Name: Geofilum rubicundum JAM-BA0501
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 133723

Type strain:

Species: Geofilum rubicundum

Strain Designation: JAM-BA0501

Culture col. no.: JCM 15548, NCIMB 14482

Strain history: M. Miyazaki JAM-BA0501.

NCBI tax ID(s): 1236989 (strain), 472113 (species)

Section

Geofilum rubicundum JAM-BA0501 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from marine sediment.

Gram-negative
motile
rod-shaped
facultative anaerobe
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	*Bacteroidia*
	Order	*Bacteroidales*
	Family	*Marinilabiliaceae*
	Genus	*Geofilum*
	Species	**Geofilum rubicundum**
	Full Scientific Name (LPSN)	Geofilum rubicundum Miyazaki et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #30279]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %100

[Ref.: #30279]	Cell length	13 µm

[Ref.: #30279]	Cell width	0.3 µm

[Ref.: #30279]	Cell shape	rod-shaped

[Ref.: #30279]	Motility	yes

[Ref.: #30279]	Flagellum arrangement	gliding

[Ref.: #30279]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #30279]	growth	10-36 °C
[Ref.: #30279]	optimum	33 °C
[Ref.: #67770]	growth	33 °C

[Ref.: #30279]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30279]			optimum	7.8
[Ref.: #30279]			growth	6.9-9.3

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30279]	Oxygen tolerance	facultative anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %97.456

[Ref.: #30279]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.984

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30279]		NaCl		growth	0.5-6	%

[Ref.: #67770]

Observation

quinones: MK-7

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #30279]	cellobiose ChEBI	+	carbon source
[Ref.: #30279]	fructose ChEBI	+	carbon source
[Ref.: #30279]	galactose ChEBI	+	carbon source
[Ref.: #30279]	lactose ChEBI	+	carbon source
[Ref.: #30279]	mannose ChEBI	+	carbon source
[Ref.: #30279]	nitrate ChEBI	+	reduction
[Ref.: #30279]	rhamnose ChEBI	+	carbon source
[Ref.: #30279]	trehalose ChEBI	+	carbon source
[Ref.: #30279]	xylose ChEBI	+	carbon source

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #30279]		catalase	+	1.11.1.6
[Ref.: #30279]		gelatinase	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cellulose degradation	100	5 of 5
[Ref.: #66794]	starch degradation	100	10 of 10
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	lipoate biosynthesis	100	5 of 5
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	propanol degradation	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	degradation of sugar alcohols	81.25	13 of 16
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	vitamin K metabolism	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	alanine metabolism	79.31	23 of 29
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	pyrimidine metabolism	77.78	35 of 45
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	biotin biosynthesis	75	3 of 4
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	sulfate reduction	69.23	9 of 13
[Ref.: #66794]	leucine metabolism	69.23	9 of 13
[Ref.: #66794]	histidine metabolism	68.97	20 of 29
[Ref.: #66794]	lipid metabolism	67.74	21 of 31
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	lysine metabolism	66.67	28 of 42
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	CO2 fixation in Crenarchaeota	66.67	6 of 9
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	62.5	5 of 8
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	coenzyme M biosynthesis	60	6 of 10
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of hexoses	55.56	10 of 18
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	methionine metabolism	53.85	14 of 26
[Ref.: #66794]	oxidative phosphorylation	52.75	48 of 91
[Ref.: #66794]	tryptophan metabolism	52.63	20 of 38
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	degradation of sugar acids	48	12 of 25
[Ref.: #66794]	ascorbate metabolism	45.45	10 of 22
[Ref.: #66794]	nitrate assimilation	44.44	4 of 9
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	arginine metabolism	41.67	10 of 24
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	polyamine pathway	39.13	9 of 23
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	androgen and estrogen metabolism	37.5	6 of 16
[Ref.: #66794]	vitamin B12 metabolism	35.29	12 of 34
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	33.33	2 of 6
[Ref.: #66794]	L-lactaldehyde degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
		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.: #30279]	Sample type/isolated from	marine sediment

[Ref.: #67770]	Sample type/isolated from	Deep subseafloor sediment (247 m below the seafloor,1,180 m)
[Ref.: #67770]	Geographic location (country and/or sea, region)	Shimokita Peninsula
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	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 AB362265 (>99% sequence identity) for Geofilum rubicundum subclade from Microbeatlas

Aquatic Samples	1182
Soil Samples	299
Animal Samples	978
Plant Samples	70
Total Samples	2529

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.: #30279]	Geofilum rubicundum JCM 15548 gene for 16S rRNA, partial sequence	AB362265	1440	GenBank	1236989 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Geofilum rubicundum JCM 15548	GCA_000974365	contig	GenBank	1236989 tax ID
[Ref.: #66792]	Geofilum rubicundum JCM 15548	1236989.10	wgs	PATRIC	1236989 tax ID	*
[Ref.: #66792]	Geofilum rubicundum JCM 15548	2627853860	draft	JGI IMG/M	1236989 tax ID	*

[Ref.: #30279]	GC-content	42.9 mol%
[Ref.: #67770]	GC-content	42.9 mol%	high performance liquid chromatography (HPLC)

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: Geofilum rubicundum JCM 15548 PATRIC: 1236989.10
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Geofilum rubicundum JCM 15548 PATRIC: 1236989.10
[Ref.: #69480]	motile	no	75.613	no
[Ref.: #69480]	gram-positive	no	97.056	yes
[Ref.: #69480]	anaerobic	yes	58.769	yes
[Ref.: #69480]	aerobic	no	81.877	no
[Ref.: #69480]	halophile	no	77.773	no
[Ref.: #69480]	spore-forming	no	94.262	no
[Ref.: #69480]	thermophile	no	98.83	no
[Ref.: #69480]	glucose-util	yes	91.265	no
[Ref.: #69480]	flagellated	no	94.258	yes
[Ref.: #69480]	glucose-ferment	no	55.139	no

Availability in culture collections External links

[Ref.: #30279]

Culture collection no.

JCM 15548, NCIMB 14482

Literature:

Topic	Title	Authors	Journal	DOI	Year
Genetics	Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes.	Inoue J, Oshima K, Suda W, Sakamoto M, Iino T, Noda S, Hongoh Y, Hattori M, Ohkuma M	Microbes Environ	10.1264/jsme2.ME14142	2015	*
Phylogeny	Geofilum rhodophaeum sp. nov., isolated from coastal sediment.	Mu X, Xu ZX, Mu DS, Chen GJ, Du ZJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002223	2017	*
Phylogeny	Geofilum rubicundum gen. nov., sp. nov., isolated from deep subseafloor sediment.	Miyazaki M, Koide O, Kobayashi T, Mori K, Shimamura S, Nunoura T, Imachi H, Inagaki F, Nagahama T, Nogi Y, Deguchi S, Takai K	Int J Syst Evol Microbiol	10.1099/ijs.0.032326-0	2011	*

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 )

#30279

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 #26620 (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 )

#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 .

#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 )

#26620

IJSEM 1075 2012 ( DOI 10.1099/ijs.0.032326-0 , PubMed 21705444 )

* These data were automatically processed and therefore are not curated

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Geofilum rubicundum JCM 15548

Geofilum rubicundum JCM 15548

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