Archive BacDiveID:10.13145/bacdive17036.20230509.8.1

Strain identifier

BacDive ID: 17036

Type strain:

Species: Fervidobacterium gondwanense

Strain Designation: AB39

Strain history: <- ACM <- K. T. Andrews and B. K. C. Patel, Griffith Univ., Brisbane, Australia; AB39

NCBI tax ID(s): 1121883 (strain), 44754 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.

General

@ref: 4873

BacDive-ID: 17036

DSM-Number: 13020

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, thermophilic, Gram-negative

description: Fervidobacterium gondwanense AB39 is an anaerobe, thermophilic, Gram-negative bacterium that was isolated from geothermal water.

NCBI tax id

NCBI tax id	Matching level
44754	species
1121883	strain

strain history

@ref: 4873
history: <- ACM <- K. T. Andrews and B. K. C. Patel, Griffith Univ., Brisbane, Australia; AB39

doi: 10.13145/bacdive17036.20230509.8.1

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 gondwanense
full scientific name: Fervidobacterium gondwanense Andrews and Patel 1996

@ref: 4873

domain: Bacteria

phylum: Thermotogae

class: Thermotogae

order: Thermotogales

family: Fervidobacteriaceae

genus: Fervidobacterium

species: Fervidobacterium gondwanense

full scientific name: Fervidobacterium gondwanense Andrews and Patel 1996

strain designation: AB39

type strain: yes

Morphology

cell morphology

@ref: 69480
gram stain: negative
confidence: 99.739

Culture and growth conditions

culture medium

@ref: 4873
name: FERVIDOBACTERIUM TF(A) MEDIUM (DSMZ Medium 740)
growth: yes
link: https://mediadive.dsmz.de/medium/740
composition: Name: FERVIDOBACTERIUM TF(A) MEDIUM (DSMZ Medium 740) Composition: D-Glucose 2.96736 g/l Trypticase peptone 1.97824 g/l Yeast extract 1.97824 g/l K2HPO4 1.58259 g/l Na2HPO4 x H2O 0.98912 g/l NH4Cl 0.49456 g/l L-Cysteine HCl x H2O 0.296736 g/l Na2S x 9 H2O 0.296736 g/l CaCl2 x 2 H2O 0.0593472 g/l MgSO4 x 7 H2O 0.0296736 g/l Nitrilotriacetic acid 0.0148368 g/l NaCl 0.0098912 g/l MnSO4 x H2O 0.0049456 g/l ZnSO4 x 7 H2O 0.00178042 g/l CoSO4 x 7 H2O 0.00178042 g/l FeSO4 x 7 H2O 0.00098912 g/l Sodium resazurin 0.00049456 g/l NiCl2 x 6 H2O 0.000296736 g/l AlK(SO4)2 x 12 H2O 0.000197824 g/l CuSO4 x 5 H2O 9.8912e-05 g/l H3BO3 9.8912e-05 g/l Na2MoO4 x 2 H2O 9.8912e-05 g/l Pyridoxine hydrochloride 9.8912e-05 g/l Riboflavin 4.9456e-05 g/l (DL)-alpha-Lipoic acid 4.9456e-05 g/l Thiamine HCl 4.9456e-05 g/l p-Aminobenzoic acid 4.9456e-05 g/l Nicotinic acid 4.9456e-05 g/l Calcium D-(+)-pantothenate 4.9456e-05 g/l Biotin 1.97824e-05 g/l Folic acid 1.97824e-05 g/l Na2WO4 x 2 H2O 3.95648e-06 g/l Na2SeO3 x 5 H2O 2.96736e-06 g/l Vitamin B12 9.8912e-07 g/l Distilled water

culture temp

@ref	growth	type	temperature	range	confidence
4873	positive	growth	65	thermophilic
69480				thermophilic	100

Physiology and metabolism

oxygen tolerance

@ref	oxygen tolerance	confidence
4873	anaerobe
69480	anaerobe	100

spore formation

@ref	spore formation	confidence
69481	no	96
69480	no	99.72

compound production

@ref: 4873
compound: restriction endonuclease FgoI

Isolation, sampling and environmental information

isolation

@ref: 4873
sample type: geothermal water
geographic location: Great Artesian Basin
country: Australia
origin.country: AUS
continent: Australia and Oceania

isolation source categories

Cat1: #Environmental
Cat2: #Aquatic

taxonmaps

@ref: 69479
File name: preview.99_85185.png
url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_134;96_9552;97_45085;98_59002;99_85185&stattab=map
Last taxonomy: Fervidobacterium gondwanense
16S sequence: Z49117
Sequence Identity:
Total samples: 68
soil counts: 2
aquatic counts: 54
animal counts: 1
plant counts: 11

Safety information

risk assessment

@ref: 4873
biosafety level: 1
biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@ref: 4873
description: F.gondwanalandicum gene for 16S ribosomal RNA
accession: Z49117
length: 1478
database: ena
NCBI tax ID: 44754

Genome sequences

@ref	description	accession	assembly level	database	NCBI tax ID
66792	Fervidobacterium gondwanense DSM 13020	GCA_900143265	scaffold	ncbi	1121883
66792	Fervidobacterium gondwanense DSM 13020	1121883.3	wgs	patric	1121883
66792	Fervidobacterium gondwanense DSM 13020	2582580731	draft	img	1121883

GC content

@ref: 4873
GC-content: 35
method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

trait	prediction	confidence	training_data
spore-forming	no	96	no
motile	yes	87.377	no
flagellated	no	90.62	no
gram-positive	no	93.414	no
anaerobic	yes	99.616	yes
aerobic	no	98.479	yes
halophile	no	91.666	no
spore-forming	no	89.339	no
thermophile	yes	100	yes
glucose-util	yes	91.473	no
glucose-ferment	yes	64.214	no

External links

@ref: 4873

culture collection no.: DSM 13020, ACM 5017

straininfo link

@ref: 86036
straininfo: 49387

literature

topic	Pubmed-ID	title	authors	journal	DOI	year	mesh	topic2
Phylogeny	8573506	Fervidobacterium gondwanense sp. nov., a new thermophilic anaerobic bacterium isolated from nonvolcanically heated geothermal waters of the Great Artesian Basin of Australia.	Andrews KT, Patel BK	Int J Syst Bacteriol	10.1099/00207713-46-1-265	1996	Australia, Base Composition, Base Sequence, DNA, Bacterial/genetics, Fermentation, Gram-Negative Anaerobic Bacteria/*classification/genetics/isolation & purification/metabolism/ultrastructure, Microbial Sensitivity Tests, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sulfides, Water Microbiology	Genetics
Phylogeny	12361295	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	Bacteria, 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 Specificity	Genetics

Reference

@id	authors	catalogue	doi/url	title
4873	Curators of the DSMZ	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13020)	https://www.dsmz.de/collection/catalogue/details/culture/DSM-13020
20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.		10.1099/ijsem.0.004332	List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69479	João 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
69480	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann		https://diaspora-project.de/progress.html#genomes	Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481	Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch		10.21203/rs.3.rs-2527258/v1	Predictions based on the model GenomeNet Sporulation v. 1
86036	Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.		10.60712/SI-ID49387.1	StrainInfo: A central database for resolving microbial strain identifiers