Name: Ruthenibacterium lactatiformans 585-1
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 132588

Type strain:

Species: Ruthenibacterium lactatiformans

Strain Designation: 585-1

Culture col. no.: DSM 100348, VKM B-2901

Strain history: <- V. Shcherbakova, Russian Academy of Sciences, Inst. of Biochem. and Physiology, Moscow, Russia; 585-1 <- B.A. Efimov, Russian Natl. Res. Med. Univ., Moscow

NCBI tax ID(s): 1550024 (species)

SI-ID 401423

DSM 100348

Special Collections

Other strains from Ruthenibacterium lactatiformans

Section

Ruthenibacterium lactatiformans 585-1 is an obligate anaerobe, chemoorganoheterotroph, Gram-negative bacterium that forms circular colonies and was isolated from faeces of healthy men.

colony-forming
Gram-negative
rod-shaped
chemoorganoheterotroph
obligate anaerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacillota*
	Class	*Clostridia*
	Order	*Eubacteriales*
	Family	*Oscillospiraceae*
	Genus	*Ruthenibacterium*
	Species	**Ruthenibacterium lactatiformans**
	Full Scientific Name (LPSN)	Ruthenibacterium lactatiformans Shkoporov et al. 2016

Information on morphological and physiological properties Morphology

[Ref.: #43087]	Gram stain	negative

[Ref.: #43087]	Cell length	1.3-1.9 µm

[Ref.: #43087]	Cell width	0.3-0.5 µm

[Ref.: #43087]	Cell shape	rod-shaped

[Ref.: #43087]	Motility	no

[Ref.: #43087]	Type of hemolysis	gamma
[Ref.: #43087]	Colony size	0.15-0.4 mm
[Ref.: #43087]	Colony color	colourless
[Ref.: #43087]	Colony shape	circular
[Ref.: #43087]	Incubation period	3-4 days
[Ref.: #43087]	Cultivation medium used	EG blood agar

Information on culture and growth conditions Culture and growth conditions

[Ref.: #43087]

Culture medium

EG blood agar

[Ref.: #43087]

Culture medium growth

[Ref.: #43087]

Culture medium

MRS broth

[Ref.: #43087]

Culture medium growth

[Ref.: #24377]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #24377]

Culture medium growth

[Ref.: #24377]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24377]

Culture medium composition

expand / minimize

[Ref.: #24377]

Culture medium

RUMEN BACTERIA MEDIUM (DSMZ Medium 330)

[Ref.: #24377]

Culture medium growth

[Ref.: #24377]

Culture medium link

Medium recipe at MediaDive

[Ref.: #24377]

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #24377]			growth	37 °C
[Ref.: #43087]			optimum	37 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43087]

Oxygen tolerance

obligate anaerobe

[Ref.: #43087]

Nutrition type

chemoorganoheterotroph

[Ref.: #43087]	Type of spore	spore
[Ref.: #43087]	Ability of spore formation	no

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68380]	arginine ChEBI	-	hydrolysis	* from API rID32A
[Ref.: #43087]	D-galactose ChEBI	+	builds acid from
[Ref.: #43087]	D-glucose ChEBI	+	builds acid from
[Ref.: #43087]	D-mannitol ChEBI	-	builds acid from
[Ref.: #68380]	D-mannose ChEBI	-	fermentation	* from API rID32A
[Ref.: #43087]	esculin ChEBI	+	hydrolysis
[Ref.: #43087]	gelatin ChEBI	-	degradation
[Ref.: #43087]	L-arabinose ChEBI	-	builds acid from
[Ref.: #68380]	L-glutamate ChEBI	-	degradation	* from API rID32A
[Ref.: #43087]	L-rhamnose ChEBI	+	builds acid from
[Ref.: #43087]	lactose ChEBI	-	builds acid from
[Ref.: #43087]	maltose ChEBI	+	builds acid from
[Ref.: #68380]	nitrate ChEBI	-	reduction	* from API rID32A
[Ref.: #43087]	raffinose ChEBI	-	builds acid from
[Ref.: #68380]	raffinose ChEBI	-	fermentation	* from API rID32A
[Ref.: #43087]	ribitol ChEBI	-	builds acid from
[Ref.: #43087]	salicin ChEBI	+	builds acid from
[Ref.: #43087]	starch ChEBI	+	hydrolysis
[Ref.: #43087]	trehalose ChEBI	-	builds acid from
[Ref.: #68380]	tryptophan ChEBI	-	energy source	* from API rID32A
[Ref.: #68380]	urea ChEBI	-	hydrolysis	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Antibiotic resistance
[Ref.: #43087]	amikacin ChEBI		yes
[Ref.: #43087]	amoxicillin ChEBI	yes
[Ref.: #43087]	ampicillin ChEBI		yes
[Ref.: #43087]	azithromycin ChEBI		yes
[Ref.: #43087]	cephalothin ChEBI		yes
[Ref.: #43087]	clindamycin ChEBI		yes
[Ref.: #43087]	levofloxacin ChEBI		yes
[Ref.: #43087]	linezolid ChEBI		yes
[Ref.: #43087]	penicillin g ChEBI		yes
[Ref.: #43087]	vancomycin ChEBI	yes

	Metabolite	Production
[Ref.: #43087]	(R)-lactate ChEBI	yes
[Ref.: #43087]	indole ChEBI	no
[Ref.: #43087]	succinate ChEBI	yes
[Ref.: #68380]	indole ChEBI	no	* from API rID32A

	Physiological tests	Metabolite	Indole test
[Ref.: #68380]		indole ChEBI	-	* from API rID32A

	Enzyme	Enzyme activity	EC number
[Ref.: #68380]	alanine arylamidase	-	3.4.11.2	* from API rID32A
[Ref.: #68380]	alkaline phosphatase	-	3.1.3.1	* from API rID32A
[Ref.: #43087]	alpha-arabinosidase	-	3.2.1.55
[Ref.: #68380]	alpha-arabinosidase	-	3.2.1.55	* from API rID32A
[Ref.: #43087]	alpha-fucosidase	-	3.2.1.51
[Ref.: #68380]	alpha-fucosidase	-	3.2.1.51	* from API rID32A
[Ref.: #43087]	alpha-galactosidase	+	3.2.1.22
[Ref.: #68380]	alpha-galactosidase	+	3.2.1.22	* from API rID32A
[Ref.: #43087]	alpha-glucosidase	+	3.2.1.20
[Ref.: #68380]	alpha-glucosidase	+	3.2.1.20	* from API rID32A
[Ref.: #68380]	arginine dihydrolase	-	3.5.3.6	* from API rID32A
[Ref.: #43087]	beta-galactosidase	+	3.2.1.23
[Ref.: #68380]	beta-galactosidase	+	3.2.1.23	* from API rID32A
[Ref.: #68380]	beta-Galactosidase 6-phosphate	-		* from API rID32A
[Ref.: #43087]	beta-glucosidase	+	3.2.1.21
[Ref.: #68380]	beta-glucosidase	+	3.2.1.21	* from API rID32A
[Ref.: #43087]	beta-glucuronidase	+	3.2.1.31
[Ref.: #68380]	beta-glucuronidase	-	3.2.1.31	* from API rID32A
[Ref.: #43087]	catalase	-	1.11.1.6
[Ref.: #68380]	glutamate decarboxylase	-	4.1.1.15	* from API rID32A
[Ref.: #68380]	glutamyl-glutamate arylamidase	-		* from API rID32A
[Ref.: #68380]	glycin arylamidase	-		* from API rID32A
[Ref.: #68380]	histidine arylamidase	-		* from API rID32A
[Ref.: #68380]	L-arginine arylamidase	-		* from API rID32A
[Ref.: #68380]	leucine arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #68380]	leucyl glycin arylamidase	-	3.4.11.1	* from API rID32A
[Ref.: #43087]	N-acetyl-beta-glucosaminidase	+	3.2.1.52
[Ref.: #68380]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API rID32A
[Ref.: #68380]	phenylalanine arylamidase	-		* from API rID32A
[Ref.: #68380]	proline-arylamidase	-	3.4.11.5	* from API rID32A
[Ref.: #68380]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API rID32A
[Ref.: #68380]	serine arylamidase	-		* from API rID32A
[Ref.: #68380]	tryptophan deaminase	-	4.1.99.1	* from API rID32A
[Ref.: #68380]	tyrosine arylamidase	-		* from API rID32A
[Ref.: #43087]	urease	-	3.5.1.5
[Ref.: #68380]	urease	-	3.5.1.5	* from API rID32A
	Only first 10 entries are displayed. Click here to see all.

API® rID32A:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Urease/urea hydrolysisURE	Arginine dihydrolaseADH (Arg)	alpha-Galactosidasealpha GAL	beta-Galactosidasebeta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha-Glucosidasealpha GLU	beta-Glucosidasebeta GLU	alpha-Arabinosidasealpha ARA	beta-Glucuronidasebeta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	Fermentation of D-mannoseMNE	Fermentation of raffinoseRAF	Glutamate decarboxylaseGDC	alpha-Fucosidasealpha FUC	Reduction of nitrateNIT	Indole productionIND	Alkaline phosphatasePAL	L-arginine arylamidaseArgA	Proline arylamidaseProA	Leucyl glycin arylamidaseLGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	Pyrrolidonyl arylamidasePyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
[Ref.: #24377]	12882	-	-	+	+	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #24377]	Sample type/isolated from	faeces of healthy men
[Ref.: #24377]	Geographic location (country and/or sea, region)	Moscow
[Ref.: #24377]	Country	Russia
[Ref.: #24377]	Country ISO 3 Code	RUS
[Ref.: #24377]	Continent	Europe

[Ref.: #43087]	Sample type/isolated from	stool sample of a 31-year-old healthy Russian male
[Ref.: #43087]	Country	Russia
[Ref.: #43087]	Country ISO 3 Code	RUS
* marker position based on {}

Isolation sources categories

#Infection	#Patient	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)
#Host	#Human	#Male

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KM098109 (>99% sequence identity) for Ruthenibacterium lactatiformans subclade from Microbeatlas

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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #24377]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #24377]	Ruthenibacterium lactatiformans strain 585-1 16S ribosomal RNA gene, partial sequence	KM098109	1519	GenBank ENA	1550024 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ruthenibacterium lactatiformans 585-1	GCA_000949455	contig	GenBank ENA	1550024 tax ID	*
[Ref.: #66792]	Ruthenibacterium lactatiformans 585-1	2630968832	draft	JGI IMG/M	1550024 tax ID	*

[Ref.: #43087]	GC-content	56.4-56.6 mol%
[Ref.: #24377]	GC-content	56.5 mol%	sequence analysis

Availability in culture collections External links

[Ref.: #24377]

Culture collection no.

DSM 100348, VKM B-2901

[Ref.: #90905]

SI-ID 401423

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ruthenibacterium lactatiformans gen. nov., sp. nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces.	Shkoporov AN, Chaplin AV, Shcherbakova VA, Suzina NE, Kafarskaia LI, Bozhenko VK, Efimov BA	Int J Syst Evol Microbiol	10.1099/ijsem.0.001143	2016	*

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 )

#24377

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 100348

#43087

Andrei N. Shkoporov, Andrei V. Chaplin, Victoria A. Shcherbakova, Natalia E. Suzina, Lyudmila I. Kafarskaia, Vladimir K. Bozhenko and Boris A. Efimov: Ruthenibacterium lactatiformans gen. nov., sp. nov., an anaerobic, lactate-producing member of the family Ruminococcaceae isolated from human faeces. IJSEM 66: 3041 - 3049 2016 ( DOI 10.1099/ijsem.0.001143 , PubMed 27154556 )

#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) .

#68380

Automatically annotated from API rID32A .

#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 .

#90905

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID401423.1 )

* These data were automatically processed and therefore are not curated

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