Strain identifier

BacDive ID: 12583

Type strain: Yes

Species: Isoptericola variabilis

Strain Designation: MX5

Strain history: CIP <- 2005, JCM <- H. König <- A. Schäfer: strain MX5

NCBI tax ID(s): 1305623 (strain), 139208 (species)

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General

@ref: 3841

BacDive-ID: 12583

DSM-Number: 10177

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive

description: Isoptericola variabilis MX5 is a facultative anaerobe, mesophilic, Gram-positive bacterium that was isolated from hindgut of termite Mastotermes darwiniensis.

NCBI tax id

NCBI tax idMatching level
1305623strain
139208species

strain history

@refhistory
3841<- H. König <- A. Schäfer; MX5
67770DSM 10177 <-- H. König <-- A. Schäfer MX5.
123799CIP <- 2005, JCM <- H. König <- A. Schäfer: strain MX5

doi: 10.13145/bacdive12583.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Promicromonosporaceae
  • genus: Isoptericola
  • species: Isoptericola variabilis
  • full scientific name: Isoptericola variabilis (Bakalidou et al. 2002) Stackebrandt et al. 2004

  • synonyms

    @refsynonym
    20215Cellulosimicrobium variabile
    20215Cellulomonas variformis

@ref: 3841

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Promicromonosporaceae

genus: Isoptericola

species: Isoptericola variabilis

full scientific name: Isoptericola variabilis (Bakalidou et al. 2002) Stackebrandt et al. 2004

strain designation: MX5

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
22921positive
123799positiveoval-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18428Colorless10-14 daysISP 2
18428Beige (1001)10-14 daysISP 3
18428Beige (1001)10-14 daysISP 4
18428Beige (1001)10-14 daysISP 5
18428Beige (1001)10-14 daysISP 6
18428Beige (1001)10-14 daysISP 7
22921yellowPYGV medium

multicellular morphology

@refforms multicellular complexmedium name
18428noISP 2
18428noISP 3
18428noISP 4
18428noISP 5
18428noISP 6
18428noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3841TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
18428ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18428ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18428ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18428ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18428ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18428ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
22921PYGV mediumyes
40114MEDIUM 112 - for JanibacteryesDistilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (1.000 g);Agar (20.000 g);Yeast extract (5.000 g);Peptone (10.000 g);Tween 80 (50.000 mg);Glycerol (2.000 g);Malt extract (5.000 g);Beef extract (2.000 g);Casamino acids (5.000 g);Ca
123799CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
3841positivegrowth28mesophilic
18428positiveoptimum28mesophilic
40114positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123799
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.997

murein

@refmurein short keytype
3841A11.31A4alpha L-Lys-D-Asp
22922A11.31A4alpha L-Lys-D-Asp

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1842862968cellulose+
1842816634raffinose+
1842826546rhamnose+
1842828757fructose+
1842829864mannitol+
1842817268myo-inositol-
1842818222xylose-
1842817992sucrose+
1842822599arabinose+
1842817234glucose+
2292127856acetamide-growth
2292115963ribitol-growth
2292162968cellulose+growth
2292128757fructose+growth
2292128260galactose+growth
2292117268myo-inositol-growth
2292117306maltose-builds acid from
2292117306maltose+growth
2292129864mannitol-growth
2292137684mannose+growth
2292126546rhamnose-growth
2292117814salicin+growth
2292130911sorbitol-growth
2292117992sucrose+growth
2292127082trehalose+growth
2292128017starch-hydrolysis
2292153424tween 20-hydrolysis
2292153426tween 80-hydrolysis
2292116199urea-hydrolysis
2292117234glucose-fermentation
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin-builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837117924D-sorbitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837130849L-arabinose+builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
12379917632nitrate+reduction
12379916301nitrite-reduction
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose+fermentation
6837916899D-mannitol-fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

metabolite production

@refChebi-IDmetaboliteproduction
2292116136hydrogen sulfideno
2292135581indoleno
2292115688acetoinno
2292189634melaninno
12379935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
2292115688acetoin-
2292117234glucose-

enzymes

@refvalueactivityec
22921alpha-glucosidase+3.2.1.20
22921arginine Dihydrolase-3.5.3.6
22921beta-galactosidase+3.2.1.23
22921beta-glucosidase+3.2.1.21
22921catalase+1.11.1.6
22921lipase (C 14)+
22921lysine decarboxylase+4.1.1.18
22921ornithine decarboxylase-4.1.1.17
22921cytochrome oxidase-1.9.3.1
22921urease-3.5.1.5
22921L-aspartate arylamidase+3.4.11.21
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase-3.4.19.3
68379pyrazinamidase-3.5.1.B15
123799oxidase+
123799catalase+1.11.1.6
123799urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase+3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-mannosidase+3.2.1.24

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18428+--+-+++++++-+-++++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18428+++-++++-++++++++++
123799+++-++++-+++++++++--

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123799+/---++/-+--+/-++++-+/---+/--+/-+/-+/-+++++++/-+/-++-++++-+++/-+/---+/--+/---

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
3841hindgut of termite Mastotermes darwiniensisMastotermes darwiniensisGermanyDEUEurope
67770Hindgut contents of Australian termite Mastotermes darwiniensisMastotermes darwiniensisGermanyDEUEurope
123799Hindgut of termite, Mastotermes darwiniensisGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host#Arthropoda#Insecta
#Host Body-Site#Gastrointestinal tract

taxonmaps

  • @ref: 69479
  • File name: preview.99_3403.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1778;97_2128;98_2608;99_3403&stattab=map
  • Last taxonomy: Isoptericola
  • 16S sequence: AJ298873
  • Sequence Identity:
  • Total samples: 1061
  • soil counts: 472
  • aquatic counts: 100
  • animal counts: 365
  • plant counts: 124

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184281German classification
38411Risk group (German classification)
1237991Risk group (French classification)

Sequence information

16S sequences

  • @ref: 3841
  • description: Cellulomonas variformis 16S rRNA gene, strain MX5
  • accession: AJ298873
  • length: 1472
  • database: ena
  • NCBI tax ID: 139208

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Isoptericola variabilis JCM 11754GCA_001313765contigncbi1305623
66792Isoptericola variabilis JCM 117541305623.3wgspatric1305623
66792Isoptericola variabilis JCM 117542734481962draftimg1305623

GC content

@refGC-contentmethod
384170
6777070-72high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.865no
gram-positiveyes69.361no
anaerobicno96.788no
halophileno80.52no
spore-formingno93.871no
thermophileno97.012yes
glucose-utilyes86.239no
flagellatedno95.486no
aerobicyes72.599no
glucose-fermentyes64.608no

External links

@ref: 3841

culture collection no.: DSM 10177, ATCC BAA 303, CIP 109082, JCM 11754, KCTC 9985, NBRC 104115

straininfo link

  • @ref: 81797
  • straininfo: 100586

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143008Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov.Stackebrandt E, Schumann P, Cui XLInt J Syst Evol Microbiol10.1099/ijs.0.02878-02004Actinomycetales/*classification/genetics/metabolism, Amino Acid Sequence, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Peptidoglycan/chemistry, Phospholipids/chemistry, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicMetabolism
Phylogeny16166680Isoptericola halotolerans sp. nov., a novel actinobacterium isolated from saline soil from Qinghai Province, north-west China.Zhang YQ, Schumann P, Li WJ, Chen GZ, Tian XP, Stackebrandt E, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63641-02005Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Bacterial Typing Techniques, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil MicrobiologyGenetics
Phylogeny27045419Isoptericola cucumis sp. nov., isolated from the root tissue of cucumber (Cucumis sativus).Kampfer P, Glaeser SP, Kloepper JW, Hu CH, McInroy JA, Martin K, Busse HJInt J Syst Evol Microbiol10.1099/ijsem.0.0010552016Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Cucumis sativus/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, Polyamines/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny32306134Lactococcus protaetiae sp. nov. and Xylanimonas protaetiae sp. nov., isolated from gut of larvae of Protaetia brevitarsis seulensis.Heo J, Kim SJ, Kim MA, Tamura T, Saitou S, Hamada M, Kim JS, Hong SB, Kwon SWAntonie Van Leeuwenhoek10.1007/s10482-020-01413-62020Actinobacteria/*classification/genetics/*isolation & purification, Actinomycetales/classification, Animals, Bacterial Typing Techniques, Base Composition, Coleoptera/*microbiology, DNA, Bacterial/genetics, Fatty Acids/analysis, *Gastrointestinal Microbiome, Lactococcus/*classification/genetics/*isolation & purification, Larva/*microbiology, Peptidoglycan, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3841Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10177)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10177
18428Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM10177.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
22921Yu-Qin Zhang, Peter Schumann, Wen-Jun Li, Guo-Zhong Chen, Xin-Peng Tian, Erko Stackebrandt, Li-Hua Xu, Cheng-Lin Jiang10.1099/ijs.0.63641-0Isoptericola halotolerans sp. nov., a novel actinobacterium isolated from saline soil from Qinghai Province, north-west ChinaIJSEM 55: 1867-1870 200516166680
22922Erko Stackebrandt, Peter Schumann, Xiao-Long Cui10.1099/ijs.0.02878-0Reclassification of Cellulosimicrobium variabile Bakalidou et al. 2002 as Isoptericola variabilis gen. nov., comb. nov.IJSEM 54: 685-688 200415143008
40114Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6784
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68371Automatically annotated from API 50CH acid
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
81797Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100586.1StrainInfo: A central database for resolving microbial strain identifiers
123799Curators of the CIPCollection of Institut Pasteur (CIP 109082)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109082