Hyphomonas neptunia (DSM 5154, ATCC 15444, IFAM LE670)

Name: Hyphomonas neptunia (DSM 5154, ATCC 15444, IFAM LE670)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6205

Type strain

Strain Designation 14-15

Culture col. no. DSM 5154 ATCC 15444 IFAM LE670 14-15

NCBI tax ID(s) 228405 81032

Special Collections DSMZ

History <- ATCC <- E. Leifson, 14-15 (Hyphomicrobium neptunium)

Links

Hyphomonas neptunia 14-15 is a bacterium that was isolated from seawater.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 36374

ATCC 15444,DSM 5154,NCIMB 2023,IFO 14232,NBRC 14232,BCRC 10690,CCRC 10690

@ref 20215

Last LPSN update 2026-02-09 11:19:09

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Caulobacterales

Family Hyphomonadaceae

Genus Hyphomonas

Species Hyphomonas neptunia

Full scientific name Hyphomonas neptunia corrig. (Leifson 1964) Moore et al. 1984

Synonyms (2)

Hyphomonas neptunium
Hyphomicrobium neptunium

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.802
125439	negative	98.1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1936	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)		Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
1936	positive	growth	26

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	95.5

Spore formation

@ref	Spore formation	Confidence
125439		90.4

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	gluconeogenesis	100	8 of 8
66794	ethanol fermentation	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	CMP-KDO biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	L-lactaldehyde degradation	100	3 of 3
66794	cardiolipin biosynthesis	100	7 of 7
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	Entner Doudoroff pathway	100	10 of 10
66794	kanosamine biosynthesis II	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	methylglyoxal degradation	100	5 of 5
66794	valine metabolism	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	ppGpp biosynthesis	100	4 of 4
66794	folate polyglutamylation	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	taurine degradation	100	1 of 1
66794	palmitate biosynthesis	95.45	21 of 22
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	leucine metabolism	92.31	12 of 13
66794	phenylalanine metabolism	92.31	12 of 13
66794	threonine metabolism	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	CO2 fixation in Crenarchaeota	88.89	8 of 9
66794	isoleucine metabolism	87.5	7 of 8
66794	propanol degradation	85.71	6 of 7
66794	photosynthesis	85.71	12 of 14
66794	citric acid cycle	85.71	12 of 14
66794	NAD metabolism	83.33	15 of 18
66794	alanine metabolism	82.76	24 of 29
66794	peptidoglycan biosynthesis	80	12 of 15
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	phenylacetate degradation (aerobic)	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	purine metabolism	78.72	74 of 94
66794	tyrosine metabolism	78.57	11 of 14
66794	serine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	vitamin B1 metabolism	76.92	10 of 13
66794	histidine metabolism	75.86	22 of 29
66794	glutamate and glutamine metabolism	75	21 of 28
66794	lactate fermentation	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	flavin biosynthesis	73.33	11 of 15
66794	proline metabolism	72.73	8 of 11
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glutathione metabolism	71.43	10 of 14
66794	heme metabolism	71.43	10 of 14
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	methionine metabolism	69.23	18 of 26
66794	lipid metabolism	67.74	21 of 31
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	IAA biosynthesis	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	acetoin degradation	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	non-pathway related	65.79	25 of 38
66794	tryptophan metabolism	65.79	25 of 38
66794	isoprenoid biosynthesis	65.38	17 of 26
66794	lysine metabolism	64.29	27 of 42
66794	pentose phosphate pathway	63.64	7 of 11
66794	vitamin B6 metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	4-hydroxyphenylacetate degradation	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	cellulose degradation	60	3 of 5
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	degradation of sugar alcohols	56.25	9 of 16
66794	androgen and estrogen metabolism	56.25	9 of 16
66794	cysteine metabolism	55.56	10 of 18
66794	sulfate reduction	53.85	7 of 13
66794	urea cycle	53.85	7 of 13
66794	catecholamine biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	butanoate fermentation	50	2 of 4
66794	cyclohexanol degradation	50	2 of 4
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	toluene degradation	50	2 of 4
66794	bile acid biosynthesis, neutral pathway	47.06	8 of 17
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	degradation of pentoses	46.43	13 of 28
66794	metabolism of disaccharids	45.45	5 of 11
66794	degradation of hexoses	44.44	8 of 18
66794	arachidonic acid metabolism	44.44	8 of 18
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	vitamin B12 metabolism	44.12	15 of 34
66794	degradation of sugar acids	44	11 of 25
66794	polyamine pathway	43.48	10 of 23
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	reductive acetyl coenzyme A pathway	42.86	3 of 7
66794	oxidative phosphorylation	42.86	39 of 91
66794	gallate degradation	40	2 of 5
66794	glycine betaine biosynthesis	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	phenol degradation	40	8 of 20
66794	glycine metabolism	40	4 of 10
66794	creatinine degradation	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	carnitine metabolism	37.5	3 of 8
66794	ascorbate metabolism	36.36	8 of 22
66794	d-xylose degradation	36.36	4 of 11
66794	sulfoquinovose degradation	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	sphingosine metabolism	33.33	2 of 6
66794	enterobactin biosynthesis	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	phosphatidylethanolamine bioynthesis	30.77	4 of 13
66794	coenzyme M biosynthesis	30	3 of 10
66794	chlorophyll metabolism	27.78	5 of 18
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	glycogen biosynthesis	25	1 of 4
66794	vitamin E metabolism	25	1 of 4
66794	carotenoid biosynthesis	22.73	5 of 22
66794	daunorubicin biosynthesis	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
1936	seawater	Spain	ESP	Europe

Taxonmaps

69479

Global distribution of 16S sequence AF082798 (>99% sequence identity) for Hyphomonas from Microbeatlas

Aquatic Samples	3479
Soil Samples	403
Animal Samples	324
Plant Samples	59
Total Samples	4265

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1936	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1302v1 assembly for Hyphomonas neptunium ATCC 15444	complete	GCA_000013025	228405.9	637000135	228405	99.57

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Hyphomonas neptunium 16S ribosomal RNA gene, partial sequence	AF082798	1316	81032
20218	Hyphomonas neptunium gene for 16S rRNA, partial sequence, strain: NBRC 14232	AB680593	1380	81032
1936	Hyphomonas neptunium strain DSM 5154 16S ribosomal RNA gene, partial sequence	KF863147	1419	81032
124043	Hyphomonas neptunium strain ATCC 15444 16S ribosomal RNA gene, partial sequence.	OR841470	1318	81032

GC content

@ref	GC-content (mol%)	Method
1936	61.9	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hyphomonas neptunium ATCC 15444
PATRIC: 228405.9

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	90.40	no
125439	motility	BacteriaNetⓘ	yes	57.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	95.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hyphomonas neptunium ATCC 15444 ATCC 15444
NCBI: GCA_000013025.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.80	no
125438	anaerobic	anaerobicⓘ	no	97.87	no
125438	aerobic	aerobicⓘ	yes	87.99	no
125438	spore-forming	spore-formingⓘ	no	88.91	no
125438	thermophilic	thermophileⓘ	no	98.64	yes
125438	flagellated	motile2+ⓘ	yes	54.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Genomic analysis reveals versatile organisms for quorum quenching enzymes: acyl-homoserine lactone-acylase and -lactonase.	Kalia VC, Raju SC, Purohit HJ	Open Microbiol J	10.2174/1874285801105010001	2011
Enzymology	[An oxidation enzyme for hydrogen sulfide from Hyphomicrobium neptunium ATCC15444].	Sasahira T, Matsui K, Arai T	Yakugaku Zasshi	10.1248/yakushi1947.113.1_79	1993
	[Oxidation of hydrogen sulfide with cell-free extract of Hyphomicrobium neptunium ATCC 15444].	Sasahira T, Matsui K, Arai T	Yakugaku Zasshi	10.1248/yakushi1947.112.5_332	1992
	Development of Defined, Minimal, and Complete Media for the Growth of Hyphomicrobium neptunium.	Havenner JA, McCardell BA, Weiner RM	Appl Environ Microbiol	10.1128/aem.38.1.18-23.1979	1979
	Cell wall composition of Hypomicrobium species.	Jones HE, Hirsch P	J Bacteriol	10.1128/jb.96.4.1037-1041.1968	1968

References

#1936	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5154
#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 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Hyphomonas neptunia (DSM 5154, ATCC 15444, IFAM LE670)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000013025

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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