Strain identifier

BacDive ID: 6139

Type strain: Yes

Species: Tepidiphilus margaritifer

Strain Designation: N2-214

Strain history: <- C. M. Manaia; N2-214

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 5722

BacDive-ID: 6139

DSM-Number: 15129

keywords: genome sequence, 16S sequence, Bacteria, thermophilic, motile

description: Tepidiphilus margaritifer N2-214 is a thermophilic, motile bacterium that was isolated from thermophilic digester of wastewater-treatment sludge.

NCBI tax id

NCBI tax idMatching level
203471species
1123354strain

strain history

  • @ref: 5722
  • history: <- C. M. Manaia; N2-214

doi: 10.13145/bacdive6139.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Hydrogenophilia
  • order: Hydrogenophilales
  • family: Hydrogenophilaceae
  • genus: Tepidiphilus
  • species: Tepidiphilus margaritifer
  • full scientific name: Tepidiphilus margaritifer Manaia et al. 2003

@ref: 5722

domain: Bacteria

phylum: Proteobacteria

class: Hydrogenophilalia

order: Hydrogenophilales

family: Hydrogenophilaceae

genus: Tepidiphilus

species: Tepidiphilus margaritifer

full scientific name: Tepidiphilus margaritifer Manaia et al. 2003 emend. Poddar et al. 2014

strain designation: N2-214

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes98.249
69480100negative

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_15129_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15129_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15129_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15129_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_15129_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 5722
  • name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/381
  • composition: Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water

culture temp

  • @ref: 5722
  • growth: positive
  • type: growth
  • temperature: 50
  • range: thermophilic

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.995

Isolation, sampling and environmental information

isolation

  • @ref: 5722
  • sample type: thermophilic digester of wastewater-treatment sludge
  • geographic location: Porto
  • country: Portugal
  • origin.country: PRT
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation
#Engineered#Waste#Wastewater
#Environmental#Terrestrial#Mud (Sludge)
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1062.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16099;96_612;97_715;98_834;99_1062&stattab=map
  • Last taxonomy: Tepidiphilus margaritifer
  • 16S sequence: AJ504663
  • Sequence Identity:
  • Total samples: 645
  • soil counts: 18
  • aquatic counts: 415
  • animal counts: 193
  • plant counts: 19

Safety information

risk assessment

  • @ref: 5722
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 5722
  • description: Tepidiphilus margaritifer partial 16S rRNA gene, type strain N2-214T
  • accession: AJ504663
  • length: 1456
  • database: ena
  • NCBI tax ID: 1123354

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Tepidiphilus margaritifer DSM 15129GCA_000425565scaffoldncbi1123354
66792Tepidiphilus margaritifer DSM 151291123354.4wgspatric1123354
66792Tepidiphilus margaritifer DSM 151292524023151draftimg1123354

GC content

  • @ref: 5722
  • GC-content: 64.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno84no
motileyes92.956no
flagellatedyes75.927no
gram-positiveno99.08no
anaerobicno88.631no
aerobicno65.668no
halophileno93.589no
spore-formingno95.375no
thermophileyes99.421yes
glucose-utilno83.274no
glucose-fermentno87.659no

External links

@ref: 5722

culture collection no.: DSM 15129, LMG 21637

straininfo link

  • @ref: 75626
  • straininfo: 87495

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130025Tepidiphilus margaritifer gen. nov., sp. nov., isolated from a thermophilic aerobic digester.Manaia CM, Nogales B, Nunes OCInt J Syst Evol Microbiol10.1099/ijs.0.02538-02003Betaproteobacteria, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Hot Temperature, Hydrogenophilaceae/classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sewage/microbiologyStress
Phylogeny21831630Characterization of a microbial consortium capable of degrading lignocellulose.Wang W, Yan L, Cui Z, Gao Y, Wang Y, Jing RBioresour Technol10.1016/j.biortech.2011.07.0652011Bacteria/genetics/*metabolism, Base Sequence, Biodegradation, Environmental, *Bioreactors, Cluster Analysis, Computational Biology, DNA Primers/genetics, Denaturing Gradient Gel Electrophoresis, Lignin/*metabolism, Molecular Sequence Data, Oryza/*chemistry, Phylogeny, Plant Stems/*chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Phylogeny24048864Taxonomic study of the genus Tepidiphilus: transfer of Petrobacter succinatimandens to the genus Tepidiphilus as Tepidiphilus succinatimandens comb. nov., emended description of the genus Tepidiphilus and description of Tepidiphilus thermophilus sp. nov., isolated from a terrestrial hot spring.Poddar A, Lepcha RT, Das SKInt J Syst Evol Microbiol10.1099/ijs.0.056424-02013Bacterial Typing Techniques, Base Composition, Betaproteobacteria/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/microbiology, Hot Springs/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny32318862Tepidiphilus baoligensis sp. nov., a Novel Bacterium of the Family Hydrogenophilaceae Isolated from an Oil Reservoir.Zhang X, Wang G, Ma X, Yu J, You J, Xue Y, Ma YCurr Microbiol10.1007/s00284-020-01983-82020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrogenophilaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny32579101Tepidiphilus olei sp. nov., isolated from the production water of a water-flooded oil reservoir in PR China.Wang XT, Shan JJ, Li XZ, Lin W, Xiu JL, Li DA, Zhang YZ, Wang LInt J Syst Evol Microbiol10.1099/ijsem.0.0042972020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hydrogenophilaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Oil and Gas Fields/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry, Water/analysisTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5722Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15129)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15129
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
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75626Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87495.1StrainInfo: A central database for resolving microbial strain identifiers