Name: Fervidobacterium nodosum Rt17-B1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17033

Type strain:

Species: Fervidobacterium nodosum

Strain Designation: Rt17-B1

Culture col. no.: DSM 5306, ATCC 35602

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

NCBI tax ID(s): 2424 (species)

SI-ID 41188

ATCC 35602, DSM 5306

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Thermotogota*
	Class	*Thermotogae*
	Order	*Thermotogales*
	Family	*Fervidobacteriaceae*
	Genus	*Fervidobacterium*
	Species	**Fervidobacterium nodosum**
	Full Scientific Name (LPSN)	Fervidobacterium nodosum Patel et al. 1985

Information on morphological and physiological properties Morphology

[Ref.: #43352]	Gram stain	negative

[Ref.: #43352]	Cell length	1.0-2.5 µm

[Ref.: #43352]	Cell width	0.5-0.55 µm

[Ref.: #43352]	Cell shape	rod-shaped

[Ref.: #43352]	Motility	yes

[Ref.: #43352]	Colony size	1 mm
[Ref.: #43352]	Colony color	creamish white
[Ref.: #43352]	Colony shape	circular
[Ref.: #43352]	Incubation period	2 days
[Ref.: #43352]	Cultivation medium used	TYEG agar deep (2%; 65°C)

Information on culture and growth conditions Culture and growth conditions

[Ref.: #1984]

Culture medium

THERMOANAEROBACTER BROCKII MEDIUM (DSMZ Medium 144)

[Ref.: #1984]

Culture medium growth

[Ref.: #1984]

Culture medium link

Medium recipe at MediaDive

[Ref.: #1984]

Culture medium composition

expand / minimize

[Ref.: #43352]

Culture medium

TYEG agar deep (2%; 65°C)

[Ref.: #43352]

Culture medium growth

[Ref.: #43352]

Culture medium

TYEG medium

[Ref.: #43352]

Culture medium growth

	Kind of temperature		Temperature
[Ref.: #1984]		growth	70 °C
[Ref.: #43352]		optimum	70 °C
[Ref.: #43352]	no	growth	85 °C
[Ref.: #43352]	no	growth	40 °C
[Ref.: #43352]		growth	47 °C

[Ref.: #1984]	Temperature range	thermophilic
[Ref.: #43352]	Temperature range	thermophilic
[Ref.: #43352]	Temperature range	hyperthermophilic
[Ref.: #43352]	Temperature range	thermophilic

	pH	Kind of pH		pH
[Ref.: #43352]			optimum	7
[Ref.: #43352]			growth	6-8

Information on physiology and metabolism Physiology and metabolism

[Ref.: #1984]	Oxygen tolerance	anaerobe
[Ref.: #43352]	Oxygen tolerance	obligate anaerobe

[Ref.: #43352]

Nutrition type

chemoorganotroph

[Ref.: #43352]

Ability of spore formation

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43352]	acetate ChEBI	-	growth
[Ref.: #43352]	arabinose ChEBI	+	assimilation
[Ref.: #43352]	arginine ChEBI	-	growth
[Ref.: #43352]	carrageenan ChEBI	-	growth
[Ref.: #43352]	cellulose ChEBI	-	degradation
[Ref.: #43352]	citrate ChEBI	-	growth
[Ref.: #43352]	dextrin ChEBI	-	growth
[Ref.: #43352]	formate ChEBI	-	growth
[Ref.: #43352]	fructose ChEBI	+	assimilation
[Ref.: #43352]	fumarate ChEBI	-	growth
[Ref.: #43352]	galactose ChEBI	+	assimilation
[Ref.: #43352]	glucose ChEBI	+	assimilation
[Ref.: #43352]	glutamine ChEBI	-	growth
[Ref.: #43352]	glycerol ChEBI	+	assimilation
[Ref.: #43352]	glycine ChEBI	-	growth
[Ref.: #43352]	inulin ChEBI	-	growth
[Ref.: #43352]	lactate ChEBI	-	growth
[Ref.: #43352]	lactose ChEBI	+	assimilation
[Ref.: #43352]	maltose ChEBI	+	assimilation
[Ref.: #43352]	mannose ChEBI	+	assimilation
[Ref.: #43352]	oxalate ChEBI	-	growth
[Ref.: #43352]	pectin ChEBI	+	assimilation
[Ref.: #43352]	pyruvate ChEBI	+/-	assimilation
[Ref.: #43352]	raffinose ChEBI	+	assimilation
[Ref.: #43352]	rhamnose ChEBI	+/-	assimilation
[Ref.: #43352]	ribose ChEBI	-	assimilation
[Ref.: #43352]	serine ChEBI	-	growth
[Ref.: #43352]	sorbitol ChEBI	+	assimilation
[Ref.: #43352]	succinate ChEBI	-	growth
[Ref.: #43352]	sucrose ChEBI	+	assimilation
[Ref.: #43352]	xanthan ChEBI	-	growth
[Ref.: #43352]	xylitol ChEBI	-	growth
[Ref.: #43352]	xylose ChEBI	-	assimilation
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #43352]	chloramphenicol ChEBI	yes	10	µg/mL
[Ref.: #43352]	d-cycloserine				yes	100	µg/mL
[Ref.: #43352]	d-cycloserine				yes	10	µg/mL
[Ref.: #43352]	neomycin ChEBI				yes	10	µg/mL
[Ref.: #43352]	penicillin ChEBI	yes	10	µg/mL
[Ref.: #43352]	sodium azide ChEBI	yes	500	µg/mL
[Ref.: #43352]	sodium azide ChEBI				yes	250	µg/mL
[Ref.: #43352]	streptomycin ChEBI				yes	10	µg/mL
[Ref.: #43352]	sulfate ChEBI	yes	100	µg/mL
[Ref.: #43352]	tetracycline ChEBI	yes	10	µg/mL

	Metabolite	Production
[Ref.: #43352]	acetate ChEBI	yes
[Ref.: #43352]	carbon dioxide ChEBI	yes
[Ref.: #43352]	dihydrogen ChEBI	yes
[Ref.: #43352]	ethanol ChEBI	yes
[Ref.: #43352]	lactate ChEBI	yes

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #1984]	Sample type/isolated from	hot spring
[Ref.: #1984]	Country	New Zealand
[Ref.: #1984]	Country ISO 3 Code	NZL
[Ref.: #1984]	Continent	Australia and Oceania

[Ref.: #43352]	Sample type/isolated from	Hot Spring
[Ref.: #43352]	Geographic location (country and/or sea, region)	New Zealand
[Ref.: #43352]	Country	New Zealand
[Ref.: #43352]	Country ISO 3 Code	NZL
[Ref.: #43352]	Continent	Australia and Oceania
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #1984]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #20218]	F.nodosum 16S ribosomal RNA	M59177	1456	ENA	2424 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Fervidobacterium nodosum Rt17-B1	GCA_000017545	complete	GenBank	381764 tax ID	*
[Ref.: #66792]	Fervidobacterium nodosum Rt17-B1	381764.8	complete	PATRIC	381764 tax ID	*
[Ref.: #66792]	Fervidobacterium nodosum Rt17-B1	640753026	complete	JGI IMG/M	381764 tax ID	*

[Ref.: #1984]	GC-content	33.7 mol%
[Ref.: #43352]	GC-content	33.7 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Fervidobacterium nodosum Rt17-B1 Rt17-B1 NCBI: GCA_000017545.1
[Ref.: #69480]	motile	yes	87.78	yes
[Ref.: #69480]	flagellated	no	88.961	no
[Ref.: #69480]	gram-positive	no	95.034	no
[Ref.: #69480]	anaerobic	yes	99.629	yes
[Ref.: #69480]	aerobic	no	98.477	yes
[Ref.: #69480]	halophile	no	90.439	no
[Ref.: #69480]	spore-forming	no	91.641	yes
[Ref.: #69480]	thermophile	yes	100	yes
[Ref.: #69480]	glucose-util	yes	90.27	no
[Ref.: #69480]	glucose-ferment	yes	65.84	no

Availability in culture collections External links

[Ref.: #1984]

Culture collection no.

DSM 5306, ATCC 35602

[Ref.: #86033]

SI-ID 41188

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
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) .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#86033

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID41188.1 )

* These data were automatically processed and therefore are not curated

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Fervidobacterium nodosum Rt17-B1 Rt17-B1

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