Geofilum rubicundum (JCM 15548, NCIMB 14482, JAM-BA0501)

Name: Geofilum rubicundum (JCM 15548, NCIMB 14482, JAM-BA0501)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 133723

Type strain

Strain Designation JAM-BA0501

Culture col. no. JCM 15548 NCIMB 14482 JAM-BA0501

NCBI tax ID(s) 1236989 472113

Special Collections JCM Literature strains

History M. Miyazaki JAM-BA0501.

Links

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 genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 393477

JCM 15548,NCIMB 14482

@ref 20215

Last LPSN update 2026-02-09 11:32:01

Domain Bacteria

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Marinilabiliaceae

Genus Geofilum

Species Geofilum rubicundum

Full scientific name Geofilum rubicundum Miyazaki et al. 2012

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Flagellum arrangement	Confidence
30279	negative	13 µm	0.3 µm	rod-shaped		gliding
125439	negative						98.2

Pigmentation

30279

Productionyes

Culture and growth conditions

Culture temp

@ref	Growth	Type	Temperature (°C)
30279	positive	growth	10-36
30279	positive	optimum	33
67770	positive	growth	33

Culture pH

@ref	Ability	Type	PH	PH range
30279	positive	optimum	7.8
30279	positive	growth	6.9-9.3	alkaliphile

Physiology and metabolism

Oxygen tolerance

30279

Oxygen tolerancefacultative anaerobe

Spore formation

@ref	Spore formation	Confidence
30279
125439		99.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
30279	NaCl	positive	growth	0.5-6 %

Observation

67770

Observationquinones: MK-7

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
30279	17057 ChEBI	cellobiose	+	carbon source
30279	28757 ChEBI	fructose	+	carbon source
30279	28260 ChEBI	galactose	+	carbon source
30279	17716 ChEBI	lactose	+	carbon source
30279	37684 ChEBI	mannose	+	carbon source
30279	17632 ChEBI	nitrate	+	reduction
30279	26546 ChEBI	rhamnose	+	carbon source
30279	27082 ChEBI	trehalose	+	carbon source
30279	18222 ChEBI	xylose	+	carbon source

Enzymes

@ref	Value	Activity	Ec
30279	catalase	+	1.11.1.6
30279	gelatinase	+

Pathway annotation

Computationally determined by

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

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
30279	marine sediment
67770	Deep subseafloor sediment (247 m below the seafloor,1,180 m)	Shimokita Peninsula	Japan	JPN	Asia

Taxonmaps

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

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM97436v1 assembly for Geofilum rubicundum JCM 15548	contig	GCA_000974365	1236989.10	2627853860	1236989	30.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
30279	Geofilum rubicundum JCM 15548 gene for 16S rRNA, partial sequence	AB362265	1440		1236989

GC content

@ref	GC-content (mol%)	Method
30279	42.9
67770	42.9	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Geofilum rubicundum JCM 15548
NCBI: GCA_000974365

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.20	no
125439	motility	BacteriaNetⓘ	no	58.20	no
125439	gram_stain	BacteriaNetⓘ	negative	98.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	62.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Geofilum rubicundum JCM 15548
PATRIC: 1236989.10

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	84.07	no
125438	anaerobic	anaerobicⓘ	no	72.05	yes
125438	spore-forming	spore-formingⓘ	no	88.92	no
125438	aerobic	aerobicⓘ	no	62.14	yes
125438	thermophilic	thermophileⓘ	no	92.90	yes
125438	flagellated	motile2+ⓘ	no	77.13	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	The Characterization of Novel Tissue Microbiota Using an Optimized 16S Metagenomic Sequencing Pipeline.	Lluch J, Servant F, Paisse S, Valle C, Valiere S, Kuchly C, Vilchez G, Donnadieu C, Courtney M, Burcelin R, Amar J, Bouchez O, Lelouvier B.	PLoS One	10.1371/journal.pone.0142334	2015
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 )
#26620	IJSEM 1075 2012 ( DOI 10.1099/ijs.0.032326-0 , PubMed 21705444 )
#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
#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 .
#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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Geofilum rubicundum (JCM 15548, NCIMB 14482, JAM-BA0501)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

Genome sequences

Genome browser: GCA_000974365

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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