Strain identifier
BacDive ID: 6139
Type strain:
Species: Tepidiphilus margaritifer
Strain Designation: N2-214
Strain history: <- C. M. Manaia; N2-214
NCBI tax ID(s): 1123354 (strain), 203471 (species)
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 id | Matching level |
---|---|
203471 | species |
1123354 | strain |
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
@ref | motility | confidence | gram stain |
---|---|---|---|
69480 | yes | 98.249 | |
69480 | 100 | negative |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_15129_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15129_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15129_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15129_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15129_5.jpg | electron 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
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Tepidiphilus margaritifer DSM 15129 | GCA_000425565 | scaffold | ncbi | 1123354 |
66792 | Tepidiphilus margaritifer DSM 15129 | 1123354.4 | wgs | patric | 1123354 |
66792 | Tepidiphilus margaritifer DSM 15129 | 2524023151 | draft | img | 1123354 |
GC content
- @ref: 5722
- GC-content: 64.8
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 84 | no |
motile | yes | 92.956 | no |
flagellated | yes | 75.927 | no |
gram-positive | no | 99.08 | no |
anaerobic | no | 88.631 | no |
aerobic | no | 65.668 | no |
halophile | no | 93.589 | no |
spore-forming | no | 95.375 | no |
thermophile | yes | 99.421 | yes |
glucose-util | no | 83.274 | no |
glucose-ferment | no | 87.659 | no |
External links
@ref: 5722
culture collection no.: DSM 15129, LMG 21637
straininfo link
- @ref: 75626
- straininfo: 87495
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 13130025 | Tepidiphilus margaritifer gen. nov., sp. nov., isolated from a thermophilic aerobic digester. | Manaia CM, Nogales B, Nunes OC | Int J Syst Evol Microbiol | 10.1099/ijs.0.02538-0 | 2003 | Betaproteobacteria, 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/microbiology | Stress |
Phylogeny | 21831630 | Characterization of a microbial consortium capable of degrading lignocellulose. | Wang W, Yan L, Cui Z, Gao Y, Wang Y, Jing R | Bioresour Technol | 10.1016/j.biortech.2011.07.065 | 2011 | Bacteria/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, DNA | Metabolism |
Phylogeny | 24048864 | Taxonomic 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 SK | Int J Syst Evol Microbiol | 10.1099/ijs.0.056424-0 | 2013 | Bacterial 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, DNA | Genetics |
Phylogeny | 32318862 | Tepidiphilus 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 Y | Curr Microbiol | 10.1007/s00284-020-01983-8 | 2020 | Bacterial 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 | Transcriptome |
Phylogeny | 32579101 | Tepidiphilus 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 L | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004297 | 2020 | Bacterial 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/analysis | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5722 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15129) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15129 | |||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
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) | |||
75626 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID87495.1 | StrainInfo: A central database for resolving microbial strain identifiers |