Cite this strain

Tetragenococcus halophilus subsp. halophilus (DSM 20339, ATCC 33315, IAM 1676)

Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5255

Type strain

Strain Designation T11

Culture col. no. DSM 20339 ATCC 33315 IAM 1676 LMG 11490 NCDO 1635 12 more

NCBI tax ID(s) 1123358 51669 1513897

Special Collections DSMZ CCUG JCM CIP

Links

Name and taxonomic classification

Tetragenococcus halophilus subsp. halophilus T11 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from salted anchovy.

Gram-positive coccus-shaped facultative anaerobe mesophilic genome sequence 16S sequence Bacteria

SI-ID 343333

LMG 10477, ATCC 33315, LMG 11490, CCM 3458, CIP 102263, DSM 20339, IAM 12284, IAM 1676, JCM 5888, NCFB 1635, NCIMB 12011, NCDO 1635, CCUG 32204, NCIB 12011, CCRC 12550, CECT 4792, VTT E-88314, NBRC 100498, BCRC 12550

Last LPSN update 2024-12-09 10:43:42

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
5253	T. halophilus subsp. halophilus dl 2, TVA 7-16, DSM 20337, JCM 20252, IAM ...
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	Cell shape	Motility
119820	positive	coccus-shaped
125438	positive

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
8744	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
34907	MEDIUM 63 - for Tetragenococcus halophilus		Distilled water make up to (1000.000 ml);Sodium chloride (30.000 g);ManRogosa Sharp broth (55.000 g)
119820	CIP Medium 63	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
8744	positive	growth	30	mesophilic
34907	positive	growth	30	mesophilic
50895	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
119820	positive	growth	22-37
119820	negative	growth	10
119820	negative	growth	41
119820	negative	growth	45

Physiology and metabolism

Halophily

@ref	Salt	Growth	Tested relation	Concentration
50895	NaCl	positive	growth	5 %
119820	NaCl	positive	growth	0-10 %

Murein

@ref	Murein short key	Type
8744	A11.31	A4alpha L-Lys-D-Asp

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
119820	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	-	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
119820	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
119820	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
119820	caseinase	-	3.4.21.50
119820	catalase	-	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
119820	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	-		from API zym
119820	gamma-glutamyltransferase	+	2.3.2.2
119820	gelatinase	-
119820	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
119820	lipase	-
68382	lipase (C 14)	-		from API zym
119820	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
119820	ornithine decarboxylase	-	4.1.1.17
119820	oxidase	-
119820	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	-	3.4.21.4	from API zym
119820	tween esterase	-
119820	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

Metabolite production

@ref	Chebi-ID	Metabolite	Production
119820	35581 ChEBI	indole

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
119820	606565 ChEBI	hippurate	+	hydrolysis
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
119820	17632 ChEBI	nitrate	-	reduction
119820	16301 ChEBI	nitrite	-	reduction
68371		Potassium 2-ketogluconate	-	builds acid from	from API 50CH acid
68371		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

Oxygen tolerance

@ref	Oxygen tolerance
119820	facultative anaerobe
125439	obligate aerobe

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
119820	-	-	+	-	-	+	+	-	-	-	+	+	-	-	-	+	+	-	-	-

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
8744	-	-	-	-	+	+	-	-	-	-	+	+	+	+	-	-	-	-	-	-	-	-	+	+	+	+	+	+	+	-	-	-	+	-	-	-	-	-	-	+	+	-	+	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Host	#Fishes
#Condition	#Saline

Isolation

8744

Sample typesalted anchovy

Taxonmaps

69479

Global distribution of 16S sequence LC071840 (>99% sequence identity) for Tetragenococcus halophilus from Microbeatlas

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

Safety information

Risk assessment

@ref	Biosafety level	Biosafety level comment
8744	1	Risk group (German classification) According to TRBA 466
119820	1	Risk group (French classification) According to TRBA 466

Sequence information

GC content

@ref	GC-content (mol%)
8744	36
67770	36.8

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Tetragenococcus halophilus 16S rRNA gene, strain DSM 20339	AJ301843	1653	1123358
8744	Tetragenococcus halophilus subsp. halophilus gene for 16S ribosomal RNA	D88668	1522	1513897
8744	Tetragenococcus halophilus strain LMG 11490 16S ribosomal RNA gene, partial sequence	EU689052	1357	1123358
67770	Tetragenococcus halophilus gene for 16S rRNA, partial sequence, strain: JCM 5888	AB596938	1481	1123358
67770	Tetragenococcus halophilus subsp. halophilus gene for 16S ribosomal RNA, partial sequence, strain: JCM 5888	LC071840	1486	1513897

Genome sequences

@ref	Description	Accession	Assembly level	Database	NCBI tax ID
66792	Tetragenococcus halophilus subsp. halophilus DSM 20339	1123358.5	wgs	PATRIC	1123358
66792	Tetragenococcus halophilus DSM 20339	2574179712	draft	JGI IMG/M	1123358
66792	Tetragenococcus halophilus DSM 20339	2835202559	draft	JGI IMG/M	1123358
67770	Tetragenococcus halophilus subsp. halophilus DSM 20339	GCA_003841405	contig		1123358

Genome-based predictions

Predictions

Predictions from Diaspora project based on:
Tetragenococcus halophilus subsp. halophilus DSM 20339
NCBI: GCA_003841405

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	96.50	no
125439	gram_stain	BacteriaNetⓘ	variable	75.40	no
125439	motility	BacteriaNetⓘ	yes	79.60	no
125439	spore_formation	BacteriaNetⓘ	yes	88.60	no

Predictions from Diaspora project based on:
Tetragenococcus halophilus subsp. halophilus DSM 20339
PATRIC: 1123358.5

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	91.67	no
125438	anaerobic	anaerobicⓘ	no	85.22	yes
125438	spore-forming	spore-formingⓘ	no	82.44	no
125438	aerobic	aerobicⓘ	no	90.75	no
125438	thermophilic	thermophileⓘ	no	94.50	yes
125438	flagellated	motile2+ⓘ	no	88.50	no

External links

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Genomic and metabolic features of Tetragenococcus halophilus as revealed by pan-genome and transcriptome analyses.	Chun BH, Han DM, Kim KH, Jeong SE, Park D, Jeon CO	Food Microbiol	10.1016/j.fm.2019.04.009	2019
Metabolism	Proteinase-producing halophilic lactic acid bacteria isolated from fish sauce fermentation and their ability to produce volatile compounds.	Udomsil N, Rodtong S, Tanasupawat S, Yongsawatdigul J	Int J Food Microbiol	10.1016/j.ijfoodmicro.2010.05.016	2010
	Effect of heterologous expression of molecular chaperone DnaK from Tetragenococcus halophilus on salinity adaptation of Escherichia coli.	Sugimoto S, Nakayama J, Fukuda D, Sonezaki S, Watanabe M, Tosukhowong A, Sonomoto K	J Biosci Bioeng	10.1016/s1389-1723(03)90114-9	2003
Genetics	Molecular analysis of the replication region of the theta-replicating plasmid pUCL287 from Tetragenococcus (Pediococcus) halophilus ATCC33315.	Benachour A, Frere J, Flahaut S, Novel G, Auffray Y	Mol Gen Genet	10.1007/s004380050523	1997
Genetics	pUCL287 plasmid from Tetragenococcus halophila (Pediococcus halophilus) ATCC 33315 represents a new theta-type replicon family of lactic acid bacteria.	Benachour A, Frere J, Novel G	FEMS Microbiol Lett	10.1111/j.1574-6968.1995.tb07518.x	1995
Genetics	Characterization and replication mode determination of the minimal replicon of Tetragenococcus halophila ATCC33315 plasmid pUCL287.	Benachour A, Frere J, Boutibonnes P, Auffray Y	Biochimie	10.1016/0300-9084(95)90005-5	1995
Phylogeny	Characterization of Tetragenococcus strains from sugar thick juice reveals a novel species, Tetragenococcus osmophilus sp. nov., and divides Tetragenococcus halophilus into two subspecies, T. halophilus subsp. halophilus subsp. nov. and T. halophilus subsp. flandriensis subsp. nov.	Juste A, Van Trappen S, Verreth C, Cleenwerck I, De Vos P, Lievens B, Willems KA	Int J Syst Evol Microbiol	10.1099/ijs.0.029157-0	2011
Phylogeny	Tetragenococcus koreensis sp. nov., a novel rhamnolipid-producing bacterium.	Lee M, Kim MK, Vancanneyt M, Swings J, Kim SH, Kang MS, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63448-0	2005

Straininfo Link

@ref	Straininfo	Culture collections
74745	343333	LMG 10477, ATCC 33315, LMG 11490, CCM 3458, CIP 102263, DSM 20339, IAM 12284, IAM 1676, JCM 5888, NCFB 1635, NCIMB 12011, NCDO 1635, CCUG 32204, NCIB 12011, CCRC 12550, CECT 4792, VTT E-88314, NBRC 100498, BCRC 12550

Culture collection no.

Culture collection no.
DSM 20339
ATCC 33315
IAM 1676
LMG 11490
NCDO 1635
CCUG 32204
CCM 3458
TC 1
T11
JCM 5888
BCRC 12550
CECT 4792
CIP 102263
IAM 12284
NBRC 100498
NCFB 1635
NCIMB 12011

References

#8744	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 20339
#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 )
#34907	; Curators of the CIP;
#50895	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 32204
#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 .
#68382	Automatically annotated from API zym .
#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 .
#74745	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-ID343333.1 )
#119820	Collection of Institut Pasteur ; Curators of the CIP; CIP 102263
#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 .

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