Hyphomonas hirschiana (DSM 5152, ATCC 33886, CIP 106773)

Name: Hyphomonas hirschiana (DSM 5152, ATCC 33886, CIP 106773)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6203

Type strain

Strain Designation VP5

Culture col. no. DSM 5152 ATCC 33886 CIP 106773 VP5

NCBI tax ID(s) 81032

Special Collections DSMZ CIP

History DSMZ <- ATCC <- R.M. Wainer, VP5 <- J. Poindexter. CIP <- 2000, DSMZ <- ATCC <- R.M. Weiner: strain VP5 <- J. Poindexter

Links

Hyphomonas hirschiana VP5 is an obligate aerobe, Gram-negative, motile bacterium that was isolated from mussel bed in thermal vent.

Gram-negative motile rod-shaped obligate aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 46768

ATCC 33886,CIP 106773,DSM 5152

@ref 20215

Last LPSN update 2026-05-29 08:26:21

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Caulobacterales

Family Hyphomonadaceae

Genus Hyphomonas

Species Hyphomonas hirschiana

Full scientific name Hyphomonas hirschiana Weiner et al. 1985

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
119911	negative	rod-shaped
125439	negative		98.306
125438	negative		97.802

Pigmentation

@ref	Production	Name
119911		Pyoverdine

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1934	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
39514	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
119911	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
1934	positive	growth	30
39514	positive	growth	30
119911	positive	growth	25-37
119911	negative	growth	5
119911	negative	growth	10
119911	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
119911	obligate aerobe
125439	obligate aerobe	98.607

Spore formation

@ref	Spore formation	Confidence
125439		96.772

Halophily

@ref	Salt	Growth	Tested relation	Concentration
119911	NaCl	positive	growth	2 %
119911	NaCl		growth	0 %
119911	NaCl		growth	4 %
119911	NaCl		growth	6 %
119911	NaCl		growth	8 %
119911	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
119911	4853 ChEBI	esculin	+	hydrolysis
119911	17632 ChEBI	nitrate	+	reduction
119911	17632 ChEBI	nitrate	-	respiration
119911	16301 ChEBI	nitrite	-	reduction

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
119911	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119911	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119911	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
119911	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
119911	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119911	caseinase	-	3.4.21.50
119911	catalase	+	1.11.1.6
68382	cystine arylamidase	+	3.4.11.3	from API zym
119911	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
119911	gelatinase	-
119911	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119911	lipase	-
68382	lipase (C 14)	-		from API zym
119911	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119911	ornithine decarboxylase	-	4.1.1.17
119911	oxidase	+
119911	protease	-
68382	trypsin	+	3.4.21.4	from API zym
119911	tryptophan deaminase	-
119911	tween esterase	-
119911	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119911	-	+	+	+	-	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
119911	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Hydrothermal vent
#Host	#Invertebrates (Other)	#Mollusca
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1934	mussel bed in thermal vent
119911	Mussel bed in thermal vent	Galápagos Islands	Ecuador	ECU	Middle and South America

Taxonmaps

69479

Global distribution of 16S sequence AF082794 (>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
1934	1	Risk group (German classification) According to TRBA 466
119911	1	Risk group (French 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	SOAPdenovo v1.05 assembly for Hyphomonas hirschiana VP5	contig	GCA_000685255	1280951.3	2576861493	1280951	72.17

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Hyphomonas hirschiana strain DSM 5152 16S ribosomal RNA gene, partial sequence	KF863145	1419		81030
20218	Hyphomonas hirschiana 16S ribosomal RNA gene, partial sequence	AF082794	1334		81030

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: SOAPdenovo v1.05 assembly for Hyphomonas hirschiana VP5
NCBI: GCA_000685255

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.61	no
125439	gram_stain	BacteriaNetⓘ	negative	98.31	no
125439	motility	BacteriaNetⓘ	yes	50.05	no
125439	spore_formation	BacteriaNetⓘ	no	96.77	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hyphomonas hirschiana VP5
PATRIC: 1280951.3

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

Literature

References

#1934	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5152
#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 )
#39514	; Curators of the CIP;
#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) .
#68382	Automatically annotated from API zym .
#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 .
#119911	Collection of Institut Pasteur ; Curators of the CIP; CIP 106773
#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 )

Rate our new design

Content

About us