Name: Methyloceanibacter caenitepidi Gela4
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 24750

Type strain:

Species: Methyloceanibacter caenitepidi

Strain Designation: Gela4

Culture col. no.: DSM 27242, NBRC 109540

Strain history: <- M. Takeuchi, Natl. Inst. Advanced Industrial Sci. and Technol., Tsukuba, Japan; Gela4

NCBI tax ID(s): 1384459 (species)

SI-ID 392242

NBRC 109540, DSM 27242, LMG 28723

Section

Methyloceanibacter caenitepidi Gela4 is a mesophilic, Gram-negative bacterium that was isolated from marine surface sediment near a hydrothermal vent.

Gram-negative
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Hyphomicrobiaceae*
	Genus	*Methyloceanibacter*
	Species	**Methyloceanibacter caenitepidi**
	Full Scientific Name (LPSN)	Methyloceanibacter caenitepidi Takeuchi et al. 2014

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	negative Confidence in %99.997

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21308]

Culture medium

METHYLOCEANUS CENITEPIDUS MEDIUM (DSMZ Medium 1488)

[Ref.: #21308]

Culture medium growth

[Ref.: #21308]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21308]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #21308]			growth	35 °C

[Ref.: #21308]

Temperature range

mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.996

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	methane metabolism	100	3 of 3
[Ref.: #66794]	photosynthesis	92.86	13 of 14
[Ref.: #66794]	pentose phosphate pathway	90.91	10 of 11
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	d-mannose degradation	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	vitamin B12 metabolism	88.24	30 of 34
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	ethylmalonyl-CoA pathway	80	4 of 5
[Ref.: #66794]	Entner Doudoroff pathway	80	8 of 10
[Ref.: #66794]	methanofuran biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	glutathione metabolism	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	citric acid cycle	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	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]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	purine metabolism	68.09	64 of 94
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	histidine metabolism	62.07	18 of 29
[Ref.: #66794]	isoprenoid biosynthesis	61.54	16 of 26
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	cysteine metabolism	61.11	11 of 18
[Ref.: #66794]	flavin biosynthesis	60	9 of 15
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	cellulose degradation	60	3 of 5
[Ref.: #66794]	phenylacetate degradation (aerobic)	60	3 of 5
[Ref.: #66794]	methanogenesis from CO2	58.33	7 of 12
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	nitrate assimilation	55.56	5 of 9
[Ref.: #66794]	tryptophan metabolism	55.26	21 of 38
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	tyrosine metabolism	50	7 of 14
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	lysine metabolism	50	21 of 42
[Ref.: #66794]	oxidative phosphorylation	48.35	44 of 91
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	cholesterol biosynthesis	45.45	5 of 11
[Ref.: #66794]	cardiolipin biosynthesis	42.86	3 of 7
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	41.18	7 of 17
[Ref.: #66794]	ascorbate metabolism	40.91	9 of 22
[Ref.: #66794]	glycine betaine biosynthesis	40	2 of 5
[Ref.: #66794]	phenol degradation	40	8 of 20
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	3-phenylpropionate degradation	40	6 of 15
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	40	2 of 5
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	dTDPLrhamnose biosynthesis	37.5	3 of 8
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	degradation of pentoses	35.71	10 of 28
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[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]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	aclacinomycin biosynthesis	28.57	2 of 7
[Ref.: #66794]	mevalonate metabolism	28.57	2 of 7
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	alginate biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of sugar alcohols	25	4 of 16
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
		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.: #21308]	Sample type/isolated from	marine surface sediment near a hydrothermal vent
[Ref.: #21308]	Geographic location (country and/or sea, region)	Kagoshima Bay, north of the Wakamiko crater (31° 41' 09'' N 130° 47' 124'' E, at 161 m water depth)
[Ref.: #21308]	Country	Japan
[Ref.: #21308]	Country ISO 3 Code	JPN
[Ref.: #21308]	Continent	Asia
[Ref.: #21308]	Geographic location	31.6858°/130.8180°
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Hydrothermal vent
#Environmental	#Aquatic	#Marine
#Environmental	#Aquatic	#Sediment
#Condition	#Thermophilic (>45°C)	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB794104 (>99% sequence identity) for Methyloceanibacter from Microbeatlas

Aquatic Samples	2801
Soil Samples	926
Animal Samples	106
Plant Samples	64
Total Samples	3897

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

[Ref.: #21308]

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.: #21308]	Methyloceanibacter caenitepidi gene for 16S ribosomal RNA, partial sequence	AB794104	1485	ENA	1384459 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Methyloceanibacter caenitepidi Gela4	GCA_000828475	complete	GenBank	1384459 tax ID	*
[Ref.: #66792]	Methyloceanibacter caenitepidi Gela4	1384459.3	complete	PATRIC	1384459 tax ID	*
[Ref.: #66792]	Methyloceanibacter caenitepidi Gela4	2630968843	complete	JGI IMG/M	1384459 tax ID	*

[Ref.: #21308]

GC-content

63.9 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: Methyloceanibacter caenitepidi Gela4 NCBI: GCA_000828475.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Methyloceanibacter caenitepidi Gela4 NCBI: GCA_000828475.1
[Ref.: #69480]	motile	no	79.93	no
[Ref.: #69480]	flagellated	no	95.873	no
[Ref.: #69480]	gram-positive	no	98.609	no
[Ref.: #69480]	anaerobic	no	94.771	no
[Ref.: #69480]	aerobic	yes	78.229	no
[Ref.: #69480]	halophile	no	55.5	no
[Ref.: #69480]	spore-forming	no	96.538	no
[Ref.: #69480]	glucose-util	yes	72.084	no
[Ref.: #69480]	thermophile	no	86.484	yes
[Ref.: #69480]	glucose-ferment	no	92.429	no

Availability in culture collections External links

[Ref.: #21308]

Culture collection no.

DSM 27242, NBRC 109540

[Ref.: #88578]

SI-ID 392242

Literature:

	Title	Authors	Journal	DOI	Year
Phylogeny	Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent.	Takeuchi M, Katayama T, Yamagishi T, Hanada S, Tamaki H, Kamagata Y, Oshima K, Hattori M, Marumo K, Nedachi M, Maeda H, Suwa Y, Sakata S	Int J Syst Evol Microbiol	10.1099/ijs.0.053397-0	2013	*
	Acetate excretion by a methanotroph, Methylocaldum marinum S8, under aerobic conditions.	Takeuchi M, Yoshioka H	Biosci Biotechnol Biochem	10.1093/bbb/zbab150	2021	*
	Correction: Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.	Takeuchi M, Ozaki H, Hiraoka S, Kamagata Y, Sakata S, Yoshioka H, Iwasaki W	PLoS One	10.1371/journal.pone.0251538	2021	*
	Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8.	Takeuchi M, Ozaki H, Hiraoka S, Kamagata Y, Sakata S, Yoshioka H, Iwasaki W	PLoS One	10.1371/journal.pone.0213535	2019	*

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 )

#21308

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 27242

#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 )

#88578

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-ID392242.1 )

* These data were automatically processed and therefore are not curated

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