Strain identifier

BacDive ID: 17033

Type strain: Yes

Species: Fervidobacterium nodosum

Strain Designation: Rt17-B1

Strain history: <- ATCC <- B.K.C. Patel, Rt17-B1

NCBI tax ID(s): 2424 (species)

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General

@ref: 1984

BacDive-ID: 17033

DSM-Number: 5306

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, chemoorganotroph, thermophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Fervidobacterium nodosum Rt17-B1 is an anaerobe, chemoorganotroph, thermophilic bacterium that forms circular colonies and was isolated from hot spring.

NCBI tax id

  • NCBI tax id: 2424
  • Matching level: species

strain history

  • @ref: 1984
  • history: <- ATCC <- B.K.C. Patel, Rt17-B1

doi: 10.13145/bacdive17033.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/thermotogota
  • domain: Bacteria
  • phylum: Thermotogota
  • class: Thermotogae
  • order: Thermotogales
  • family: Fervidobacteriaceae
  • genus: Fervidobacterium
  • species: Fervidobacterium nodosum
  • full scientific name: Fervidobacterium nodosum Patel et al. 1985

@ref: 1984

domain: Bacteria

phylum: Thermotogae

class: Thermotogae

order: Thermotogales

family: Fervidobacteriaceae

genus: Fervidobacterium

species: Fervidobacterium nodosum

full scientific name: Fervidobacterium nodosum Patel et al. 1985

strain designation: Rt17-B1

type strain: yes

Morphology

cell morphology

  • @ref: 43352
  • gram stain: negative
  • cell length: 1.0-2.5 µm
  • cell width: 0.5-0.55 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 43352
  • colony size: 1 mm
  • colony color: creamish white
  • colony shape: circular
  • incubation period: 2 days
  • medium used: TYEG agar deep (2%; 65°C)

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1984THERMOANAEROBACTER BROCKII MEDIUM (DSMZ Medium 144)yeshttps://mediadive.dsmz.de/medium/144Name: THERMOANAEROBACTER BROCKII MEDIUM (DSMZ Medium 144) Composition: Trypticase peptone 10.0 g/l D-Glucose 5.0 g/l Yeast extract 3.0 g/l K2HPO4 1.5 g/l Na2S x 9 H2O 1.0 g/l NH4Cl 0.9 g/l KH2PO4 0.75 g/l MgCl2 x 6 H2O 0.4 g/l Nitrilotriacetic acid 0.1152 g/l NaCl 0.009 g/l FeSO4 x 7 H2O 0.003 g/l FeCl2 x 4 H2O 0.0018 g/l CoCl2 x 6 H2O 0.00153 g/l MnCl2 x 4 H2O 0.0009 g/l CaCl2 x 2 H2O 0.0009 g/l ZnCl2 0.0009 g/l Sodium resazurin 0.0005 g/l NiCl2 x 6 H2O 0.00027 g/l Na2SeO3 x 5 H2O 0.00027 g/l CuCl2 0.00018 g/l H3BO3 9e-05 g/l Na2MoO4 x 2 H2O 9e-05 g/l Pyridoxine hydrochloride 5e-05 g/l p-Aminobenzoic acid 2.5e-05 g/l (DL)-alpha-Lipoic acid 2.5e-05 g/l Riboflavin 2.5e-05 g/l Calcium D-(+)-pantothenate 2.5e-05 g/l Thiamine HCl 2.5e-05 g/l Nicotinic acid 2.5e-05 g/l Biotin 1e-05 g/l Folic acid 1e-05 g/l Vitamin B12 5e-07 g/l Distilled water
43352TYEG agar deep (2%; 65°C)yes
43352TYEG mediumyes

culture temp

@refgrowthtypetemperaturerange
1984positivegrowth70thermophilic
43352positiveoptimum70thermophilic
43352nogrowth85hyperthermophilic
43352nogrowth40thermophilic
43352positivegrowth47thermophilic

culture pH

@refabilitytypepH
43352positivegrowth6-8
43352positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
1984anaerobe
43352obligate anaerobe

nutrition type

  • @ref: 43352
  • type: chemoorganotroph

spore formation

  • @ref: 43352
  • spore formation: no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4335230089acetate-growth
4335222599arabinose+assimilation
4335229016arginine-growth
433523435carrageenan-growth
4335262968cellulose-degradation
4335216947citrate-growth
4335223652dextrin-growth
4335224996lactate-growth
4335215740formate-growth
4335228757fructose+assimilation
4335229806fumarate-growth
4335228260galactose+assimilation
4335217234glucose+assimilation
4335228300glutamine-growth
4335217754glycerol+assimilation
4335215428glycine-growth
4335215443inulin-growth
4335217716lactose+assimilation
4335217306maltose+assimilation
4335237684mannose+assimilation
4335230623oxalate-growth
4335217309pectin+assimilation
4335215361pyruvate+/-assimilation
4335216634raffinose+assimilation
4335226546rhamnose+/-assimilation
4335233942ribose-assimilation
4335217822serine-growth
4335230911sorbitol+assimilation
4335230031succinate-growth
4335217992sucrose+assimilation
4335210057xanthan-growth
4335217151xylitol-growth
4335218222xylose-assimilation

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
43352278547sodium azideyesyes500 µg/mL
4335216189sulfateyesyes100 µg/mL
4335217698chloramphenicolyesyes10 µg/mL
4335217334penicillinyesyes10 µg/mL
4335227902tetracyclineyesyes10 µg/mL
43352278547sodium azideyesyes250 µg/mL
43352d-cycloserineyesyes100 µg/mL
43352d-cycloserineyesyes10 µg/mL
433527507neomycinyesyes10 µg/mL
4335217076streptomycinyesyes10 µg/mL

metabolite production

@refChebi-IDmetaboliteproduction
4335230089acetateyes
4335216526carbon dioxideyes
4335218276dihydrogenyes
4335216236ethanolyes
4335224996lactateyes

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
1984hot springNew ZealandNZLAustralia and Oceania
43352Hot SpringNew ZealandNZLAustralia and OceaniaNew Zealand

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

Safety information

risk assessment

  • @ref: 1984
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: F.nodosum 16S ribosomal RNA
  • accession: M59177
  • length: 1456
  • database: ena
  • NCBI tax ID: 2424

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Fervidobacterium nodosum Rt17-B1GCA_000017545completencbi381764
66792Fervidobacterium nodosum Rt17-B1381764.8completepatric381764
66792Fervidobacterium nodosum Rt17-B1640753026completeimg381764

GC content

@refGC-contentmethod
198433.7
4335233.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.78yes
flagellatedno88.961no
gram-positiveno95.034no
anaerobicyes99.629yes
aerobicno98.477yes
halophileno90.439no
spore-formingno91.641yes
thermophileyes100yes
glucose-utilyes90.27no
glucose-fermentyes65.84no

External links

@ref: 1984

culture collection no.: DSM 5306, ATCC 35602

straininfo link

  • @ref: 86033
  • straininfo: 41188

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361295Development of fluorescent adjacent hybridization probes and their application in real-time PCR for the simultaneous detection and identification of Fervidobacterium and Caloramator.Connolly GR, Patel BKCInt J Syst Evol Microbiol10.1099/00207713-52-5-18372002Bacteria, Anaerobic/classification/*genetics/isolation & purification, Base Sequence, Carbocyanines, DNA Primers, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fluorescein-5-isothiocyanate, *Fluorescent Dyes, Molecular Probe Techniques, Molecular Sequence Data, Nucleic Acid Hybridization, *Oligonucleotide Probes, Polymerase Chain Reaction, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species SpecificityGenetics
Enzymology19255469Crystallization and preliminary crystallographic analysis of thermophilic cellulase from Fervidobacterium nodosum Rt17-B1.Zheng B, Yang W, Wang Y, Feng Y, Lou ZActa Crystallogr Sect F Struct Biol Cryst Commun10.1107/S17443091090013162009Bacteria/*enzymology, Cellulase/*chemistry, Crystallization, Crystallography, X-Ray, *Temperature
Enzymology20383468Gene cloning and characterization of a novel thermophilic esterase from Fervidobacterium nodosum Rt17-B1.Yu S, Zheng B, Zhao X, Feng YActa Biochim Biophys Sin (Shanghai)10.1093/abbs/gmq0202010Amino Acid Sequence, Aspergillus/enzymology, Catalysis, *Cloning, Molecular, Computational Biology/*methods, Escherichia coli/metabolism, Esterases/*genetics, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/enzymology/*genetics, Kinetics, Molecular Sequence Data, Mutagenesis, Site-Directed, Mutation, Recombinant Proteins/chemistry, Sequence Homology, Amino Acid, Substrate SpecificityGenetics
Metabolism22102031Influence of the N-terminal peptide on the cocrystallization of a thermophilic endo-beta-1,4-glucanase with polysaccharide substrates.Zheng B, Yang W, Wang Y, Lou Z, Feng YActa Crystallogr Sect F Struct Biol Cryst Commun10.1107/S17443091110335502011Bacteria/*enzymology, Cellulase/*chemistry/metabolism, Crystallization, Crystallography, X-Ray, Polysaccharides/*chemistry/metabolism, Substrate SpecificityEnzymology
Enzymology22128157Crystal structure of hyperthermophilic endo-beta-1,4-glucanase: implications for catalytic mechanism and thermostability.Zheng B, Yang W, Zhao X, Wang Y, Lou Z, Rao Z, Feng YJ Biol Chem10.1074/jbc.M111.2663462011Adaptation, Physiological/*physiology, Binding Sites, Catalysis, Cellulase/*chemistry/genetics, Crystallography, X-Ray, Enzyme Stability/physiology, Glucose/*chemistry, Gram-Negative Anaerobic Straight, Curved, and Helical Rods/*enzymology/genetics, *Hot Temperature, Hydrogen Bonding, Substrate SpecificityStress
Metabolism22944207Thermorecovery of cyanobacterial fatty acids at elevated temperatures.Liu X, Curtiss R 3rdJ Biotechnol10.1016/j.jbiotec.2012.08.0132012Bacterial Proteins/genetics/*metabolism, Biofuels, Cyanobacteria/genetics/*metabolism, Fatty Acids, Nonesterified/*metabolism, Hot Temperature, Lipase/genetics/*metabolismStress
Enzymology24326351Characterization of a thermostable 2,4-diaminopentanoate dehydrogenase from Fervidobacterium nodosum Rt17-B1.Fukuyama S, Mihara H, Miyake R, Ueda M, Esaki N, Kurihara TJ Biosci Bioeng10.1016/j.jbiosc.2013.11.0022013Amino Acid Oxidoreductases/*chemistry/genetics/isolation & purification/*metabolism, Amino Acids, Diamino/metabolism, Bacteria/*enzymology/genetics, Cloning, Molecular, Enzyme Stability, Escherichia coli/genetics/metabolism, Hydrogen-Ion Concentration, Kinetics, Ornithine/metabolism, Recombinant Proteins/chemistry/genetics/isolation & purification/metabolism, Substrate Specificity, TemperatureMetabolism
Enzymology31783074Identification of a novel type I pullulanase from Fervidobacterium nodosum Rt17-B1, with high thermostability and suitable optimal pH.Yang Y, Zhu Y, Obaroakpo JU, Zhang S, Lu J, Yang L, Ni D, Pang X, Lv JInt J Biol Macromol10.1016/j.ijbiomac.2019.10.1122019Bacteria/*enzymology/genetics, Bacterial Proteins/*chemistry/genetics, Enzyme Stability, Glycoside Hydrolases/*chemistry/genetics, *Hot Temperature, Hydrogen-Ion Concentration, Recombinant Proteins/chemistry/geneticsStress

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1984Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 5306)https://www.dsmz.de/collection/catalogue/details/culture/DSM-5306
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
43352B. K. C. Patel, H. W. Morgan, R. M. Daniel10.1007/BF00446741Fervidobacterium nodosum gen. nov. and spec. nov., a new chemoorganotrophic, caldoactive, anaerobic bacteriumArch Microbiol 141: 63-69 1985
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)
86033Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID41188.1StrainInfo: A central database for resolving microbial strain identifiers