Butyricimonas synergistica (DSM 23225, CCUG 56610, JCM 15148)

Name: Butyricimonas synergistica (DSM 23225, CCUG 56610, JCM 15148)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 12522

Type strain

Strain Designation MT01

Culture col. no. DSM 23225 CCUG 56610 JCM 15148 MT01 KCTC 15147

NCBI tax ID(s) 1121129 544644

Special Collections DSMZ CCUG JCM KCTC Literature strains

Links

Butyricimonas synergistica MT01 is an anaerobe, mesophilic, Gram-negative prokaryote that was isolated from rat faeces.

Gram-negative rod-shaped anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 406189

JCM 15148,DSM 23225,CCUG 56610

@ref 20215

Last LPSN update 2025-12-16 09:49:52

Domain Pseudomonadati

Phylum Bacteroidota

Class Bacteroidia

Order Bacteroidales

Family Odoribacteraceae

Genus Butyricimonas

Species Butyricimonas synergistica

Full scientific name Butyricimonas synergistica Sakamoto et al. 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
29161	negative	1.5 µm	1 µm	rod-shaped
125439	negative					98

Colony morphology

@ref	Type of hemolysis	Incubation period
16756	gamma
61041		2 days

Pigmentation

29161

Productionyes

Multimedia

@ref:	66793
multimedia content:	EM_DSM_23225_1.jpg
multimedia.multimedia content:	EM_DSM_23225_1.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_23225_2.jpg
multimedia.multimedia content:	EM_DSM_23225_2.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_23225_3.jpg
multimedia.multimedia content:	EM_DSM_23225_3.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_23225_4.jpg
multimedia.multimedia content:	EM_DSM_23225_4.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

@ref:	66793
multimedia content:	EM_DSM_23225_5.jpg
multimedia.multimedia content:	EM_DSM_23225_5.jpg
caption:	electron microscopic image
intellectual property rights:	© HZI/Manfred Rohde
manual_annotation:	1

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
16756	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase 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 Tween 80 Vitamin K1 NaOH Distilled water
16756	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)		Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
16756	positive	growth	37	mesophilic
61041	positive	growth	37	mesophilic
67770	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
16756	anaerobe
29161	anaerobe
61041	anaerobe
125439	anaerobe	99.2

Spore formation

@ref	Spore formation	Confidence
29161
125439		92.4

Observation

@ref	Observation
29161	aggregates in clumps
67770	quinones: MK-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29161	30089 ChEBI	acetate	+	carbon source
29161	16449 ChEBI	alanine	+	carbon source
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68367	65327 ChEBI	D-xylose	-	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
29161	17234 ChEBI	glucose	+	carbon source
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
68380	29985 ChEBI	L-glutamate	+	degradation	from API rID32A
68367	62345 ChEBI	L-rhamnose	-	builds acid from	from API 20A
68367	17716 ChEBI	lactose	-	builds acid from	from API 20A
68367	17306 ChEBI	maltose	-	builds acid from	from API 20A
29161	37684 ChEBI	mannose	+	carbon source
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
29161	506227 ChEBI	N-acetylglucosamine	+	carbon source
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
29161	17272 ChEBI	propionate	+	carbon source
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68367	16634 ChEBI	raffinose	-	builds acid from	from API 20A
68367	17814 ChEBI	salicin	-	builds acid from	from API 20A
68367	30911 ChEBI	sorbitol	-	builds acid from	from API 20A
29161	30031 ChEBI	succinate	+	carbon source
68367	17992 ChEBI	sucrose	-	builds acid from	from API 20A
68367	27082 ChEBI	trehalose	-	builds acid from	from API 20A
68380	27897 ChEBI	tryptophan	+	energy source	from API rID32A
68367	27897 ChEBI	tryptophan	+	energy source	from API 20A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite
29161	35581 ChEBI	indole
68380	35581 ChEBI	indole	from API rID32A
68367	35581 ChEBI	indole	from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
29161	35581 ChEBI	indole	+
68380	35581 ChEBI	indole	+	from API rID32A
68367	35581 ChEBI	indole	+	from API 20A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	+	3.4.11.2	from API rID32A
29161	alkaline phosphatase	+	3.1.3.1
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	-	3.2.1.51	from API rID32A
29161	alpha-galactosidase	+	3.2.1.22
68380	alpha-galactosidase	+	3.2.1.22	from API rID32A
68380	alpha-glucosidase	-	3.2.1.20	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	-	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68367	beta-glucosidase	+	3.2.1.21	from API 20A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
16756	catalase	-	1.11.1.6
68367	catalase	-	1.11.1.6	from API 20A
16756	cytochrome-c oxidase	-	1.9.3.1
29161	gelatinase	+
68367	gelatinase	-		from API 20A
68380	glutamate decarboxylase	+	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	+		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	+	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	-	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	+	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	-		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A
68367	urease	-	3.5.1.5	from API 20A

API 20A

@ref	IND	URE	GLU	MAN	LAC	SAC	MAL	SAL	XYL	ARA	GEL	ESC	GLY	CEL	MNE	MLZ	RAF	SOR	RHA	TRE	CAT	Spores presentSPOR	GramGRAM	Morphology coccus="+" rod="-"COCC
16756	+	-	+/-	-	-	-	-	-	-	-	-	+	-	-	+/-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
16756	-	-	+	-	-	-	-	-	-	+	-	-	+	-	-	+	+	-	-	+	-	-	-	-	+	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Mammals	#Muridae (Mouse/Rat)
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

@ref	Sample type	Sampling date	Country	Country ISO 3 Code	Continent
16756	rat faeces		Japan	JPN	Asia
61041	Mouse feces	2007-12-01	Japan	JPN	Asia
67770	Rat feces

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
16756	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
67770	ASM37966v1 assembly for Butyricimonas synergistica DSM 23225	scaffold	GCA_000379665	1121129.3	2515154026	1121129	74.92

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
16756	Butyricimonas synergistica gene for 16S ribosomal RNA, partial sequence	AB443948	1484		544644

GC content

@ref	GC-content (mol%)	Method
16756	46.4	high performance liquid chromatography (HPLC)
29161	46.4
16756	44.8	high performance liquid chromatography (HPLC)
16756	44.8	sequence analysis

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Butyricimonas synergistica DSM 23225
NCBI: GCA_000379665

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	92.40	no
125439	motility	BacteriaNetⓘ	no	56.90	no
125439	gram_stain	BacteriaNetⓘ	negative	98.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.20	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Butyricimonas synergistica DSM 23225
PATRIC: 1121129.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	84.43	yes
125438	anaerobic	anaerobicⓘ	yes	88.81	yes
125438	spore-forming	spore-formingⓘ	no	88.71	yes
125438	aerobic	aerobicⓘ	no	94.19	yes
125438	thermophilic	thermophileⓘ	no	94.22	yes
125438	flagellated	motile2+ⓘ	no	83.50	yes

Literature

Topic	Title	Authors	Journal	DOI	Year
	A biosynthetic pathway for the selective sulfonation of steroidal metabolites by human gut bacteria.	Yao L, D'Agostino GD, Park J, Hang S, Adhikari AA, Zhang Y, Li W, Avila-Pacheco J, Bae S, Clish CB, Franzosa EA, Huttenhower C, Huh JR, Devlin AS.	Nat Microbiol	10.1038/s41564-022-01176-y	2022
Genetics	Two new bacteria isolated from vagina of a patient with vaginosis: Atopobium massiliense sp. nov. and Butyricimonas vaginalis sp. nov.	Bordigoni A, Lo CI, Yimagou EK, Nicaise B, Diop K, Raoult D, Desnues C, Fenollar F.	New Microbes New Infect	10.1016/j.nmni.2020.100771	2020
Phylogeny	Butyricimonas faecihominis sp. nov. and Butyricimonas paravirosa sp. nov., isolated from human faeces, and emended description of the genus Butyricimonas.	Sakamoto M, Tanaka Y, Benno Y, Ohkuma M	Int J Syst Evol Microbiol	10.1099/ijs.0.065318-0	2014
Phylogeny	Butyricimonas synergistica gen. nov., sp. nov. and Butyricimonas virosa sp. nov., butyric acid-producing bacteria in the family 'Porphyromonadaceae' isolated from rat faeces.	Sakamoto M, Takagaki A, Matsumoto K, Kato Y, Goto K, Benno Y	Int J Syst Evol Microbiol	10.1099/ijs.0.007674-0	2009

References

#16756	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23225
#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 )
#29161	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 #25585 (see below)
#61041	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 56610
#66793	Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68367	Automatically annotated from API 20A .
#68380	Automatically annotated from API rID32A .
#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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Butyricimonas synergistica (DSM 23225, CCUG 56610, JCM 15148)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Multimedia

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20A

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000379665

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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