Hyphomicrobium facile (DSM 1565, ATCC 27485, NCIB 10342)

Name: Hyphomicrobium facile (DSM 1565, ATCC 27485, NCIB 10342)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 6181

Type strain

Strain Designation H-526

Culture col. no. DSM 1565 ATCC 27485 NCIB 10342 H-526

NCBI tax ID(s) 51670 582841

Special Collections DSMZ

Links

Hyphomicrobium facile H-526 is a mesophilic prokaryote that was isolated from soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 39026

ATCC 27485,DSM 1565,NCIB 10342,NCIMB 10342

@ref 20215

Last LPSN update 2025-12-16 09:48:15

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Hyphomicrobiaceae

Genus Hyphomicrobium

Species Hyphomicrobium facile

Full scientific name Hyphomicrobium facile corrig. Hirsch 1989

Synonyms (1)

Hyphomicrobium facilis

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	negative	97.833
125439	negative	99.6

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
823	HYPHOMICROBIUM MEDIUM (DSMZ Medium 162)		Medium recipe at MediaDive	Name: HYPHOMICROBIUM MEDIUM (DSMZ Medium 162) Composition: Methylamine hydrochloride 3.38 g/l Na2HPO4 2.13 g/l KH2PO4 1.36 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Yeast extract 0.1 g/l CaCl2 x 2 H2O 0.006 g/l FeSO4 x 7 H2O 0.003 g/l Na2MoO4 x 2 H2O 0.0015 g/l MnSO4 x H2O 0.001 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
823	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	99.1

Spore formation

@ref	Spore formation	Confidence
125439		98.4

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	ethanol fermentation	100	2 of 2
66794	ppGpp biosynthesis	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	valine metabolism	100	9 of 9
66794	methylglyoxal degradation	100	5 of 5
66794	biotin biosynthesis	100	4 of 4
66794	formaldehyde oxidation	100	3 of 3
66794	coenzyme A metabolism	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	suberin monomers biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	adipate degradation	100	2 of 2
66794	palmitate biosynthesis	100	22 of 22
66794	photosynthesis	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	pentose phosphate pathway	90.91	10 of 11
66794	threonine metabolism	90	9 of 10
66794	molybdenum cofactor biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	alanine metabolism	82.76	24 of 29
66794	vitamin B12 metabolism	82.35	28 of 34
66794	glutamate and glutamine metabolism	82.14	23 of 28
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	cellulose degradation	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	citric acid cycle	78.57	11 of 14
66794	tetrahydrofolate metabolism	78.57	11 of 14
66794	lipid A biosynthesis	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	leucine metabolism	76.92	10 of 13
66794	purine metabolism	75.53	71 of 94
66794	CMP-KDO biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	acetate fermentation	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	vitamin B6 metabolism	72.73	8 of 11
66794	proline metabolism	72.73	8 of 11
66794	heme metabolism	71.43	10 of 14
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	ubiquinone biosynthesis	71.43	5 of 7
66794	glycolysis	70.59	12 of 17
66794	vitamin B1 metabolism	69.23	9 of 13
66794	histidine metabolism	68.97	20 of 29
66794	serine metabolism	66.67	6 of 9
66794	methane metabolism	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	octane oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	d-mannose degradation	66.67	6 of 9
66794	cyanate degradation	66.67	2 of 3
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	non-pathway related	65.79	25 of 38
66794	lipid metabolism	64.52	20 of 31
66794	pyrimidine metabolism	64.44	29 of 45
66794	arginine metabolism	62.5	15 of 24
66794	isoleucine metabolism	62.5	5 of 8
66794	urea cycle	61.54	8 of 13
66794	phosphatidylethanolamine bioynthesis	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	phenylacetate degradation (aerobic)	60	3 of 5
66794	methanofuran biosynthesis	60	3 of 5
66794	Entner Doudoroff pathway	60	6 of 10
66794	lipoate biosynthesis	60	3 of 5
66794	propionate fermentation	60	6 of 10
66794	methanogenesis from CO2	58.33	7 of 12
66794	glutathione metabolism	57.14	8 of 14
66794	tyrosine metabolism	57.14	8 of 14
66794	propanol degradation	57.14	4 of 7
66794	degradation of sugar alcohols	56.25	9 of 16
66794	lysine metabolism	54.76	23 of 42
66794	sulfate reduction	53.85	7 of 13
66794	isoprenoid biosynthesis	53.85	14 of 26
66794	oxidative phosphorylation	52.75	48 of 91
66794	polyamine pathway	52.17	12 of 23
66794	pantothenate biosynthesis	50	3 of 6
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	aminopropanol phosphate biosynthesis	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	ketogluconate metabolism	50	4 of 8
66794	glycogen biosynthesis	50	2 of 4
66794	3-phenylpropionate degradation	46.67	7 of 15
66794	metabolism of disaccharids	45.45	5 of 11
66794	phenol degradation	45	9 of 20
66794	4-hydroxymandelate degradation	44.44	4 of 9
66794	nitrate assimilation	44.44	4 of 9
66794	benzoyl-CoA degradation	42.86	3 of 7
66794	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
66794	factor 420 biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	glycogen metabolism	40	2 of 5
66794	O-antigen biosynthesis	40	2 of 5
66794	arachidonic acid metabolism	38.89	7 of 18
66794	degradation of hexoses	38.89	7 of 18
66794	carnitine metabolism	37.5	3 of 8
66794	carotenoid biosynthesis	36.36	8 of 22
66794	cholesterol biosynthesis	36.36	4 of 11
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	allantoin degradation	33.33	3 of 9
66794	androgen and estrogen metabolism	31.25	5 of 16
66794	coenzyme M biosynthesis	30	3 of 10
66794	degradation of pentoses	28.57	8 of 28
66794	chlorophyll metabolism	27.78	5 of 18
66794	ascorbate metabolism	27.27	6 of 22
66794	cyclohexanol degradation	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	bile acid biosynthesis, neutral pathway	23.53	4 of 17

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
823	soil	New Hampshire	USA	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence Y14309 (>99% sequence identity) for Hyphomicrobium from Microbeatlas

Aquatic Samples	115
Soil Samples	239
Animal Samples	98
Plant Samples	98
Total Samples	550

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
823	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	IMG-taxon 2636416034 annotated assembly for Hyphomicrobium facile DSM 1565	contig	GCA_900116175	51670.3	2636416034	51670	76.5

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
823	Hyphomicrobium facile subsp. facile partial 16S rRNA gene, type strain IFAM H-526T	Y14309	1423		582841

GC content

823

GC-content (mol%)60.2

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Hyphomicrobium facile DSM 1565
NCBI: GCA_900116175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.40	no
125439	motility	BacteriaNetⓘ	yes	72.80	no
125439	gram_stain	BacteriaNetⓘ	negative	99.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Hyphomicrobium facile strain DSM 1565
PATRIC: 51670.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	97.83	no
125438	anaerobic	anaerobicⓘ	no	88.23	no
125438	spore-forming	spore-formingⓘ	no	85.30	no
125438	aerobic	aerobicⓘ	yes	85.18	no
125438	thermophilic	thermophileⓘ	no	97.03	yes
125438	flagellated	motile2+ⓘ	yes	70.12	no

Literature

References

#823	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 1565
#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 )
#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 .
#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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