oxidative phosphorylation	43.96	40 of 91
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	gallate degradation	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	degradation of sugar alcohols	31.25	5 of 16
[Ref.: #66794]	vitamin B1 metabolism	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	phenol degradation	25	5 of 20
[Ref.: #66794]	degradation of sugar acids	24	6 of 25
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	allantoin degradation	22.22	2 of 9
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		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.: #15512]	Sample type/isolated from	marine sediment
[Ref.: #15512]	Geographic location (country and/or sea, region)	Okinawa, Onna Village, Cape Maeda
[Ref.: #15512]	Country	Japan
[Ref.: #15512]	Country ISO 3 Code	JPN
[Ref.: #15512]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sediment
[Ref.: #67771]	Geographic location (country and/or sea, region)	the shore of Cape Maeda, Onna Village, Okinawa Pref.
[Ref.: #67771]	Country	Japan
[Ref.: #67771]	Country ISO 3 Code	JPN
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB270585 (>99% sequence identity) for Robiginitalea myxolifaciens subclade from Microbeatlas

Aquatic Samples	2673
Soil Samples	113
Animal Samples	196
Plant Samples	28
Total Samples	3010

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

[Ref.: #15512]

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.: #15512]	Robiginitalea myxolifaciens gene for 16S rRNA, partial sequence	AB270585	1465	ENA	400055 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Robiginitalea myxolifaciens DSM 21019	GCA_900115205	scaffold	GenBank	400055 tax ID	*
[Ref.: #66792]	Robiginitalea myxolifaciens strain DSM 21019	400055.5	wgs	PATRIC	400055 tax ID	*
[Ref.: #66792]	Robiginitalea myxolifaciens DSM 21019	2636416043	draft	JGI IMG/M	400055 tax ID	*

[Ref.: #15512]	GC-content	50.1 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32509]	GC-content	50.1 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: Robiginitalea myxolifaciens DSM 21019 NCBI: GCA_900115205.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Robiginitalea myxolifaciens DSM 21019 NCBI: GCA_900115205.1
[Ref.: #69480]	motile	no	90.161	yes
[Ref.: #69480]	flagellated	no	95.411	yes
[Ref.: #69480]	gram-positive	no	97.688	yes
[Ref.: #69480]	anaerobic	no	99.122	yes
[Ref.: #69480]	aerobic	yes	86.36	no
[Ref.: #69480]	halophile	no	74.307	no
[Ref.: #69480]	spore-forming	no	96.996	yes
[Ref.: #69480]	glucose-ferment	no	89.77	no
[Ref.: #69480]	thermophile	no	97.144	yes
[Ref.: #69480]	glucose-util	yes	91.45	yes

Availability in culture collections External links

[Ref.: #15512]

Culture collection no.

DSM 21019, KCTC 22216, MBIC 06409

[Ref.: #75121]

SI-ID 401150

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Robiginitalea myxolifaciens sp. nov., a novel myxol-producing bacterium isolated from marine sediment, and emended description of the genus Robiginitalea.	Manh HD, Matsuo Y, Katsuta A, Matsuda S, Shizuri Y, Kasai H	Int J Syst Evol Microbiol	10.1099/ijs.0.65598-0	2008	*

References

#15512

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21019

#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 )

#32509

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 #28729 (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 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 )

#75121

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-ID401150.1 )

#28729

IJSEM 1660 2008 ( DOI 10.1099/ijs.0.65598-0 , PubMed 18599712 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Robiginitalea myxolifaciens in external resources:
SILVA
BRENDA
PANGAEA
StrainInfo
GBIF

Robiginitalea myxolifaciens DSM 21019

Robiginitalea myxolifaciens DSM 21019

Change proposal

Change proposal