Fervidobacterium nodosum (DSM 5306, ATCC 35602, Rt17-B1)

Name: Fervidobacterium nodosum (DSM 5306, ATCC 35602, Rt17-B1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17033

Type strain

Strain Designation Rt17-B1

Culture col. no. DSM 5306 ATCC 35602 Rt17-B1

NCBI tax ID(s) 2424

Special Collections DSMZ Literature strains

History <- ATCC <- B.K.C. Patel, Rt17-B1

Links

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

Gram-negative motile rod-shaped colony-forming anaerobe chemoorganotroph genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 41188

ATCC 35602,DSM 5306

@ref 20215

Last LPSN update 2026-02-09 11:22:07

Domain Bacteria

Phylum Thermotogota

Class Thermotogae

Order Thermotogales

Family Fervidobacteriaceae

Genus Fervidobacterium

Species Fervidobacterium nodosum

Full scientific name Fervidobacterium nodosum Patel et al. 1985

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43352	negative	1.0-2.5 µm	0.5-0.55 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43352	1 mm	creamish white	circular	2 days	TYEG agar deep (2%; 65°C)

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
1984	THERMOANAEROBACTER BROCKII MEDIUM (DSMZ Medium 144)	Medium recipe at MediaDive	Name: 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
43352	TYEG agar deep (2%; 65°C)
43352	TYEG medium

Culture temp

@ref	Growth	Type	Temperature (°C)
1984	positive	growth	70
43352	positive	optimum	70
43352	negative	growth	85
43352	negative	growth	40
43352	positive	growth	47

Culture pH

@ref	Ability	Type	PH
43352	positive	optimum	7
43352	positive	growth	6-8

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
1984	anaerobe
43352	obligate anaerobe
125438	anaerobe	93.939

Nutrition type

43352

Typechemoorganotroph

Spore formation

@ref	Spore formation	Confidence
43352
125439		90.3

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43352	30089 ChEBI	acetate	-	growth
43352	22599 ChEBI	arabinose	+	assimilation
43352	29016 ChEBI	arginine	-	growth
43352	3435 ChEBI	carrageenan	-	growth
43352	62968 ChEBI	cellulose	-	degradation
43352	16947 ChEBI	citrate	-	growth
43352	23652 ChEBI	dextrin	-	growth
43352	15740 ChEBI	formate	-	growth
43352	28757 ChEBI	fructose	+	assimilation
43352	29806 ChEBI	fumarate	-	growth
43352	28260 ChEBI	galactose	+	assimilation
43352	17234 ChEBI	glucose	+	assimilation
43352	28300 ChEBI	glutamine	-	growth
43352	17754 ChEBI	glycerol	+	assimilation
43352	15428 ChEBI	glycine	-	growth
43352	15443 ChEBI	inulin	-	growth
43352	24996 ChEBI	lactate	-	growth
43352	17716 ChEBI	lactose	+	assimilation
43352	17306 ChEBI	maltose	+	assimilation
43352	37684 ChEBI	mannose	+	assimilation
43352	30623 ChEBI	oxalate	-	growth
43352	17309 ChEBI	pectin	+	assimilation
43352	15361 ChEBI	pyruvate	+/-	assimilation
43352	16634 ChEBI	raffinose	+	assimilation
43352	26546 ChEBI	rhamnose	+/-	assimilation
43352	33942 ChEBI	ribose	-	assimilation
43352	17822 ChEBI	serine	-	growth
43352	30911 ChEBI	sorbitol	+	assimilation
43352	30031 ChEBI	succinate	-	growth
43352	17992 ChEBI	sucrose	+	assimilation
43352	10057 ChEBI	xanthan	-	growth
43352	17151 ChEBI	xylitol	-	growth
43352	18222 ChEBI	xylose	-	assimilation

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43352	17698	chloramphenicol	10 µg/mL
43352		d-cycloserine		100 µg/mL
43352		d-cycloserine		10 µg/mL
43352	7507	neomycin		10 µg/mL
43352	17334	penicillin	10 µg/mL
43352	278547	sodium azide	500 µg/mL
43352	278547	sodium azide		250 µg/mL
43352	17076	streptomycin		10 µg/mL
43352	16189	sulfate	100 µg/mL
43352	27902	tetracycline	10 µg/mL

Metabolite production

@ref	Chebi-ID	Metabolite
43352	30089 ChEBI	acetate
43352	16526 ChEBI	carbon dioxide
43352	18276 ChEBI	dihydrogen
43352	16236 ChEBI	ethanol
43352	24996 ChEBI	lactate

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Thermal spring
#Condition	#Thermophilic (>45°C)	-

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
1984	hot spring		New Zealand	NZL	Australia and Oceania
43352	Hot Spring	New Zealand	New Zealand	NZL	Australia and Oceania

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
1984	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM1754v1 assembly for Fervidobacterium nodosum Rt17-B1	complete	GCA_000017545	381764.8	640753026	381764	99.45

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	F.nodosum 16S ribosomal RNA	M59177	1456		2424

GC content

@ref	GC-content (mol%)	Method
1984	33.7
43352	33.7	thermal denaturation, midpoint method (Tm)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Fervidobacterium nodosum Rt17-B1
PATRIC: 381764.8

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	90.30	no
125439	motility	BacteriaNetⓘ	no	74.50	no
125439	gram_stain	BacteriaNetⓘ	negative	77.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative aerobe	85.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Fervidobacterium nodosum Rt17-B1 Rt17-B1
NCBI: GCA_000017545.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	64.76	no
125438	anaerobic	anaerobicⓘ	yes	93.94	yes
125438	aerobic	aerobicⓘ	no	97.08	yes
125438	spore-forming	spore-formingⓘ	no	81.91	no
125438	thermophilic	thermophileⓘ	yes	77.07	yes
125438	flagellated	motile2+ⓘ	yes	56.09	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Structural and functional diversity among Type III restriction-modification systems that confer host DNA protection via methylation of the N4 atom of cytosine.	Murray IA, Luyten YA, Fomenkov A, Dai N, Correa IR, Farmerie WG, Clark TA, Korlach J, Morgan RD, Roberts RJ.	PLoS One	10.1371/journal.pone.0253267	2021
	Purification and Properties of a Thermostable Pullulanase from a Newly Isolated Thermophilic Anaerobic Bacterium, Fervidobacterium pennavorans Ven5.	Koch R, Canganella F, Hippe H, Jahnke KD, Antranikian G.	Appl Environ Microbiol	10.1128/aem.63.3.1088-1094.1997	1997
	Keratin Degradation by Fervidobacterium pennavorans, a Novel Thermophilic Anaerobic Species of the Order Thermotogales.	Friedrich AB, Antranikian G.	Appl Environ Microbiol	10.1128/aem.62.8.2875-2882.1996	1996
Metabolism	Chimeric cellulase matrix for investigating intramolecular synergism between non-hydrolytic disruptive functions of carbohydrate-binding modules and catalytic hydrolysis.	Wang Y, Tang R, Tao J, Wang X, Zheng B, Feng Y.	J Biol Chem	10.1074/jbc.m111.320358	2012
	Compilation of small ribosomal subunit RNA structures.	Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R.	Nucleic Acids Res	10.1093/nar/21.13.3025	1993
Enzymology	Crystal 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 Y	J Biol Chem	10.1074/jbc.M111.266346	2011
Phylogeny	Development 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 BKC	Int J Syst Evol Microbiol	10.1099/00207713-52-5-1837	2002
Enzymology	Identification 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 J	Int J Biol Macromol	10.1016/j.ijbiomac.2019.10.112	2019
Enzymology	Characterization of a thermostable 2,4-diaminopentanoate dehydrogenase from Fervidobacterium nodosum Rt17-B1.	Fukuyama S, Mihara H, Miyake R, Ueda M, Esaki N, Kurihara T	J Biosci Bioeng	10.1016/j.jbiosc.2013.11.002	2013
Metabolism	Thermorecovery of cyanobacterial fatty acids at elevated temperatures.	Liu X, Curtiss R 3rd	J Biotechnol	10.1016/j.jbiotec.2012.08.013	2012
Metabolism	Influence 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 Y	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309111033550	2011
Enzymology	Gene cloning and characterization of a novel thermophilic esterase from Fervidobacterium nodosum Rt17-B1.	Yu S, Zheng B, Zhao X, Feng Y	Acta Biochim Biophys Sin (Shanghai)	10.1093/abbs/gmq020	2010
Enzymology	Crystallization and preliminary crystallographic analysis of thermophilic cellulase from Fervidobacterium nodosum Rt17-B1.	Zheng B, Yang W, Wang Y, Feng Y, Lou Z	Acta Crystallogr Sect F Struct Biol Cryst Commun	10.1107/S1744309109001316	2009

References

#1984	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 5306
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#20218	Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )
#43352	B. K. C. Patel, H. W. Morgan, R. M. Daniel: Fervidobacterium nodosum gen. nov. and spec. nov., a new chemoorganotrophic, caldoactive, anaerobic bacterium. Arch Microbiol 141: 63 - 69 1985 ( DOI 10.1007/BF00446741 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Fervidobacterium nodosum (DSM 5306, ATCC 35602, Rt17-B1)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Nutrition type

Spore formation

Metabolite utilization

Antibiotic resistance

Metabolite production

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000017545

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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