Name: Aminivibrio pyruvatiphilus 4F6E
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24744

Type strain:

Species: Aminivibrio pyruvatiphilus

Strain Designation: 4F6E

Culture col. no.: DSM 25964, JCM 18417

Strain history: A. Tonouchi 4F6E.

NCBI tax ID(s): 1005740 (species)

SI-ID 407815

DSM 25964

Special Collections

Section

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
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	*Synergistota*
	Class	*Synergistia*
	Order	*Synergistales*
	Family	*Synergistaceae*
	Genus	*Aminivibrio*
	Species	**Aminivibrio pyruvatiphilus**
	Full Scientific Name (LPSN)	Aminivibrio pyruvatiphilus Honda et al. 2013

Information on morphological and physiological properties Morphology

[Ref.: #31105]	Gram stain	negative

[Ref.: #31105]	Cell length	2.25 µm

[Ref.: #31105]	Cell width	0.8 µm

[Ref.: #31105]	Cell shape	rod-shaped

[Ref.: #31105]	Motility	yes

[Ref.: #21278]

Incubation period

3-7 days

[Ref.: #31105]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21278]

Culture medium

ANAEROBIC FRESHWATER (FWM) MEDIUM (DSMZ Medium 503)

[Ref.: #21278]

Culture medium growth

[Ref.: #21278]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21278]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21278]	growth	37 °C
[Ref.: #31105]	growth	20-42 °C
[Ref.: #31105]	optimum	38.5 °C
[Ref.: #67770]	growth	37 °C

	pH	Kind of pH		pH
[Ref.: #31105]			optimum	7.3
[Ref.: #31105]			growth	6.4-8.4

Information on physiology and metabolism Physiology and metabolism

[Ref.: #21278]	Oxygen tolerance	anaerobe
[Ref.: #31105]	Oxygen tolerance	anaerobe
[Ref.: #69480]	Oxygen tolerance	anaerobe Confidence in %93.853

[Ref.: #31105]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31105]		NaCl		growth	0-1.5	%

[Ref.: #31105]

Observation

aggregates in clumps

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31105]	alanine ChEBI	+	carbon source
[Ref.: #31105]	asparagine ChEBI	+	carbon source
[Ref.: #31105]	aspartate ChEBI	+	carbon source
[Ref.: #31105]	citrate ChEBI	+	carbon source
[Ref.: #31105]	glutamate ChEBI	+	carbon source
[Ref.: #31105]	glycine ChEBI	+	carbon source
[Ref.: #31105]	histidine ChEBI	+	carbon source
[Ref.: #31105]	leucine ChEBI	+	carbon source
[Ref.: #31105]	pyruvate ChEBI	+	carbon source
[Ref.: #31105]	serine ChEBI	+	carbon source

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	CMP-KDO biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	aminopropanol phosphate biosynthesis	100	2 of 2
[Ref.: #66794]	reductive acetyl coenzyme A pathway	100	7 of 7
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	ribulose monophosphate pathway	100	2 of 2
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	isoleucine metabolism	100	8 of 8
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	palmitate biosynthesis	90.91	20 of 22
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	valine metabolism	88.89	8 of 9
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	hydrogen production	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	molybdenum cofactor biosynthesis	77.78	7 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	urea cycle	76.92	10 of 13
[Ref.: #66794]	degradation of sugar acids	76	19 of 25
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	glutamate and glutamine metabolism	75	21 of 28
[Ref.: #66794]	butanoate fermentation	75	3 of 4
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	purine metabolism	74.47	70 of 94
[Ref.: #66794]	vitamin B12 metabolism	73.53	25 of 34
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	histidine metabolism	72.41	21 of 29
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	photosynthesis	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	pyrimidine metabolism	71.11	32 of 45
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	Entner Doudoroff pathway	70	7 of 10
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	lipid A biosynthesis	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	heme metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	degradation of sugar alcohols	62.5	10 of 16
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	arginine metabolism	62.5	15 of 24
[Ref.: #66794]	leucine metabolism	61.54	8 of 13
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	glycine metabolism	60	6 of 10
[Ref.: #66794]	factor 420 biosynthesis	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	lysine metabolism	59.52	25 of 42
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	tyrosine metabolism	57.14	8 of 14
[Ref.: #66794]	tetrahydrofolate metabolism	57.14	8 of 14
[Ref.: #66794]	oxidative phosphorylation	56.04	51 of 91
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	CO2 fixation in Crenarchaeota	55.56	5 of 9
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	degradation of pentoses	50	14 of 28
[Ref.: #66794]	coenzyme M biosynthesis	50	5 of 10
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	non-pathway related	50	19 of 38
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	methionine metabolism	46.15	12 of 26
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	metabolism of disaccharids	45.45	5 of 11
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	phenol degradation	45	9 of 20
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	ubiquinone biosynthesis	42.86	3 of 7
[Ref.: #66794]	glutathione metabolism	42.86	6 of 14
[Ref.: #66794]	bacilysin biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	ethylmalonyl-CoA pathway	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	vitamin B6 metabolism	36.36	4 of 11
[Ref.: #66794]	isoprenoid biosynthesis	34.62	9 of 26
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	sulfate reduction	30.77	4 of 13
[Ref.: #66794]	polyamine pathway	30.43	7 of 23
[Ref.: #66794]	arachidonic acid metabolism	27.78	5 of 18
[Ref.: #66794]	methanogenesis from CO2	25	3 of 12
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	biotin biosynthesis	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	23.08	3 of 13
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
		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.: #21278]	Sample type/isolated from	soil from a rice paddy field
[Ref.: #21278]	Geographic location (country and/or sea, region)	Aomori Prefecture, Asino, Kanagi, Goshogawara city
[Ref.: #21278]	Country	Japan
[Ref.: #21278]	Country ISO 3 Code	JPN
[Ref.: #21278]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Soil of a rice field in Japan
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #21278]

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.: #21278]	Aminivibrio pyruvatiphilus gene for 16S ribosomal RNA, partial sequence	AB623229	1441	GenBank ENA	1005740 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Aminivibrio pyruvatiphilus DSM 25964	GCA_004366815	scaffold	GenBank ENA	1005740 tax ID
[Ref.: #66792]	Aminivibrio pyruvatiphilus strain DSM 25964	1005740.3	wgs	PATRIC	1005740 tax ID	*
[Ref.: #66792]	Aminivibrio pyruvatiphilus DSM 25964	2756170234	draft	JGI IMG/M	1005740 tax ID	*

[Ref.: #21278]	GC-content	61.9 mol%	high performance liquid chromatography (HPLC)
[Ref.: #31105]	GC-content	61.9 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Aminivibrio pyruvatiphilus DSM 25964 NCBI: GCA_004366815.1
[Ref.: #69481]	spore-forming	spore-formingⓘ	no	100	no

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Aminivibrio pyruvatiphilus strain DSM 25964 PATRIC: 1005740.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	76.957	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	yes	93.853	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	79.3	yes
[Ref.: #69480]	aerobic	aerobicⓘ	no	92.502	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	72.729	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	61.297	no

Availability in culture collections External links

[Ref.: #21278]

Culture collection no.

DSM 25964, JCM 18417

[Ref.: #88572]

SI-ID 407815

Literature:

Topic	Title	Authors	Journal	DOI	Year
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

#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 (see below)

#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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#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 )

#88572

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-ID407815.1 )

#27434

IJSEM 3679 2013 ( DOI 10.1099/ijs.0.052225-0 , PubMed 23625260 )

* These data were automatically processed and therefore are not curated

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Aminivibrio pyruvatiphilus DSM 25964

Aminivibrio pyruvatiphilus strain DSM 25964

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