Ructibacterium gallinarum (DSM 107454, Cla-CZ-49)

Name: Ructibacterium gallinarum (DSM 107454, Cla-CZ-49)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 160181

Type strain

Strain Designation Cla-CZ-49

Culture col. no. DSM 107454 Cla-CZ-49

NCBI tax ID(s) 2779355

Special Collections DSMZ Chicken DZIF

History DSMZ <- T. Clavel, RWTH Aachen; <- C. Zenner, LMU, München;

Links

Ructibacterium gallinarum Cla-CZ-49 is a bacterium that was isolated from chicken caecal content .

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 399560

JCM 34650,DSM 107454

@ref 20215

Last LPSN update 2026-05-29 08:44:22

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Oscillospiraceae

Genus Ructibacterium

Species Ructibacterium gallinarum

Full scientific name Ructibacterium gallinarum Zenner et al. 2021

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
67085	BHI MEDIUM (DSMZ Medium 215)	Medium recipe at MediaDive	Name: BHI MEDIUM (DSMZ Medium 215; with strain-specific modifications) Composition: Brain heart infusion 37.0 g/l Arginine 10.0 g/l Distilled water
67085	GAM Broth (Gifu Anaerobic Medium Broth) (DSMZ Medium 1713)	Medium recipe at MediaDive	Name: GAM Broth (Gifu Anaerobic Medium Broth) (DSMZ Medium 1713) Composition: GAM Broth powder 59.0 g/l Distilled water
67085	MRS MEDIUM (DSMZ Medium 11)	Medium recipe at MediaDive	Name: MRS MEDIUM (DSMZ Medium 11) Composition: Glucose 20.0 g/l Casein peptone 10.0 g/l Meat extract 10.0 g/l Na-acetate 5.0 g/l Yeast extract 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)
67085	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125438	anaerobe	93.358
125439	anaerobe	99.42

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
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	16024 ChEBI	D-mannose	-	builds acid from	from API 20A
68367	4853 ChEBI	esculin	+	hydrolysis	from API 20A
68367	5291 ChEBI	gelatin	-	hydrolysis	from API 20A
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	17306 ChEBI	maltose	-	builds acid from	from API 20A
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
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
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	Production
68380	35581 ChEBI	indole		from API rID32A
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
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
68380	alkaline phosphatase	+	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
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
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	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
67085	-	-	+/-	-	+/-	-	-	-	+/-	-	-	+	-	-	-	-	-	-	-	-	not determinedn.d.	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
67085	-	-	+	+	-	-	-	-	-	-	-	-	-	+	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-
67085	-	-	+	+	-	-	-	-	-	+/-	-	-	-	+/-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
67085	chicken caecal content (age of chicken 35 days)	Munich	Germany	DEU	Europe	48.1502	11.5856 48.1502/11.5856

Interaction and safety

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1498278v1 assembly for Ructibacterium gallinarum DSM 107454	contig	GCA_014982785	2779355.3	2910157262	2779355	62.8

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
67085	Ructibacterium gallinarum strain Cla-CZ-49 16S ribosomal RNA gene, partial sequence	MN055917.1	1469		2779355

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1498278v1 assembly for Ructibacterium gallinarum DSM 107454
BV-BRC: 2779355.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	99.42	no
125439	gram_stain	BacteriaNetⓘ	variable	49.65	no
125439	spore_formation	BacteriaNetⓘ	yes	49.31	no
125439	motility	BacteriaNetⓘ	yes	59.01	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Oscillospiraceae bacterium DSM 107454
PATRIC: 2779355.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	72.77	no
125438	anaerobic	anaerobicⓘ	yes	93.36	no
125438	spore-forming	spore-formingⓘ	no	62.32	no
125438	aerobic	aerobicⓘ	no	98.97	no
125438	thermophilic	thermophileⓘ	no	82.02	yes
125438	flagellated	motile2+ⓘ	no	88.66	no

Literature

References

#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) .
#67085	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107454
#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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