Strain identifier

BacDive ID: 7502

Type strain: Yes

Species: Frondihabitans australicus

Strain Designation: E1HC-02

Strain history: CIP <- 2007, JCM <- 2006, L. Zhang, Griffith Univ., Brisbane, Australia: strain E1HC-02

NCBI tax ID(s): 386892 (species)

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General

@ref: 7224

BacDive-ID: 7502

DSM-Number: 17894

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, rod-shaped

description: Frondihabitans australicus E1HC-02 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from leaf litters.

NCBI tax id

  • NCBI tax id: 386892
  • Matching level: species

strain history

@refhistory
7224<- L. Zhang <- S. Suyambulingam, E1HC-02
67770L. Zhang E1HC-02 <-- S. Suyambulingam.
116644CIP <- 2007, JCM <- 2006, L. Zhang, Griffith Univ., Brisbane, Australia: strain E1HC-02

doi: 10.13145/bacdive7502.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Frondihabitans
  • species: Frondihabitans australicus
  • full scientific name: Frondihabitans australicus (Zhang et al. 2007) Greene et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Frondicola australicus

@ref: 7224

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Frondihabitans

species: Frondihabitans australicus

full scientific name: Frondihabitans australicus (Zhang et al. 2007) Greene et al. 2009

strain designation: E1HC-02

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31866positive0.5-1.0 µm0.2-0.4 µmrod-shapedno
69480positive100
116644positiverod-shapedyes

colony morphology

@refcolony colorincubation periodmedium used
19755Golden yellow (1004)10-14 daysISP 2
19755Golden yellow (1004)10-14 daysISP 3

multicellular morphology

@refforms multicellular complexmedium name
19755noISP 2
19755noISP 3

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7224TRYPTICASE 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
7224R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
19755ISP 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
19755ISP 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:
37337MEDIUM 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
116644CIP Medium 112yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=112

culture temp

@refgrowthtypetemperaturerange
7224positivegrowth28mesophilic
19755positiveoptimum28mesophilic
31866positivegrowth15-37
31866positiveoptimum25mesophilic
37337positivegrowth25mesophilic
67770positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
31866positivegrowth6-9.5alkaliphile
31866positiveoptimum9.1

Physiology and metabolism

oxygen tolerance

  • @ref: 31866
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31866no
69481no100
69480no99.974

murein

  • @ref: 7224
  • murein short key: B05
  • type: B2ß {Gly} [L-Hsr] D-Glu-D-Orn

observation

  • @ref: 67770
  • observation: quinones: MK-8, MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3186623652dextrin+carbon source
3186617234glucose+carbon source
3186629987glutamate+carbon source
3186617306maltose+carbon source
3186628053melibiose+carbon source
3186630031succinate+carbon source
3186617992sucrose+carbon source
3186627082trehalose+carbon source
3186653423tween 40+carbon source
3186653426tween 80+carbon source
3186627248urocanic acid+carbon source
11664417632nitrate-reduction
11664416301nitrite-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

  • @ref: 116644
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase-3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382alkaline phosphatase-3.1.3.1
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
116644oxidase+
116644catalase+1.11.1.6
116644urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19755-----++-+----------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
19755----++------+-++++-
116644-++-++-+-+--+-++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7224leaf littersSoutheast QueenslandAustraliaAUSAustralia and Oceania
67770Decaying leaf litter of a slash pine forestsoutheast QueenslandAustraliaAUSAustralia and Oceania
116644Plant, Leaf littersQueenslandAustraliaAUSAustralia and Oceania

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Decomposing plant
#Host Body-Site#Plant#Leaf (Phyllosphere)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
72241Risk group (German classification)
197551Risk group (German classification)
1166441Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7224
  • description: Frondihabitans australicus strain E1HC-02 16S ribosomal RNA gene, partial sequence
  • accession: DQ525859
  • length: 1433
  • database: ena
  • NCBI tax ID: 386892

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Frondihabitans australicus strain DSM 17894386892.3wgspatric386892
66792Frondihabitans australicus DSM 178942775506716draftimg386892
67770Frondihabitans australicus DSM 17894GCA_003634555contigncbi386892

GC content

@refGC-contentmethod
722471
3186670-72
6777070-72thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveyes90.345yes
anaerobicno99.52no
halophileno91.591no
spore-formingno88.148no
glucose-utilyes86.714no
aerobicyes90.621yes
motileno58.492yes
flagellatedno94.166no
thermophileno99.184yes
glucose-fermentno84.819no

External links

@ref: 7224

culture collection no.: DSM 17894, JCM 13598, CIP 109654

straininfo link

  • @ref: 76948
  • straininfo: 309450

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17551025Frondicola australicus gen. nov., sp. nov., isolated from decaying leaf litter from a pine forest.Zhang L, Xu Z, Patel BKCInt J Syst Evol Microbiol10.1099/ijs.0.64560-02007Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Australia, Base Composition, Carbohydrate Metabolism, Cell Wall/chemistry/ultrastructure, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Glycolipids/analysis, Hydrogen-Ion Concentration, Microscopy, Electron, Transmission, Molecular Sequence Data, Nucleic Acid Denaturation, Nucleic Acid Hybridization, Peptidoglycan/analysis, Phylogeny, Plant Leaves/microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Temperature, Trees, Vitamin K 2/analysisGenetics
Phylogeny19196793Proposal of Frondihabitans gen. nov. to replace the illegitimate genus name Frondicola Zhang et al. 2007.Greene AC, Euzeby JP, Tindall BJ, Patel BKInt J Syst Evol Microbiol10.1099/ijs.0.010934-02009Actinomycetales/*classification, Species Specificity
Phylogeny19734279Frondihabitans peucedani sp. nov., an actinobacterium isolated from rhizosphere soil, and emended description of the genus Frondihabitans Greene et al. 2009.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.017947-02009Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Magnoliopsida/microbiology, Molecular Sequence Data, Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny22140170Compostimonas suwonensis gen. nov., sp. nov., isolated from spent mushroom compost.Kim SJ, Tamura T, Hamada M, Ahn JH, Weon HY, Park IC, Suzuki KI, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.036343-02011Actinomycetales/*classification/genetics/isolation & purification, Agaricales, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny24132916Description of Galbitalea soli gen. nov., sp. nov., and Frondihabitans sucicola sp. nov.Kim SJ, Lim JM, Ahn JH, Weon HY, Hamada M, Suzuki KI, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.058339-02013Acer/*microbiology, Actinomycetales/*classification/genetics/isolation & purification, Cell Wall/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Phylogeny30387709Planctomonas deserti gen. nov., sp. nov., a new member of the family Microbacteriaceae isolated from soil of the Taklamakan desert.Liu SW, Li FN, Zheng HY, Qi X, Huang DL, Xie YY, Sun CHInt J Syst Evol Microbiol10.1099/ijsem.0.0030952018Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, DNA, Bacterial/genetics, *Desert Climate, Fatty Acids/chemistry, Glycolipids/chemistry, Gram-Positive Bacteria/*classification/isolation & purification, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7224Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17894)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17894
19755Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM17894.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
31866Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2812628776041
37337Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7421
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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
76948Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID309450.1StrainInfo: A central database for resolving microbial strain identifiers
116644Curators of the CIPCollection of Institut Pasteur (CIP 109654)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109654