Name: Tetragenococcus halophilus subsp. halophilus DSM 20338
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 5254

Type strain:

Species: Tetragenococcus halophilus subsp. halophilus

Culture col. no.: DSM 20338, IFO 12172, NBRC 12172, NCDO 1872, NCIB 9735, JCM 20259, IAM 1693, NCIMB 9735, NISL 7117

Strain history: IAM 1693 <-- K. Sakaguchi d-6 ("Pediococcus soyae").

NCBI tax ID(s): 1513897 (subspecies)

SI-ID 1239

DSM 20338, NCDO 1872, NCIB 9735, NCIMB 9735, IAM1693, IFO12172, KCTC 3720, NBRC 12172, BCRC 12576, CCRC 12576, NCFB 1872, JCM 20259

Other strains from Tetragenococcus halophilus subsp. halophilus

T. halophilus subsp. halophilus T11, DSM 20339, ATCC 33315, IAM ... (type strain)
T. halophilus subsp. halophilus dl 2, TVA 7-16, DSM 20337, JCM ...
T. halophilus subsp. halophilus JCM 2015
T. halophilus subsp. halophilus JCM 20245, ATCC 13621, IAM 1673

Section

Tetragenococcus halophilus subsp. halophilus DSM 20338 is a spore-forming, mesophilic bacterium that was isolated from Soy sauce brewing mashes.

spore-forming
mesophilic
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	*Bacillota*
	Class	*Bacilli*
	Order	*Lactobacillales*
	Family	*Enterococcaceae*
	Genus	*Tetragenococcus*
	Species	**Tetragenococcus halophilus subsp. halophilus**
	Full Scientific Name (LPSN)	Tetragenococcus halophilus subsp. halophilus (Mees 1934) Justé et al. 2012

Information on morphological and physiological properties Morphology

[Ref.: #69480]	Gram stain	positive Confidence in %99.999

[Ref.: #69480]	Motility	no Confidence in %94.266

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8729]

Culture medium

PEDIOCOCCUS HALOPHILUS MEDIUM (DSMZ Medium 227)

[Ref.: #8729]

Culture medium growth

[Ref.: #8729]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8729]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #8729]			growth	30 °C
[Ref.: #67770]			growth	30 °C

[Ref.: #8729]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #69481]	Ability of spore formation	yes Confidence in %92
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.94

[Ref.: #8729]	Murein short key	A11.31
[Ref.: #8729]	Murein types	A4alpha L-Lys-D-Asp

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	C4 and CAM-carbon fixation	100	8 of 8
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	acetoin degradation	100	3 of 3
[Ref.: #66794]	aspartate and asparagine metabolism	100	9 of 9
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	gluconeogenesis	87.5	7 of 8
[Ref.: #66794]	degradation of sugar alcohols	87.5	14 of 16
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	vitamin B1 metabolism	84.62	11 of 13
[Ref.: #66794]	pyrimidine metabolism	82.22	37 of 45
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	glycine betaine biosynthesis	80	4 of 5
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	75.53	71 of 94
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	ppGpp biosynthesis	75	3 of 4
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	reductive acetyl coenzyme A pathway	71.43	5 of 7
[Ref.: #66794]	glutathione metabolism	71.43	10 of 14
[Ref.: #66794]	glycolysis	70.59	12 of 17
[Ref.: #66794]	starch degradation	70	7 of 10
[Ref.: #66794]	formaldehyde oxidation	66.67	2 of 3
[Ref.: #66794]	NAD metabolism	66.67	12 of 18
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	selenocysteine biosynthesis	66.67	4 of 6
[Ref.: #66794]	valine metabolism	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	sphingosine metabolism	66.67	4 of 6
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	non-pathway related	63.16	24 of 38
[Ref.: #66794]	isoleucine metabolism	62.5	5 of 8
[Ref.: #66794]	oxidative phosphorylation	61.54	56 of 91
[Ref.: #66794]	degradation of pentoses	60.71	17 of 28
[Ref.: #66794]	glutamate and glutamine metabolism	60.71	17 of 28
[Ref.: #66794]	glycogen metabolism	60	3 of 5
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	methionine metabolism	57.69	15 of 26
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	cysteine metabolism	50	9 of 18
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	50	4 of 8
[Ref.: #66794]	Entner Doudoroff pathway	50	5 of 10
[Ref.: #66794]	CMP-KDO biosynthesis	50	2 of 4
[Ref.: #66794]	sulfopterin metabolism	50	2 of 4
[Ref.: #66794]	degradation of hexoses	50	9 of 18
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	citric acid cycle	50	7 of 14
[Ref.: #66794]	adipate degradation	50	1 of 2
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	leucine metabolism	46.15	6 of 13
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	arginine metabolism	45.83	11 of 24
[Ref.: #66794]	vitamin B6 metabolism	45.45	5 of 11
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	mevalonate metabolism	42.86	3 of 7
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	cellulose degradation	40	2 of 5
[Ref.: #66794]	tryptophan metabolism	36.84	14 of 38
[Ref.: #66794]	d-xylose degradation	36.36	4 of 11
[Ref.: #66794]	tetrahydrofolate metabolism	35.71	5 of 14
[Ref.: #66794]	tyrosine metabolism	35.71	5 of 14
[Ref.: #66794]	lipid metabolism	35.48	11 of 31
[Ref.: #66794]	histidine metabolism	34.48	10 of 29
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	flavin biosynthesis	33.33	5 of 15
[Ref.: #66794]	cyanate degradation	33.33	1 of 3
[Ref.: #66794]	arachidonic acid metabolism	33.33	6 of 18
[Ref.: #66794]	lipid A biosynthesis	33.33	3 of 9
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	degradation of sugar acids	32	8 of 25
[Ref.: #66794]	ascorbate metabolism	31.82	7 of 22
[Ref.: #66794]	androgen and estrogen metabolism	31.25	5 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	carotenoid biosynthesis	27.27	6 of 22
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	sulfate reduction	23.08	3 of 13
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
[Ref.: #66794]	4-hydroxymandelate degradation	22.22	2 of 9
[Ref.: #66794]	allantoin 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.: #67770]	Sample type/isolated from	Soy sauce brewing mashes
* marker position based on {}

[Ref.: #69479]

Global distribution of 16S sequence AB911555 (>99% sequence identity) for Tetragenococcus halophilus from Microbeatlas

Aquatic Samples	1678
Soil Samples	861
Animal Samples	20165
Plant Samples	532
Total Samples	23236

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

[Ref.: #8729]

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.: #67770]	Tetragenococcus halophilus gene for 16S rRNA, partial sequence, strain: JCM 20259	AB911555	1522	ENA	51669 tax ID
[Ref.: #20218]	Tetragenococcus halophilus gene for 16S rRNA, partial sequence, strain: NBRC 12172	AB680249	1484	ENA	945021 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Tetragenococcus halophilus NBRC 12172	GCA_000283615	complete	GenBank	945021 tax ID	*
[Ref.: #66792]	Tetragenococcus halophilus NBRC 12172	945021.8	complete	PATRIC	945021 tax ID	*
[Ref.: #66792]	Tetragenococcus halophilus NBRC 12172	2511231116	complete	JGI IMG/M	945021 tax ID	*

[Ref.: #67770]	GC-content	35.9 mol%
[Ref.: #67770]	GC-content	34.2 mol%	thermal denaturation, midpoint method (Tm)

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

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Tetragenococcus halophilus NBRC 12172 PATRIC: 945021.8
[Ref.: #69481]	spore-forming	yes	92	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Tetragenococcus halophilus NBRC 12172 NBRC 12172 NCBI: GCA_000283615.1
[Ref.: #69480]	motile	no	94.53	no
[Ref.: #69480]	flagellated	no	97.323	no
[Ref.: #69480]	gram-positive	yes	91.663	no
[Ref.: #69480]	anaerobic	no	89.366	no
[Ref.: #69480]	aerobic	no	96.655	no
[Ref.: #69480]	halophile	yes	92.609	no
[Ref.: #69480]	spore-forming	no	92.484	no
[Ref.: #69480]	thermophile	no	97.273	yes
[Ref.: #69480]	glucose-util	yes	89.721	no
[Ref.: #69480]	glucose-ferment	yes	87.81	no

Availability in culture collections External links

[Ref.: #8729]

Culture collection no.

DSM 20338, IFO 12172, NBRC 12172, NCDO 1872, NCIB 9735, JCM 20259, IAM 1693, NCIMB 9735, NISL 7117

[Ref.: #74744]

SI-ID 1239

References

#8729

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20338

#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 )

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

#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 .

#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 )

#74744

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-ID1239.1 )

* These data were automatically processed and therefore are not curated

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Tetragenococcus halophilus NBRC 12172

Tetragenococcus halophilus NBRC 12172 NBRC 12172

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