Saccharococcus thermophilus (DSM 4749, ATCC 43125, CCM 3586)

Name: Saccharococcus thermophilus (DSM 4749, ATCC 43125, CCM 3586)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1390

Type strain

Strain Designation 657

Culture col. no. DSM 4749 ATCC 43125 CCM 3586 657

NCBI tax ID(s) 29396

Special Collections DSMZ

History <- CCM <- R. Nystrand; 657

Links

Saccharococcus thermophilus 657 is a bacterium that was isolated from beet sugar extraction.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 41663

ATCC 43125,CCM 3586,DSM 4749

@ref 20215

Last LPSN update 2026-02-09 11:18:05

Domain Bacteria

Phylum Bacillota

Class Bacilli

Order Caryophanales

Family Bacillaceae

Genus Saccharococcus

Species Saccharococcus thermophilus

Full scientific name Saccharococcus thermophilus Nystrand 1984

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
1752	TS AGAR (DSMZ Medium 893)		Medium recipe at MediaDive	Name: TS AGAR (DSMZ Medium 893) Composition: Agar 15.0 g/l Sucrose 5.0 g/l Tryptone 5.0 g/l Beef extract 3.0 g/l Glucose 1.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
1752	positive	growth	50

Physiology and metabolism

Spore formation

@ref	Spore formation	Confidence
125438		90.986

Murein

@ref	Murein short key	Type
1752	A31	A1gamma m-Dpm-direct

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Food production	#Food
#Engineered	#Industrial	#Industrial production

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
1752	beet sugar extraction	Sweden	SWE	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1752	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
124043	ASM4268330v1 assembly for Saccharococcus thermophilus CCM 3586	contig	GCA_042683305			29396	77.51
66792	ASM1176147v1 assembly for Saccharococcus thermophilus DSM 4749	contig	GCA_011761475	29396.3	2824486690	29396	75.3
124043	ASM4265112v1 assembly for Saccharococcus thermophilus CCM 3586	contig	GCA_042651125			29396	47.71

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
20218	Saccharococcus thermophilus 16S ribosomal RNA	L09227	1538	29396
20218	S.thermophilus gene for 16S ribosomal RNA	X70430	1538	29396
124043	Saccharococcus thermophilus strain CCM 3586 16S ribosomal RNA gene, partial sequence.	MT760102	1350	29396

GC content

@ref	GC-content (mol%)	Method
1752	47.8	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Saccharococcus thermophilus DSM 4749
NCBI: GCA_011761475

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	89.60	no
125439	motility	BacteriaNetⓘ	yes	88.10	no
125439	gram_stain	BacteriaNetⓘ	variable	89.20	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	84.80	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Saccharococcus thermophilus strain DSM 4749
PATRIC: 29396.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	74.00	no
125438	anaerobic	anaerobicⓘ	no	86.70	no
125438	spore-forming	spore-formingⓘ	yes	90.99	no
125438	aerobic	aerobicⓘ	yes	66.15	no
125438	thermophilic	thermophileⓘ	yes	72.45	yes
125438	flagellated	motile2+ⓘ	yes	81.23	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Elucidating the biotechnological potential of the genera Parageobacillus and Saccharococcus through comparative genomic and pan-genome analysis.	Mol M, de Maayer P.	BMC Genomics	10.1186/s12864-024-10635-1	2024
Enzymology	Isolation, Genomic Sequence and Physiological Characterization of Parageobacillus sp. G301, an Isolate Capable of Both Hydrogenogenic and Aerobic Carbon Monoxide Oxidation.	Imaura Y, Okamoto S, Hino T, Ogami Y, Katayama YA, Tanimura A, Inoue M, Kamikawa R, Yoshida T, Sako Y.	Appl Environ Microbiol	10.1128/aem.00185-23	2023
	Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima.	Pope PB, Vivekanand V, Eijsink VG, Horn SJ.	3 Biotech	10.1007/s13205-012-0097-x	2013
Phylogeny	Anoxybacillus sediminis sp. nov., a novel moderately thermophilic bacterium isolated from a hot spring.	Khan IU, Habib N, Xiao M, Devi AM, Habib M, Hejazi MS, Salam N, Zhi XY, Li WJ	Antonie Van Leeuwenhoek	10.1007/s10482-018-1118-5	2018

References

#1752	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 4749
#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) .
#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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Saccharococcus thermophilus (DSM 4749, ATCC 43125, CCM 3586)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Spore formation

Murein

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_042683305

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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