Fretibacterium fastidiosum (DSM 25557, JCM 16858, SGP1)

Name: Fretibacterium fastidiosum (DSM 25557, JCM 16858, SGP1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 23457

Type strain

Strain Designation SGP1

Culture col. no. DSM 25557 JCM 16858 SGP1

NCBI tax ID(s) 651822

Special Collections DSMZ JCM Literature strains

History DSMZ <- W. Wade, King's College London, United Kingdom; SGP1 <- S. Vartoukian; JCM <-- S. R. Vartoukian SGP1.

Links

Fretibacterium fastidiosum SGP1 is an anaerobe, Gram-negative, motile bacterium that was isolated from subgingival plaque from a human with periodontitis.

Gram-negative motile ovoid-shaped anaerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 401326

JCM 16858,DSM 25557

@ref 20215

Last LPSN update 2026-05-29 08:30:26

Domain Bacteria

Phylum Synergistota

Class Synergistia

Order Synergistales

Family Synergistaceae

Genus Fretibacterium

Species Fretibacterium fastidiosum

Full scientific name Fretibacterium fastidiosum Vartoukian et al. 2013

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
30647	negative	7.5 µm	1.25 µm	ovoid-shaped

Colony morphology

19245

Incubation period8-14 days

Pigmentation

30647

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
19245	CHOPPED MEAT MEDIUM FOR FERTIBACTERIUM SP. (DSMZ Medium 78c)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM FOR FERTIBACTERIUM SP. (DSMZ Medium 78c) Composition: Ground beef 586.166 g/l Casein peptone 35.17 g/l Na-fumarate 7.034 g/l Na-formate 7.034 g/l Yeast extract 5.86166 g/l K2HPO4 5.86166 g/l Ethanol 2.22743 g/l L-Cysteine HCl x H2O 0.586167 g/l DL-Dithiothreitol 0.3517 g/l Haemin 0.00293083 g/l Sodium resazurin 0.000586166 g/l Pyridoxine hydrochloride 0.000117233 g/l Riboflavin 5.86166e-05 g/l Calcium D-(+)-pantothenate 5.86166e-05 g/l (DL)-alpha-Lipoic acid 5.86166e-05 g/l p-Aminobenzoic acid 5.86166e-05 g/l Nicotinic acid 5.86166e-05 g/l Thiamine HCl 5.86166e-05 g/l Biotin 2.34467e-05 g/l Folic acid 2.34467e-05 g/l Vitamin B12 1.17233e-06 g/l NaOH Vitamin K1 Horse serum Isobutyric acid DL-2-Methylbutyric acid Valeric acid Isovaleric acid Distilled water
19245	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Trypticase peptone 5.0 g/l Peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Vitamin K1 NaOH Tween 80 Clarified rumen fluid Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
19245	positive	growth	37
30647	positive	growth	25-42
30647	positive	optimum	37
67770	positive	growth	37

Culture pH

@ref	Ability	Type	PH
30647	positive	optimum	6.5
30647	positive	growth	06-08

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
19245	anaerobe
30647	anaerobe
125439	facultative anaerobe	95.9

Observation

30647

Observationaggregates in clumps

Metabolite production

@ref	Chebi-ID	Metabolite	Production
30647	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
30647	acid phosphatase	+	3.1.3.2
30647	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Infection	#Inflammation	-
#Host	#Human	-
#Host Body-Site	#Oral cavity and airways	#Plaque

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
19245	subgingival plaque from a human with periodontitis	Homo sapiens	London	United Kingdom	GBR	Europe
67770	Subgingival plaque from a human with periodontitis	Homo sapiens

Taxonmaps

69479

Global distribution of 16S sequence GQ149247 (>99% sequence identity) for Fretibacterium fastidiosum subclade from Microbeatlas

Aquatic Samples	51
Soil Samples	100
Animal Samples	6307
Plant Samples	32
Total Samples	6490

Interaction and safety

Risk assessment

@ref	Pathogenicity human	Biosafety level	Biosafety level comment
19245	yes, in single cases	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	ASM21071v1 assembly for Fretibacterium fastidiosum SGP1	chromosome	GCA_000210715	651822.3	650377983	651822	0

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
19245	Fretibacterium fastidiosum strain SGP1 16S ribosomal RNA gene, partial sequence	GQ149247	1440		651822

GC content

@ref	GC-content (mol%)	Method
19245	63	sequence analysis
30647	63
67770	63	genome sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM21071v1 assembly for Fretibacterium fastidiosum SGP1
NCBI: GCA_000210715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	95.90	no
125439	motility	BacteriaNetⓘ	no	64.47	no
125439	gram_stain	BacteriaNetⓘ	positive	65.10	no
125439	spore_formation	BacteriaNetⓘ	no	81.69	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Laser-assisted microbial culturomics.	Qu T, Koch L, Mukherjee R, Tu Y, Seidel AL, Puttmann LD, Winkel A, Yang I, Grischke J, Liu D, Wolkers WF, Kittler S, Chichkov B, Stiesch M, Szafranski SP.	Nat Commun	10.1038/s41467-025-66804-7	2025
Genetics	Closed genome sequence of Fretibacterium fastidiosum, a potential contributor to periodontal disease.	Mori A, Kudoh M, Kuboniwa M, Ruckert-Reed C, Busche T, Eisenhut M, Fukusaki E, Brautigam A, Laker B.	Microbiol Resour Announc	10.1128/mra.00004-25	2025
Phylogeny	Fretibacterium fastidiosum gen. nov., sp. nov., isolated from the human oral cavity.	Vartoukian SR, Downes J, Palmer RM, Wade WG	Int J Syst Evol Microbiol	10.1099/ijs.0.041038-0	2012

References

#19245	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25557
#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 )
#26978	IJSEM 458 2013 ( DOI 10.1099/ijs.0.041038-0 , PubMed 22493171 )
#30647	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 #26978
#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;
#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 .
#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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Fretibacterium fastidiosum (DSM 25557, JCM 16858, SGP1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Observation

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000210715

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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