Strain identifier
BacDive ID: 130290
Type strain: 
Species: Thiogranum longum
Strain Designation: gps52
Strain history: <- K. Mori, NBRC; NBRC 101260 <- K. Mori and S. Hanada, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan; gps52 {2003}
NCBI tax ID(s): 1537524 (species)
version 9.3 (current version)
General
@ref: 22132
BacDive-ID: 130290
DSM-Number: 19610
keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative
description: Thiogranum longum gps52 is a microaerophile, mesophilic, Gram-negative bacterium that was isolated from rock samples from a deep-sea hydrothermal field.
NCBI tax id
- NCBI tax id: 1537524
- Matching level: species
strain history
- @ref: 22132
- history: <- K. Mori, NBRC; NBRC 101260 <- K. Mori and S. Hanada, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan; gps52 {2003}
doi: 10.13145/bacdive130290.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Ectothiorhodospiraceae
- genus: Thiogranum
- species: Thiogranum longum
- full scientific name: Thiogranum longum Mori et al. 2015
@ref: 22132
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Ectothiorhodospiraceae
genus: Thiogranum
species: Thiogranum longum
full scientific name: Thiogranum longum Mori et al. 2015
strain designation: gps52
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 97.1 |
| 125438 | negative | 99.494 |
colony morphology
- @ref: 22132
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 22132
- name: THIOGRANUM MEDIUM (DSMZ Medium 1570)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1570
- composition: Name: THIOGRANUM MEDIUM (DSMZ Medium 1570) Composition: MgCl2 x 6 H2O 3.00197 g/l Na2S2O3 x 5 H2O 1.47638 g/l Na2CO3 0.984252 g/l (NH4)2SO4 0.649606 g/l KH2PO4 0.58563 g/l KCl 0.324803 g/l K2HPO4 0.103346 g/l MgSO4 x 7 H2O 0.0295276 g/l Nitrilotriacetic acid 0.0147638 g/l NaCl 0.00984252 g/l MnSO4 x H2O 0.00492126 g/l ZnSO4 x 7 H2O 0.00177165 g/l CoSO4 x 7 H2O 0.00177165 g/l FeSO4 x 7 H2O 0.000984252 g/l CaCl2 x 2 H2O 0.000984252 g/l NiCl2 x 6 H2O 0.000295276 g/l AlK(SO4)2 x 12 H2O 0.00019685 g/l Pyridoxine hydrochloride 9.84252e-05 g/l CuSO4 x 5 H2O 9.84252e-05 g/l Na2MoO4 x 2 H2O 9.84252e-05 g/l H3BO3 9.84252e-05 g/l (DL)-alpha-Lipoic acid 4.92126e-05 g/l p-Aminobenzoic acid 4.92126e-05 g/l Calcium D-(+)-pantothenate 4.92126e-05 g/l Nicotinic acid 4.92126e-05 g/l Riboflavin 4.92126e-05 g/l Thiamine HCl 4.92126e-05 g/l Folic acid 1.9685e-05 g/l Biotin 1.9685e-05 g/l Na2WO4 x 2 H2O 3.93701e-06 g/l Na2SeO3 x 5 H2O 2.95276e-06 g/l Vitamin B12 9.84252e-07 g/l Distilled water
culture temp
- @ref: 22132
- growth: positive
- type: growth
- temperature: 30
Physiology and metabolism
oxygen tolerance
- @ref: 22132
- oxygen tolerance: microaerophile
spore formation
- @ref: 125439
- spore formation: no
- confidence: 99.1
Isolation, sampling and environmental information
isolation
- @ref: 22132
- sample type: rock samples from a deep-sea hydrothermal field
- geographic location: off the eastern coast, Suiyo Seamount
- country: Japan
- origin.country: JPN
- continent: Asia
- latitude: 28.6
- longitude: 140.633
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Hydrothermal vent |
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Geologic |
| #Condition | #Thermophilic (>45°C) |
taxonmaps
- @ref: 69479
- File name: preview.99_14134.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_159;96_7298;97_8748;98_10722;99_14134&stattab=map
- Last taxonomy: Thiogranum longum subclade
- 16S sequence: AB983478
- Sequence Identity:
- Total samples: 2140
- soil counts: 79
- aquatic counts: 1926
- animal counts: 132
- plant counts: 3
Safety information
risk assessment
- @ref: 22132
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22132
- description: Thiogranum longum gene for 16S ribosomal RNA, partial sequence
- accession: AB983478
- length: 1508
- database: nuccore
- NCBI tax ID: 1537524
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thiogranum longum DSM 19610 | GCA_004339085 | scaffold | ncbi | 1537524 |
| 66792 | Thiogranum longum strain DSM 19610 | 1537524.3 | wgs | patric | 1537524 |
| 66792 | Thiogranum longum DSM 19610 | 2770939547 | draft | img | 1537524 |
GC content
- @ref: 22132
- GC-content: 53.8
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 99.494 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 85.766 | yes |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 50.442 | yes |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.922 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 90.206 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | yes | 69.476 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 99.1 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 79.5 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 97.1 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | aerobe | 81.6 |
External links
@ref: 22132
culture collection no.: DSM 19610, NBRC 101260
straininfo link
- @ref: 88825
- straininfo: 402744
literature
- topic: Phylogeny
- Pubmed-ID: 25336721
- title: Thiogranum longum gen. nov., sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing bacterium of the family Ectothiorhodospiraceae isolated from a deep-sea hydrothermal field, and an emended description of the genus Thiohalomonas.
- authors: Mori K, Suzuki KI, Yamaguchi K, Urabe T, Hanada S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.070599-0
- year: 2014
- mesh: Bacterial Typing Techniques, Base Composition, Chemoautotrophic Growth, DNA, Bacterial/genetics, Ectothiorhodospiraceae/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Hydrothermal Vents/*microbiology, Molecular Sequence Data, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sulfur/*metabolism, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 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 | 10.1099/ijsem.0.004332 | |||
| 22132 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19610 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19610) | |||
| 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) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 88825 | 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 | 10.60712/SI-ID402744.1 | |||
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | 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 | https://github.com/GenomeNet/deepG |