Name: Rarobacter incanus YLM-32
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13531

Type strain:

Species: Rarobacter incanus

Strain Designation: YLM-32

Culture col. no.: DSM 10596, ATCC 51544, CIP 104132, JCM 6350, IFO 16149, IFO 16558, NBRC 101357, NBRC 16149, NBRC 16558

Strain history: CIP <- 1996, DSMZ <- JCM <- 1987, S. Sato, Nat. Res. Inst. of Brewing, Tokyo, Japan: strain YLM-32 <- T. Hasuo, Japan

NCBI tax ID(s): 153494 (species)

SI-ID 43043

ATCC 51544, JCM 6350, CIP 104132, DSM 10596, IFO 16149, IFO 16558, NBRC 16558, NBRC 16149, NBRC 101357

Other strains from Rarobacter incanus

R. incanus JCM 9462
R. incanus JCM 9463
R. incanus JCM 9464

Section

Rarobacter incanus YLM-32 is an anaerobe, mesophilic bacterium that was isolated from activated sludge; waste-water treatment systems of alcoholic beverage.

anaerobe
mesophilic
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	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micrococcales*
	Family	*Rarobacteraceae*
	Genus	*Rarobacter*
	Species	**Rarobacter incanus**
	Full Scientific Name (LPSN)	Rarobacter incanus Yamamoto et al. 1994

Information on morphological and physiological properties Morphology

[Ref.: #120071]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #120071]	Cell shape	rod-shaped

[Ref.: #120071]	Motility	no
[Ref.: #69480]	Motility	no Confidence in %92.823

Information on culture and growth conditions Culture and growth conditions

[Ref.: #3981]

Culture medium

PYG MEDIUM (MODIFIED) (DSMZ Medium 104)

[Ref.: #3981]

Culture medium growth

[Ref.: #3981]

Culture medium link

Medium recipe at MediaDive

[Ref.: #3981]

Culture medium composition

expand / minimize

[Ref.: #38167]

Culture medium

MEDIUM 137 - for Ruminococcus hansenii and Rarobacter incanus

[Ref.: #38167]

Culture medium growth

[Ref.: #38167]

Culture medium composition

expand / minimize

[Ref.: #120071]

Culture medium

CIP Medium 137

[Ref.: #120071]

Culture medium growth

[Ref.: #120071]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #3981]		growth	30 °C
[Ref.: #38167]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #120071]		growth	30-37 °C
[Ref.: #120071]	no	growth	10 °C
[Ref.: #120071]	no	growth	15 °C
[Ref.: #120071]	no	growth	25 °C
[Ref.: #120071]	no	growth	41 °C
[Ref.: #120071]	no	growth	45 °C

[Ref.: #3981]	Temperature range	mesophilic
[Ref.: #38167]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #120071]	Temperature range	mesophilic
[Ref.: #120071]	Temperature range	psychrophilic
[Ref.: #120071]	Temperature range	mesophilic
[Ref.: #120071]	Temperature range	thermophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #3981]

Oxygen tolerance

anaerobe

[Ref.: #69480]

Ability of spore formation

no Confidence in %99.99

	Salt	Tested relation		Salt conc.
[Ref.: #120071]	NaCl		growth	0	%
[Ref.: #120071]	NaCl	no	growth	2	%
[Ref.: #120071]	NaCl	no	growth	4	%
[Ref.: #120071]	NaCl	no	growth	6	%
[Ref.: #120071]	NaCl	no	growth	8	%
[Ref.: #120071]	NaCl	no	growth	10	%

[Ref.: #3981]	Murein short key	A21.05
[Ref.: #3981]	Murein types	A4ß L-Orn-D-Glu

[Ref.: #67770]

Observation

quinones: MK-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #120071]	cellobiose ChEBI	-	degradation
[Ref.: #120071]	citrate ChEBI	-	carbon source
[Ref.: #120071]	D-arabinose ChEBI	+	degradation
[Ref.: #120071]	D-fructose ChEBI	+	degradation
[Ref.: #120071]	D-glucose ChEBI	+	degradation
[Ref.: #120071]	D-xylose ChEBI	+	degradation
[Ref.: #120071]	esculin ChEBI	+	hydrolysis
[Ref.: #120071]	hippurate ChEBI	+	hydrolysis
[Ref.: #120071]	lactose ChEBI	+	degradation
[Ref.: #120071]	maltose ChEBI	-	degradation
[Ref.: #120071]	nitrate ChEBI	-	reduction
[Ref.: #120071]	nitrate ChEBI	+	respiration
[Ref.: #120071]	nitrite ChEBI	-	reduction
[Ref.: #120071]	salicin ChEBI	-	degradation
[Ref.: #120071]	sucrose ChEBI	-	degradation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #120071]		indole ChEBI	no

	Physiological tests	Metabolite	Voges-Proskauer-test	Methylred-test
[Ref.: #120071]		acetoin ChEBI	-
[Ref.: #120071]		glucose ChEBI		-

	Enzyme	Enzyme activity	EC number
[Ref.: #120071]	alcohol dehydrogenase	-	1.1.1.1
[Ref.: #120071]	amylase	-
[Ref.: #120071]	caseinase	-	3.4.21.50
[Ref.: #120071]	catalase	+	1.11.1.6
[Ref.: #120071]	DNase	-
[Ref.: #120071]	gamma-glutamyltransferase	-	2.3.2.2
[Ref.: #120071]	gelatinase	+
[Ref.: #120071]	lecithinase	-
[Ref.: #120071]	lipase	-
[Ref.: #120071]	lysine decarboxylase	-	4.1.1.18
[Ref.: #120071]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #120071]	oxidase	+
[Ref.: #120071]	phenylalanine ammonia-lyase	-	4.3.1.24
[Ref.: #120071]	tryptophan deaminase	-
[Ref.: #120071]	tween esterase	-
[Ref.: #120071]	urease	-	3.5.1.5
	Only first 10 entries are displayed. Click here to see all.

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	glycogen metabolism	100	5 of 5
[Ref.: #66794]	vitamin K metabolism	100	5 of 5
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	threonine metabolism	90	9 of 10
[Ref.: #66794]	starch degradation	90	9 of 10
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	pentose phosphate pathway	81.82	9 of 11
[Ref.: #66794]	lipoate biosynthesis	80	4 of 5
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	valine metabolism	77.78	7 of 9
[Ref.: #66794]	serine metabolism	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
[Ref.: #66794]	isoleucine metabolism	75	6 of 8
[Ref.: #66794]	sulfopterin metabolism	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	alanine metabolism	72.41	21 of 29
[Ref.: #66794]	heme metabolism	71.43	10 of 14
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	tetrahydrofolate metabolism	71.43	10 of 14
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	aspartate and asparagine metabolism	66.67	6 of 9
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	enterobactin biosynthesis	66.67	2 of 3
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	gluconeogenesis	62.5	5 of 8
[Ref.: #66794]	pyrimidine metabolism	62.22	28 of 45
[Ref.: #66794]	methionine metabolism	61.54	16 of 26
[Ref.: #66794]	metabolism of amino sugars and derivatives	60	3 of 5
[Ref.: #66794]	methylglyoxal degradation	60	3 of 5
[Ref.: #66794]	purine metabolism	58.51	55 of 94
[Ref.: #66794]	arginine metabolism	58.33	14 of 24
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	citric acid cycle	57.14	8 of 14
[Ref.: #66794]	ubiquinone biosynthesis	57.14	4 of 7
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	oxidative phosphorylation	56.04	51 of 91
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	proline metabolism	54.55	6 of 11
[Ref.: #66794]	leucine metabolism	53.85	7 of 13
[Ref.: #66794]	histidine metabolism	51.72	15 of 29
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	ketogluconate metabolism	50	4 of 8
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	mannosylglycerate biosynthesis	50	1 of 2
[Ref.: #66794]	lysine metabolism	47.62	20 of 42
[Ref.: #66794]	lipid metabolism	45.16	14 of 31
[Ref.: #66794]	tryptophan metabolism	44.74	17 of 38
[Ref.: #66794]	lipid A biosynthesis	44.44	4 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	propanol degradation	42.86	3 of 7
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	41.67	5 of 12
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	propionate fermentation	40	4 of 10
[Ref.: #66794]	Entner Doudoroff pathway	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	sulfate reduction	38.46	5 of 13
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	glutathione metabolism	35.71	5 of 14
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	nitrate assimilation	33.33	3 of 9
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	33.33	2 of 6
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	degradation of pentoses	32.14	9 of 28
[Ref.: #66794]	vitamin B1 metabolism	30.77	4 of 13
[Ref.: #66794]	myo-inositol biosynthesis	30	3 of 10
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	dTDPLrhamnose biosynthesis	25	2 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	molybdenum cofactor biosynthesis	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #3981]	Sample type/isolated from	activated sludge; waste-water treatment systems of alcoholic beverage
[Ref.: #3981]	Country	Japan
[Ref.: #3981]	Country ISO 3 Code	JPN
[Ref.: #3981]	Continent	Asia

[Ref.: #120071]	Sample type/isolated from	Environment, Waste-water treatment system
[Ref.: #120071]	Country	Japan
[Ref.: #120071]	Country ISO 3 Code	JPN
[Ref.: #120071]	Continent	Asia
[Ref.: #120071]	Isolation date	1983
* marker position based on {}

Isolation sources categories

#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Industrial wastewater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB056129 (>99% sequence identity) for Rarobacter incanus subclade from Microbeatlas

Aquatic Samples	80
Soil Samples	136
Animal Samples	174
Plant Samples	70
Total Samples	460

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

[Ref.: #3981]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #120071]	Biosafety level	1	Risk group (French classification)

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.: #20218]	Rarobacter incanus gene for 16S rRNA, partial sequence	AB056129	1493	ENA	153494 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rarobacter incanus DSM 10596	GCA_006715765	contig	GenBank	153494 tax ID
[Ref.: #66792]	Rarobacter incanus strain DSM 10596	153494.3	wgs	PATRIC	153494 tax ID	*
[Ref.: #66792]	Rarobacter incanus DSM 10596	2811994875	draft	JGI IMG/M	153494 tax ID	*

[Ref.: #3981]	GC-content	65 mol%
[Ref.: #67770]	GC-content	65.2 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Rarobacter incanus strain DSM 10596 PATRIC: 153494.3
[Ref.: #69481]	spore-forming	no	89	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Rarobacter incanus strain DSM 10596 PATRIC: 153494.3
[Ref.: #69480]	motile	no	89.765	no
[Ref.: #69480]	gram-positive	yes	93.432	no
[Ref.: #69480]	anaerobic	no	84.397	yes
[Ref.: #69480]	aerobic	no	66.31	no
[Ref.: #69480]	halophile	no	70.61	no
[Ref.: #69480]	spore-forming	no	93.429	no
[Ref.: #69480]	thermophile	no	97.402	yes
[Ref.: #69480]	glucose-util	yes	84.128	no
[Ref.: #69480]	flagellated	no	97.812	no
[Ref.: #69480]	glucose-ferment	no	71.551	no

Availability in culture collections External links

[Ref.: #3981]

Culture collection no.

DSM 10596, ATCC 51544, CIP 104132, JCM 6350, IFO 16149, IFO 16558, NBRC 101357, NBRC 16149, NBRC 16558

[Ref.: #82722]

SI-ID 43043

References

#3981

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 10596

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#38167 ; Curators of the CIP;

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#82722

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-ID43043.1 )

#120071 Collection of Institut Pasteur ; Curators of the CIP; CIP 104132
* These data were automatically processed and therefore are not curated

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Rarobacter incanus strain DSM 10596

Rarobacter incanus strain DSM 10596

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