Strain identifier

BacDive ID: 13531

Type strain: Yes

Species: Rarobacter incanus

Strain Designation: YLM-32

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)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 3981

BacDive-ID: 13531

DSM-Number: 10596

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

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

NCBI tax id

  • NCBI tax id: 153494
  • Matching level: species

strain history

@refhistory
3981<- JCM <- S. Sato, YLM-32
67770S. Sato YLM-32.
120071CIP <- 1996, DSMZ <- JCM <- 1987, S. Sato, Nat. Res. Inst. of Brewing, Tokyo, Japan: strain YLM-32 <- T. Hasuo, Japan

doi: 10.13145/bacdive13531.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Rarobacteraceae
  • genus: Rarobacter
  • species: Rarobacter incanus
  • full scientific name: Rarobacter incanus Yamamoto et al. 1994

@ref: 3981

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Rarobacteraceae

genus: Rarobacter

species: Rarobacter incanus

full scientific name: Rarobacter incanus Yamamoto et al. 1994

strain designation: YLM-32

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480no92.823
69480100positive
120071nopositiverod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3981PYG MEDIUM (MODIFIED) (DSMZ Medium 104)yeshttps://mediadive.dsmz.de/medium/104Name: 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
38167MEDIUM 137 - for Ruminococcus hansenii and Rarobacter incanusyesDistilled water make up to (940.000 ml);Glucose (5.000 g);Yeast extract(10.000 g);Peptone (5.000 g);Resazurin (1.000 mg);Tween 80 (1.000 ml);Tryptone (5.000g);Beef extract (5.000 g);Cysteine hydrochloride (0.500 g);Di Potassium monohydrogenophosphate (2.0
120071CIP Medium 137yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=137

culture temp

@refgrowthtypetemperaturerange
3981positivegrowth30mesophilic
38167positivegrowth30mesophilic
67770positivegrowth30mesophilic
120071positivegrowth30-37mesophilic
120071nogrowth10psychrophilic
120071nogrowth15psychrophilic
120071nogrowth25mesophilic
120071nogrowth41thermophilic
120071nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 3981
  • oxygen tolerance: anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.99

halophily

@refsaltgrowthtested relationconcentration
120071NaClpositivegrowth0 %
120071NaClnogrowth2 %
120071NaClnogrowth4 %
120071NaClnogrowth6 %
120071NaClnogrowth8 %
120071NaClnogrowth10 %

murein

  • @ref: 3981
  • murein short key: A21.05
  • type: A4ß L-Orn-D-Glu

observation

  • @ref: 67770
  • observation: quinones: MK-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12007117108D-arabinose+degradation
12007115824D-fructose+degradation
12007117634D-glucose+degradation
12007165327D-xylose+degradation
12007117057cellobiose-degradation
12007117716lactose+degradation
12007117306maltose-degradation
12007117814salicin-degradation
12007117992sucrose-degradation
12007116947citrate-carbon source
1200714853esculin+hydrolysis
120071606565hippurate+hydrolysis
12007117632nitrate-reduction
12007116301nitrite-reduction
12007117632nitrate+respiration

metabolite production

  • @ref: 120071
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12007115688acetoin-
12007117234glucose-

enzymes

@refvalueactivityec
120071oxidase+
120071alcohol dehydrogenase-1.1.1.1
120071gelatinase+
120071amylase-
120071DNase-
120071caseinase-3.4.21.50
120071catalase+1.11.1.6
120071tween esterase-
120071gamma-glutamyltransferase-2.3.2.2
120071lecithinase-
120071lipase-
120071lysine decarboxylase-4.1.1.18
120071ornithine decarboxylase-4.1.1.17
120071phenylalanine ammonia-lyase-4.3.1.24
120071tryptophan deaminase-
120071urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
3981activated sludge; waste-water treatment systems of alcoholic beverageJapanJPNAsia
120071Environment, Waste-water treatment systemJapanJPNAsia1983

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Activated sludge
#Engineered#Waste#Industrial wastewater

taxonmaps

  • @ref: 69479
  • File name: preview.99_121871.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_33890;97_61604;98_82009;99_121871&stattab=map
  • Last taxonomy: Rarobacter incanus subclade
  • 16S sequence: AB056129
  • Sequence Identity:
  • Total samples: 460
  • soil counts: 136
  • aquatic counts: 80
  • animal counts: 174
  • plant counts: 70

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
39811Risk group (German classification)
1200711Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Rarobacter incanus gene for 16S rRNA, partial sequence
  • accession: AB056129
  • length: 1493
  • database: ena
  • NCBI tax ID: 153494

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rarobacter incanus strain DSM 10596153494.3wgspatric153494
66792Rarobacter incanus DSM 105962811994875draftimg153494
67770Rarobacter incanus DSM 10596GCA_006715765contigncbi153494

GC content

@refGC-contentmethod
398165
6777065.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno89no
motileno89.765no
gram-positiveyes93.432no
anaerobicno84.397yes
aerobicno66.31no
halophileno70.61no
spore-formingno93.429no
thermophileno97.402yes
glucose-utilyes84.128no
flagellatedno97.812no
glucose-fermentno71.551no

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

straininfo link

  • @ref: 82722
  • straininfo: 43043

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3981Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10596)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10596
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
38167Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16007
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
82722Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43043.1StrainInfo: A central database for resolving microbial strain identifiers
120071Curators of the CIPCollection of Institut Pasteur (CIP 104132)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104132