Aminivibrio pyruvatiphilus (DSM 25964, JCM 18417, 4F6E)

Name: Aminivibrio pyruvatiphilus (DSM 25964, JCM 18417, 4F6E)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 24744

Type strain

Strain Designation 4F6E

Culture col. no. DSM 25964 JCM 18417 4F6E

NCBI tax ID(s) 1005740

Special Collections DSMZ JCM Literature strains

History <- A. Tonouchi, Faculty Agriculture and Life Sci., Hirosaki University, Hirosaki, Japan; 4F6E <- T. Honda; {2010} A. Tonouchi 4F6E.

Links

Aminivibrio pyruvatiphilus 4F6E is an anaerobe, Gram-negative, motile bacterium that was isolated from soil from a rice paddy field.

Gram-negative motile rod-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 407815

JCM 18417,DSM 25964

@ref 20215

Last LPSN update 2026-02-09 11:24:03

Domain Bacteria

Phylum Synergistota

Class Synergistia

Order Synergistales

Family Synergistaceae

Genus Aminivibrio

Species Aminivibrio pyruvatiphilus

Full scientific name Aminivibrio pyruvatiphilus Honda et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
31105	negative	2.25 µm	0.8 µm	rod-shaped
125439	negative					94.3

Colony morphology

21278

Incubation period3-7 days

Pigmentation

31105

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
21278	ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)		Medium recipe at MediaDive	Name: ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503; with strain-specific modifications) Composition: Na2CO3 1.49551 g/l NaCl 0.997008 g/l KCl 0.498505 g/l Na-pyruvate 0.498504 g/l MgCl2 x 6 H2O 0.398803 g/l Na2S x 9 H2O 0.299103 g/l NH4Cl 0.249252 g/l KH2PO4 0.199402 g/l CaCl2 x 2 H2O 0.149552 g/l HCl 0.00249252 g/l FeCl2 x 4 H2O 0.00149551 g/l Sodium resazurin 0.000498505 g/l NaOH 0.000498504 g/l Pyridoxine hydrochloride 0.000299103 g/l Nicotinic acid 0.000199402 g/l Thiamine-HCl x 2 H2O 0.000199402 g/l CoCl2 x 6 H2O 0.000189432 g/l Calcium pantothenate 9.97009e-05 g/l MnCl2 x 4 H2O 9.97009e-05 g/l Vitamin B12 9.97009e-05 g/l p-Aminobenzoic acid 7.97607e-05 g/l ZnCl2 6.97906e-05 g/l Na2MoO4 x 2 H2O 3.58923e-05 g/l NiCl2 x 6 H2O 2.39282e-05 g/l D-(+)-biotin 1.99402e-05 g/l H3BO3 5.98205e-06 g/l Na2WO4 x 2 H2O 3.98804e-06 g/l Na2SeO3 x 5 H2O 2.99103e-06 g/l CuCl2 x 2 H2O 1.99402e-06 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
21278	positive	growth	37
31105	positive	growth	20-42
31105	positive	optimum	38.5
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
31105	positive	optimum	7.3
31105	positive	growth	6.4-8.4

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
21278	anaerobe
31105	anaerobe
125438	anaerobe	93.853
125439	anaerobe	99.5

Spore formation

@ref	Spore formation	Confidence
31105
125439		90.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31105	NaCl	positive	growth	0-1.5 %

Observation

31105

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31105	16449 ChEBI	alanine	+	carbon source
31105	22653 ChEBI	asparagine	+	carbon source
31105	35391 ChEBI	aspartate	+	carbon source
31105	16947 ChEBI	citrate	+	carbon source
31105	29987 ChEBI	glutamate	+	carbon source
31105	15428 ChEBI	glycine	+	carbon source
31105	27570 ChEBI	histidine	+	carbon source
31105	25017 ChEBI	leucine	+	carbon source
31105	15361 ChEBI	pyruvate	+	carbon source
31105	17822 ChEBI	serine	+	carbon source

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	ppGpp biosynthesis	100	4 of 4
66794	L-lactaldehyde degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	CMP-KDO biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	aminopropanol phosphate biosynthesis	100	2 of 2
66794	reductive acetyl coenzyme A pathway	100	7 of 7
66794	gluconeogenesis	100	8 of 8
66794	ribulose monophosphate pathway	100	2 of 2
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	isoleucine metabolism	100	8 of 8
66794	sulfopterin metabolism	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	C4 and CAM-carbon fixation	100	8 of 8
66794	suberin monomers biosynthesis	100	2 of 2
66794	palmitate biosynthesis	90.91	20 of 22
66794	threonine metabolism	90	9 of 10
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	citric acid cycle	85.71	12 of 14
66794	hydrogen production	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	starch degradation	80	8 of 10
66794	propionate fermentation	80	8 of 10
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	NAD metabolism	77.78	14 of 18
66794	vitamin B1 metabolism	76.92	10 of 13
66794	urea cycle	76.92	10 of 13
66794	degradation of sugar acids	76	19 of 25
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	glutamate and glutamine metabolism	75	21 of 28
66794	butanoate fermentation	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	purine metabolism	74.47	70 of 94
66794	vitamin B12 metabolism	73.53	25 of 34
66794	flavin biosynthesis	73.33	11 of 15
66794	histidine metabolism	72.41	21 of 29
66794	alanine metabolism	72.41	21 of 29
66794	photosynthesis	71.43	10 of 14
66794	propanol degradation	71.43	5 of 7
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	pyrimidine metabolism	71.11	32 of 45
66794	glycolysis	70.59	12 of 17
66794	Entner Doudoroff pathway	70	7 of 10
66794	phenylalanine metabolism	69.23	9 of 13
66794	selenocysteine biosynthesis	66.67	4 of 6
66794	formaldehyde oxidation	66.67	2 of 3
66794	lipid A biosynthesis	66.67	6 of 9
66794	d-mannose degradation	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	heme metabolism	64.29	9 of 14
66794	pentose phosphate pathway	63.64	7 of 11
66794	tryptophan metabolism	63.16	24 of 38
66794	degradation of sugar alcohols	62.5	10 of 16
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	leucine metabolism	61.54	8 of 13
66794	glycine betaine biosynthesis	60	3 of 5
66794	glycine metabolism	60	6 of 10
66794	factor 420 biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	glycogen metabolism	60	3 of 5
66794	gallate degradation	60	3 of 5
66794	lysine metabolism	59.52	25 of 42
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	tyrosine metabolism	57.14	8 of 14
66794	tetrahydrofolate metabolism	57.14	8 of 14
66794	oxidative phosphorylation	56.04	51 of 91
66794	cysteine metabolism	55.56	10 of 18
66794	CO2 fixation in Crenarchaeota	55.56	5 of 9
66794	adipate degradation	50	1 of 2
66794	degradation of pentoses	50	14 of 28
66794	coenzyme M biosynthesis	50	5 of 10
66794	pantothenate biosynthesis	50	3 of 6
66794	ethanol fermentation	50	1 of 2
66794	phenylmercury acetate degradation	50	1 of 2
66794	non-pathway related	50	19 of 38
66794	quinate degradation	50	1 of 2
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	lactate fermentation	50	2 of 4
66794	toluene degradation	50	2 of 4
66794	degradation of hexoses	50	9 of 18
66794	methionine metabolism	46.15	12 of 26
66794	proline metabolism	45.45	5 of 11
66794	metabolism of disaccharids	45.45	5 of 11
66794	lipid metabolism	45.16	14 of 31
66794	phenol degradation	45	9 of 20
66794	allantoin degradation	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	glutathione metabolism	42.86	6 of 14
66794	bacilysin biosynthesis	40	2 of 5
66794	lipoate biosynthesis	40	2 of 5
66794	myo-inositol biosynthesis	40	4 of 10
66794	ethylmalonyl-CoA pathway	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	4-hydroxyphenylacetate degradation	40	4 of 10
66794	d-xylose degradation	36.36	4 of 11
66794	vitamin B6 metabolism	36.36	4 of 11
66794	isoprenoid biosynthesis	34.62	9 of 26
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	cyanate degradation	33.33	1 of 3
66794	octane oxidation	33.33	1 of 3
66794	3-phenylpropionate degradation	33.33	5 of 15
66794	sphingosine metabolism	33.33	2 of 6
66794	ascorbate metabolism	31.82	7 of 22
66794	sulfate reduction	30.77	4 of 13
66794	polyamine pathway	30.43	7 of 23
66794	arachidonic acid metabolism	27.78	5 of 18
66794	methanogenesis from CO2	25	3 of 12
66794	catecholamine biosynthesis	25	1 of 4
66794	cyclohexanol degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	carnitine metabolism	25	2 of 8
66794	androgen and estrogen metabolism	25	4 of 16
66794	phosphatidylethanolamine bioynthesis	23.08	3 of 13
66794	4-hydroxymandelate degradation	22.22	2 of 9

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
21278	soil from a rice paddy field	Aomori Prefecture, Asino, Kanagi, Goshogawara city	Japan	JPN	Asia
67770	Soil of a rice field in Japan

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
21278	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM436681v1 assembly for Aminivibrio pyruvatiphilus DSM 25964	scaffold	GCA_004366815	1005740.3	2756170234	1005740	60.87

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
21278	Aminivibrio pyruvatiphilus gene for 16S ribosomal RNA, partial sequence	AB623229	1441		1005740

GC content

@ref	GC-content (mol%)	Method
21278	61.9	high performance liquid chromatography (HPLC)
31105	61.9

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Aminivibrio pyruvatiphilus DSM 25964
NCBI: GCA_004366815

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	90.90	no
125439	motility	BacteriaNetⓘ	no	53.30	no
125439	gram_stain	BacteriaNetⓘ	negative	94.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Aminivibrio pyruvatiphilus strain DSM 25964
PATRIC: 1005740.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	76.96	yes
125438	anaerobic	anaerobicⓘ	yes	93.85	no
125438	spore-forming	spore-formingⓘ	no	79.30	yes
125438	aerobic	aerobicⓘ	no	92.50	yes
125438	thermophilic	thermophileⓘ	no	72.73	yes
125438	flagellated	motile2+ⓘ	yes	61.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Identification of a Putative CodY Regulon in the Gram-Negative Phylum Synergistetes.	Geng J, Luo S, Shieh HR, Wang HY, Hu S, Chen YM.	Int J Mol Sci	10.3390/ijms23147911	2022
Phylogeny	Aminivibrio pyruvatiphilus gen. nov., sp. nov., an anaerobic, amino-acid-degrading bacterium from soil of a Japanese rice field.	Honda T, Fujita T, Tonouchi A	Int J Syst Evol Microbiol	10.1099/ijs.0.052225-0	2013

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 )
#21278	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25964
#27434	IJSEM 3679 2013 ( DOI 10.1099/ijs.0.052225-0 , PubMed 23625260 )
#31105	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 #27434
#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;
#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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Aminivibrio pyruvatiphilus (DSM 25964, JCM 18417, 4F6E)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_004366815

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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