Tetragenococcus halophilus subsp. halophilus (DSM 20337, dl 2, TVA 7-16)

Name: Tetragenococcus halophilus subsp. halophilus (DSM 20337, dl 2, TVA 7-16)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5253

Type strain

Strain Designation dl 2, TVA 7-16

Culture col. no. DSM 20337 dl 2 TVA 7-16 NISL 7128 IAM 1683 1 more

NCBI tax ID(s) 1513897

Special Collections DSMZ JCM

History DSMZ <- K. Kitahara, TVA 7-16 <- K. Sakaguchi, dl 2 (Pediococcus soyae) JCM <-- IAM 1683 <-- K. Sakaguchi dl-2 ("Pediococcus soyae").

Links

Tetragenococcus halophilus subsp. halophilus dl 2 is a bacterium that was isolated from soy sauce brewing mash.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 49608

DSM 20337,IAM 1683,JCM 20252

@ref 20215

Last LPSN update 2026-05-29 08:26:07

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Lactobacillales

Family Enterococcaceae

Genus Tetragenococcus

Species Tetragenococcus halophilus subsp. halophilus

Full scientific name Tetragenococcus halophilus subsp. halophilus (Mees 1934) Justé et al. 2012

BacDive ID	Other strains from **Tetragenococcus halophilus subsp. halophilus** (4)	Type strain
5255	T. halophilus subsp. halophilus T11, DSM 20339, ATCC 33315, IAM 1676, LMG ... (type strain)
5254	T. halophilus subsp. halophilus DSM 20338, IFO 12172, NBRC 12172, NCDO 1872, ...
162786	T. halophilus subsp. halophilus JCM 2015
162820	T. halophilus subsp. halophilus JCM 20245, ATCC 13621, IAM 1673

Morphology

Cell morphology

@ref	Gram stain	Confidence
125438	positive	92.512

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
8728	PEDIOCOCCUS HALOPHILUS MEDIUM (DSMZ Medium 227)		Medium recipe at MediaDive	Name: PEDIOCOCCUS HALOPHILUS MEDIUM (DSMZ Medium 227) Composition: NaCl 65.0 g/l Glucose 20.0 g/l Meat extract 10.0 g/l Casein peptone 10.0 g/l Yeast extract 5.0 g/l Na-acetate 5.0 g/l (NH4)3 citrate 2.0 g/l K2HPO4 2.0 g/l Tween 80 1.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
8728	positive	growth	30
67770	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	98.52

Murein

@ref	Murein short key	Type
8728	A11.31	A4alpha L-Lys-D-Asp

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68371	27613 ChEBI	amygdalin	-	builds acid from	from API 50CH acid
68371	18305 ChEBI	arbutin	-	builds acid from	from API 50CH acid
68371	17057 ChEBI	cellobiose	-	builds acid from	from API 50CH acid
68371	17108 ChEBI	D-arabinose	-	builds acid from	from API 50CH acid
68371	18333 ChEBI	D-arabitol	-	builds acid from	from API 50CH acid
68371	15824 ChEBI	D-fructose	-	builds acid from	from API 50CH acid
68371	28847 ChEBI	D-fucose	-	builds acid from	from API 50CH acid
68371	12936 ChEBI	D-galactose	-	builds acid from	from API 50CH acid
68371	17634 ChEBI	D-glucose	-	builds acid from	from API 50CH acid
68371	62318 ChEBI	D-lyxose	-	builds acid from	from API 50CH acid
68371	16899 ChEBI	D-mannitol	+	builds acid from	from API 50CH acid
68371	16024 ChEBI	D-mannose	-	builds acid from	from API 50CH acid
68371	16988 ChEBI	D-ribose	-	builds acid from	from API 50CH acid
68371	17924 ChEBI	D-sorbitol	-	builds acid from	from API 50CH acid
68371	16443 ChEBI	D-tagatose	-	builds acid from	from API 50CH acid
68371	65327 ChEBI	D-xylose	-	builds acid from	from API 50CH acid
68371	17113 ChEBI	erythritol	-	builds acid from	from API 50CH acid
68371	4853 ChEBI	esculin	+	builds acid from	from API 50CH acid
68371	16813 ChEBI	galactitol	-	builds acid from	from API 50CH acid
68371	28066 ChEBI	gentiobiose	-	builds acid from	from API 50CH acid
68371	24265 ChEBI	gluconate	-	builds acid from	from API 50CH acid
68371	17754 ChEBI	glycerol	-	builds acid from	from API 50CH acid
68371	28087 ChEBI	glycogen	-	builds acid from	from API 50CH acid
68371	15443 ChEBI	inulin	-	builds acid from	from API 50CH acid
68371	30849 ChEBI	L-arabinose	+	builds acid from	from API 50CH acid
68371	18403 ChEBI	L-arabitol	-	builds acid from	from API 50CH acid
68371	18287 ChEBI	L-fucose	-	builds acid from	from API 50CH acid
68371	62345 ChEBI	L-rhamnose	-	builds acid from	from API 50CH acid
68371	17266 ChEBI	L-sorbose	-	builds acid from	from API 50CH acid
68371	65328 ChEBI	L-xylose	-	builds acid from	from API 50CH acid
68371	17716 ChEBI	lactose	-	builds acid from	from API 50CH acid
68371	17306 ChEBI	maltose	-	builds acid from	from API 50CH acid
68371	6731 ChEBI	melezitose	-	builds acid from	from API 50CH acid
68371	28053 ChEBI	melibiose	+	builds acid from	from API 50CH acid
68371	320061 ChEBI	methyl alpha-D-glucopyranoside	-	builds acid from	from API 50CH acid
68371	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from	from API 50CH acid
68371	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from	from API 50CH acid
68371	17268 ChEBI	myo-inositol	-	builds acid from	from API 50CH acid
68371	59640 ChEBI	N-acetylglucosamine	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371	0 ChEBI	Potassium 5-ketogluconate	-	builds acid from	from API 50CH acid
68371	16634 ChEBI	raffinose	-	builds acid from	from API 50CH acid
68371	15963 ChEBI	ribitol	-	builds acid from	from API 50CH acid
68371	17814 ChEBI	salicin	-	builds acid from	from API 50CH acid
68371	28017 ChEBI	starch	-	builds acid from	from API 50CH acid
68371	17992 ChEBI	sucrose	-	builds acid from	from API 50CH acid
68371	27082 ChEBI	trehalose	-	builds acid from	from API 50CH acid
68371	32528 ChEBI	turanose	-	builds acid from	from API 50CH acid
68371	17151 ChEBI	xylitol	-	builds acid from	from API 50CH acid

API 50CHac

@ref	ControlQ	GLY	ERY	DARA	LARA	RIB	DXYL	LXYL	ADO	MDX	GAL	GLU	FRU	MNE	SBE	RHA	DUL	INO	MAN	SOR	MDM	MDG	NAG	AMY	ARB	ESC	SAL	CEL	MAL	LAC	MEL	SAC	TRE	INU	MLZ	RAF	AMD	GLYG	XLT	GEN	TUR	LYX	TAG	DFUC	LFUC	DARL	LARL	GNT	2KG	5KG
8728	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Food

Isolation

@ref	Sample type
8728	soy sauce brewing mash
67770	Soy sauce brewing mashes

Taxonmaps

69479

Global distribution of 16S sequence AB911549 (>99% sequence identity) for Tetragenococcus halophilus from Microbeatlas

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
8728	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	ASM2413720v1 assembly for Tetragenococcus halophilus DSM 20337	contig	GCA_024137205	51669.116		51669	51.45
124043	ASM289757v1 assembly for Tetragenococcus halophilus subsp. halophilus NISL 7128	contig	GCA_002897575	1513897.10	2891795932	1513897	10.29

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67770	Tetragenococcus halophilus gene for 16S rRNA, partial sequence, strain: JCM 20252	AB911549	1515		51669

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM2413720v1 assembly for Tetragenococcus halophilus DSM 20337
NCBI: GCA_024137205

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	98.52	no
125439	gram_stain	BacteriaNetⓘ	positive	55.77	no
125439	motility	BacteriaNetⓘ	yes	42.08	no
125439	spore_formation	BacteriaNetⓘ	yes	43.48	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Tetragenococcus halophilus DSM 20337
NCBI: GCA_024137205.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	92.51	no
125438	anaerobic	anaerobicⓘ	no	85.42	no
125438	aerobic	aerobicⓘ	no	92.70	no
125438	spore-forming	spore-formingⓘ	no	80.75	no
125438	thermophilic	thermophileⓘ	no	96.50	yes
125438	flagellated	motile2+ⓘ	no	89.00	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	The diversity among the species Tetragenococcus halophilus including new isolates from a lupine seed fermentation.	Link T, Vogel RF, Ehrmann MA.	BMC Microbiol	10.1186/s12866-021-02381-1	2021

References

#8728	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20337
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68371	Automatically annotated from API 50CH acid .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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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Tetragenococcus halophilus subsp. halophilus (DSM 20337, dl 2, TVA 7-16)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Metabolite utilization

API 50CHac

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_024137205

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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