Strain identifier

BacDive ID: 2987

Type strain: Yes

Species: Ramlibacter tataouinensis

Strain Designation: TTB310

Strain history: CIP <- 2005, T. Heulin, Saint-Paul-Lez-Durance, France: strain TTB310

NCBI tax ID(s): 94132 (species)

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General

@ref: 5464

BacDive-ID: 2987

DSM-Number: 14655

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

description: Ramlibacter tataouinensis TTB310 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from sub-desert soil.

NCBI tax id

  • NCBI tax id: 94132
  • Matching level: species

strain history

@refhistory
5464<- T. Heulin; TTB310
123435CIP <- 2005, T. Heulin, Saint-Paul-Lez-Durance, France: strain TTB310

doi: 10.13145/bacdive2987.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Ramlibacter
  • species: Ramlibacter tataouinensis
  • full scientific name: Ramlibacter tataouinensis Heulin et al. 2003

@ref: 5464

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Ramlibacter

species: Ramlibacter tataouinensis

full scientific name: Ramlibacter tataouinensis Heulin et al. 2003

strain designation: TTB310

type strain: yes

Morphology

cell morphology

  • @ref: 123435
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5464R2A 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
5464TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
36407MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
123435CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
5464positivegrowth30mesophilic
36407positivegrowth30mesophilic

Physiology and metabolism

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12343517632nitrate-reduction
12343516301nitrite-reduction

metabolite production

  • @ref: 123435
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
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+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
123435oxidase+
123435catalase+1.11.1.6
123435urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123435-+++-+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5464sub-desert soilTataouineTunisiaTUNAfrica
123435Environment, Sub-desert soilTataouineTunisiaTUNAfrica1999

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Desert
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_3318.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_1727;97_2068;98_2543;99_3318&stattab=map
  • Last taxonomy: Ramlibacter tataouinensis subclade
  • 16S sequence: AF144383
  • Sequence Identity:
  • Total samples: 5346
  • soil counts: 3799
  • aquatic counts: 673
  • animal counts: 342
  • plant counts: 532

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
54641Risk group (German classification)
1234351Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5464
  • description: Ramlibacter tataouinensis TTB310 16S ribosomal RNA gene, partial sequence
  • accession: AF144383
  • length: 1437
  • database: ena
  • NCBI tax ID: 365046

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ramlibacter tataouinensis TTB310GCA_000215705completencbi365046
66792Ramlibacter tataouinensis TTB310365046.3completepatric365046
66792Ramlibacter tataouinensis TTB310650716081completeimg365046

GC content

  • @ref: 5464
  • GC-content: 70

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno60.548no
flagellatedno85.508no
gram-positiveno98.321no
anaerobicno98.732no
aerobicyes96no
halophileno92.168no
spore-formingno93.127no
thermophileno96.809yes
glucose-utilyes50.535no
glucose-fermentno86.792no

External links

@ref: 5464

culture collection no.: DSM 14655, CIP 108695, ATCC BAA 407, LMG 21543

straininfo link

  • @ref: 72509
  • straininfo: 88869

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12710631Ramlibacter tataouinensis gen. nov., sp. nov., and Ramlibacter henchirensis sp. nov., cyst-producing bacteria isolated from subdesert soil in Tunisia.Heulin T, Barakat M, Christen R, Lesourd M, Sutra L, De Luca G, Achouak WInt J Syst Evol Microbiol10.1099/ijs.0.02482-02003Betaproteobacteria/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/chemistry/genetics, Fatty Acids/analysis, Microscopy, Phase-Contrast, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, *Soil Microbiology, TunisiaGenetics
Cultivation16112847A morphological transition in the pleomorphic bacterium Ramlibacter tataouinensis TTB310.Gommeaux M, Barakat M, Lesourd M, Thiery J, Heulin TRes Microbiol10.1016/j.resmic.2005.05.0102005Comamonadaceae/*growth & development/physiology/*ultrastructure, Culture Media, Microscopy, Electron, Transmission, Morphogenesis
Metabolism21912644The cyst-dividing bacterium Ramlibacter tataouinensis TTB310 genome reveals a well-stocked toolbox for adaptation to a desert environment.De Luca G, Barakat M, Ortet P, Fochesato S, Jourlin-Castelli C, Ansaldi M, Py B, Fichant G, Coutinho PM, Voulhoux R, Bastien O, Marechal E, Henrissat B, Quentin Y, Noirot P, Filloux A, Mejean V, DuBow MS, Barras F, Barbe V, Weissenbach J, Mihalcescu I, Vermeglio A, Achouak W, Heulin TPLoS One10.1371/journal.pone.00237842011Adaptation, Physiological/*genetics/radiation effects, Carbohydrate Metabolism/genetics/radiation effects, Cell Division/*genetics/radiation effects, Cell Membrane/metabolism/radiation effects, Cell Movement/genetics/radiation effects, Cell Shape/genetics/radiation effects, Circadian Rhythm/genetics/radiation effects, Comamonadaceae/*cytology/enzymology/genetics/*physiology, DNA Repair/genetics/radiation effects, DNA, Bacterial/genetics, *Desert Climate, Extracellular Space/genetics/metabolism/radiation effects, Fatty Acids/metabolism, *Genome, Bacterial, *Genomics, Hydrolysis/radiation effects, Light, Membrane Fluidity/genetics/radiation effects, Membrane Lipids/metabolism, Osmotic Pressure/radiation effects, Oxidative Stress/genetics/radiation effects, Polysaccharides, Bacterial/biosynthesis/metabolism, Protein Transport/genetics/radiation effects, Sequence Analysis, DNA, Signal Transduction/genetics/radiation effects, Trehalose/biosynthesis/metabolismGenetics
Phylogeny22450785Ramlibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity.Wang L, An DS, Kim SG, Jin FX, Kim SC, Lee ST, Im WTJ Microbiol Biotechnol10.4014/jmb.1106.060412012Biotransformation, China, Comamonadaceae/genetics/*isolation & purification/*metabolism, Ginsenosides/*metabolism, Molecular Sequence Data, Panax/growth & development/microbiology, Phylogeny, *Soil MicrobiologyMetabolism
Phylogeny24425747Ramlibacter solisilvae sp. nov., isolated from forest soil, and emended description of the genus Ramlibacter.Lee HJ, Lee SH, Lee SS, Lee JS, Kim Y, Kim SC, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.058396-02014Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees/*microbiology, Ubiquinone/chemistry, VietnamGenetics
Phylogeny28879839Ramlibacter rhizophilus sp. nov., isolated from rhizosphere soil of national flower Mugunghwa from South Korea.Yan ZF, Trinh H, Moya G, Lin P, Li CT, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0021912017Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hibiscus/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny28950933Ramlibacter monticola sp. nov., isolated from forest soil.Chaudhary DK, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0023142017Bacterial Typing Techniques, Base Composition, Comamonadaceae/classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Phylogeny31433291Ramlibacter humi sp. nov., isolated from tropical forest soil.Zhang XJ, Feng GD, Yao Q, Wang YH, Yang SZ, Zhu HHInt J Syst Evol Microbiol10.1099/ijsem.0.0036412019Bacterial Typing Techniques, Base Composition, China, Comamonadaceae/classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Tropical Climate, Ubiquinone/chemistryTranscriptome
Metabolism31712689Light on the cell cycle of the non-photosynthetic bacterium Ramlibacter tataouinensis.De Luca G, Fochesato S, Lavergne J, Forest KT, Barakat M, Ortet P, Achouak W, Heulin T, Vermeglio ASci Rep10.1038/s41598-019-52927-72019Cell Cycle/*radiation effects, Comamonadaceae/*physiology/*radiation effects, Darkness, Energy Metabolism/*radiation effects, Heme Oxygenase (Decyclizing)/metabolism, *Light, Mutation, Phenotype, Spectrum AnalysisPhenotype
Phylogeny32965207Ramlibacter pinisoli sp. nov., a novel bacterial species isolated from pine garden soil.Akter S, N A M K, Lee SY, Moon SK, Choi C, Balusamy SR, Siddiqi MZ, Ashrafudoulla M, Rahman MS, Huq MAInt J Syst Evol Microbiol10.1099/ijsem.0.0044862020Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gardens, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, *Pinus, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome
Pathogenicity36364003Production and Characterization of a Novel Exopolysaccharide from Ramlibacter tataouinensis.Jivkova D, Sathiyanarayanan G, Harir M, Hertkorn N, Schmitt-Kopplin P, Sanhaji G, Fochesato S, Berthomieu C, Heyraud A, Achouak W, Santaella C, Heulin TMolecules10.3390/molecules272171722022Humans, Gas Chromatography-Mass Spectrometry, *Comamonadaceae, Rhamnose, *Cysts, Polysaccharides, Bacterial/chemistryBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5464Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14655)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14655
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
36407Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6353
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
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
72509Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88869.1StrainInfo: A central database for resolving microbial strain identifiers
123435Curators of the CIPCollection of Institut Pasteur (CIP 108695)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108695