Ruthenibacterium lactatiformans (DSM 105274, WCA3-601-WT-6J)

Name: Ruthenibacterium lactatiformans (DSM 105274, WCA3-601-WT-6J)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 159622

Type strain

Strain Designation WCA3-601-WT-6J

Culture col. no. DSM 105274 WCA3-601-WT-6J

NCBI tax ID(s) 1550024

Special Collections DSMZ Pig DZIF

History <- T. Clavel , TU Munich, Freising-Weihenstephan, Germany; WCA3-601-WT-6J

Links

Ruthenibacterium lactatiformans WCA3-601-WT-6J is a bacterium that was isolated from pig, WT, 24 weeks old, feces.

genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 398287

DSM 105274

@ref 20215

Last LPSN update 2026-02-09 11:38:41

Domain Bacteria

Phylum Bacillota

Class Clostridia

Order Eubacteriales

Family Oscillospiraceae

Genus Ruthenibacterium

Species Ruthenibacterium lactatiformans

Full scientific name Ruthenibacterium lactatiformans Shkoporov et al. 2016

BacDive ID	Other strains from **Ruthenibacterium lactatiformans** (1)	Type strain
132588	R. lactatiformans 585-1, DSM 100348, VKM B-2901 (type strain)

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
66457	CHOPPED MEAT MEDIUM (DSMZ Medium 78)		Medium recipe at MediaDive	Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
66457	positive	growth	37

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	anaerobe	90.4

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68367	17057 ChEBI	cellobiose	-	builds acid from	from API 20A
68367	16899 ChEBI	D-mannitol	-	builds acid from	from API 20A
68367	16024 ChEBI	D-mannose	-	builds acid from	from API 20A
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
68367	17754 ChEBI	glycerol	-	builds acid from	from API 20A
68367	30849 ChEBI	L-arabinose	-	builds acid from	from API 20A
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
68367	6731 ChEBI	melezitose	-	builds acid from	from API 20A
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
68367	27897 ChEBI	tryptophan	-	energy source	from API 20A
68367	16199 ChEBI	urea	-	hydrolysis	from API 20A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68367	35581 ChEBI	indole		from API 20A

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
68367	beta-glucosidase	-	3.2.1.21	from API 20A
68367	gelatinase	-		from API 20A
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
66457	-	-	+/-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	not determinedn.d.	not determinedn.d.	not determinedn.d.	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Mammals	#Suidae (Pig,Swine)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
66457	pig, WT, 24 weeks old, feces	Kranzberg (Bavaria)	Germany	DEU	Europe

Taxonmaps

69479

Global distribution of 16S sequence MN537483 (>99% sequence identity) for Ruthenibacterium lactatiformans subclade from Microbeatlas

Aquatic Samples	6411
Soil Samples	1989
Animal Samples	296291
Plant Samples	856
Total Samples	305547

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
66457	1	Risk group (German classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM969571v1 assembly for Ruthenibacterium lactatiformans WCA3-601-WT-6J	contig	GCA_009695715	1550024.411	8074554192	1550024	65.11

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
66457	Ruthenibacterium lactatiformans strain DSM 105274 16S ribosomal RNA gene, partial sequence	MN537483	1483		1550024

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ruthenibacterium lactatiformans WCA3-601-WT-6J
NCBI: GCA_009695715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	yes	71.80	no
125439	motility	BacteriaNetⓘ	yes	66.10	no
125439	gram_stain	BacteriaNetⓘ	positive	54.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	anaerobe	90.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ruthenibacterium lactatiformans strain WCA3-601-WT-6J
PATRIC: 1550024.411

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	69.98	no
125438	anaerobic	anaerobicⓘ	yes	85.92	no
125438	spore-forming	spore-formingⓘ	no	53.13	no
125438	aerobic	aerobicⓘ	no	90.83	no
125438	thermophilic	thermophileⓘ	no	91.21	no
125438	flagellated	motile2+ⓘ	no	83.63	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 )
#66457	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 105274
#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) .
#68367	Automatically annotated from API 20A .
#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 .
#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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