Strain identifier
BacDive ID: 132651
Type strain: 
Species: Endomicrobium proavitum
Strain Designation: Rsa215
Strain history: A. Brune; Max Planck Inst. for Terrestrial Microbiol., Germany; Rsa215.
NCBI tax ID(s): 1408281 (species)
version 9.3 (current version)
General
@ref: 24440
BacDive-ID: 132651
DSM-Number: 29378
keywords: genome sequence, Bacteria, anaerobe, mesophilic, Gram-negative
description: Endomicrobium proavitum Rsa215 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from filtered gut homogenate of starch-fed termite Reticulitermes santonensis .
NCBI tax id
- NCBI tax id: 1408281
- Matching level: species
strain history
| @ref | history |
|---|---|
| 24440 | <- A. Brune, MPI, Marburg, Germany; Rsa215 <- H. Zheng |
| 67770 | A. Brune; Max Planck Inst. for Terrestrial Microbiol., Germany; Rsa215. |
doi: 10.13145/bacdive132651.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/elusimicrobiota
- domain: Bacteria
- phylum: Elusimicrobiota
- class: Endomicrobiia
- order: Endomicrobiales
- family: Endomicrobiaceae
- genus: Endomicrobium
- species: Endomicrobium proavitum
- full scientific name: Endomicrobium proavitum Zheng et al. 2018
@ref: 24440
domain: Bacteria
phylum: Elusimicrobia
class: Endomicrobia
order: Endomicrobiales
family: Endomicrobiaceae
genus: Endomicrobium
species: Endomicrobium proavitum
full scientific name: Endomicrobium proavitum Zheng et al. 2018
strain designation: Rsa215
type strain: no
Morphology
cell morphology
- @ref: 125438
- gram stain: negative
- confidence: 93.423
Culture and growth conditions
culture medium
- @ref: 24440
- name: OMIZ-PAT (DSMZ Medium 1494)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1494
- composition: Name: . OMIZ-PAT Medium (modified) (DSMZ Medium 1494) Composition: (NH4)6Mo7O24 x 4 H2O 12.4 g/l Yeast extract 3.0 g/l Fe SO4 x 7 H2O 2.78015 g/l D-Glucose 2.0 g/l D-Mannose 2.0 g/l D-Arabinose 2.0 g/l L-Fucose 2.0 g/l D-Trehalose 2.0 g/l D-Sucrose 2.0 g/l L-Rhamnose 2.0 g/l NH4Cl 1.6 g/l Glutathione 1.5366 g/l Ascorbic acid 1.0 g/l NaHCO3 1.0 g/l Ethanol 1.0 g/l KCl 0.968 g/l D-Maltose 0.8 g/l D-glucuronic acid 0.8 g/l D-Mannitol 0.8 g/l D-galacturonic acid 0.8 g/l D-Fructose 0.8 g/l L-Glutamine 0.68 g/l L-Histidine 0.62 g/l NaVO3 0.61 g/l D 0.56 g/l Pyruvic acid 0.55 g/l L-Serine 0.525 g/l Fumaric acid 0.5 g/l HCl 0.3646 g/l L-Cysteine HCl 0.35 g/l L-Glutamic acid 0.3 g/l Formic acid 0.3 g/l ZnSO4 x 7 H2O 0.287 g/l MgSO4 x 7 H2O 0.25 g/l DL-carnitine 0.2 g/l N-Acetylglucosamine 0.2 g/l Citric acid 0.2 g/l L-Lysine HCl 0.182 g/l L-Arginine 0.175 g/l L-Ornithine HCl 0.17 g/l L-Phenylalanine 0.165 g/l CaCl2 x H2O 0.15 g/l L-Methionine 0.15 g/l L-Asparagine 0.15 g/l NaH2PO4 x H2O 0.14 g/l L-Leucine 0.131 g/l L-Isoleucine 0.131 g/l NiSO4 x 6 H2O 0.131 g/l L-Threonine 0.12 g/l L-Aspartic acid 0.118 g/l SnCl2 x 2 H2O 0.118 g/l L-Valine 0.117 g/l L-Proline 0.115 g/l L-Tryptophan 0.102 g/l Nicotinic acid 0.1 g/l Folinic acid 0.1 g/l L-Tyrosine 0.09 g/l NaOH 0.079994 g/l Glycine 0.075 g/l Nicotinamide 0.05 g/l Folic acid 0.05 g/l D-(+)-biotin 0.05 g/l Vitamine B12 0.05 g/l Choline chloride 0.05 g/l Myo-inositol 0.05 g/l L-Alanine 0.045 g/l Hemin 0.026076 g/l N-acetylmuramic acid 0.025 g/l Na2SeO3 0.0173 g/l MnSO4 x H2O 0.0169 g/l Riboflavine 0.01 g/l 2-Mercaptoethanesulfonic acid 0.01 g/l Phenol red 0.01 g/l Putrescine 2 HCl 0.005 g/l Pyridoxal hydrochloride 0.005 g/l Pyridoxal phosphate 0.005 g/l Calcium D-(+)-pantothenate 0.005 g/l Thiamine HCl 0.005 g/l Thiamin pyrophosphate 0.005 g/l Thymidine 0.0024 g/l N-(2-acetamido)-2-aminoethanesulfonic acid 0.0018 g/l Hypoxanthine 0.0014 g/l Uracil 0.0011 g/l Flavin adenine dinucleotide 0.001 g/l ß-nicotinamide adenine dinucleotide 0.001 g/l Coenzym A 0.001 g/l CuSO4 0.000789 g/l Cholesterol Asialofetuin 2-Mercaptoethanol Isovaleric acid Valeric acid 2-Methylbutyric acid Isobutyric acid DL-alpha-lipoic acid Rabbit serum Distilled water
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 24440 | positive | growth | 30 |
| 67770 | positive | growth | 30 |
Physiology and metabolism
oxygen tolerance
- @ref: 125438
- oxygen tolerance: anaerobe
- confidence: 93.222
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 125439 | no | 96.4 |
| 125438 | no | 93.185 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 24440 | filtered gut homogenate (0.22 µm pore size) of starch-fed termite Reticulitermes santonensis (Isoptera: Rhinotermitidae) | Reticulitermes santonensis | Saint-Georges-d'Oléron | France | FRA | Europe |
| 67770 | Hindgut of the termite Reticulitermes santonensis | Reticulitermes santonensis |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Arthropoda | #Insecta |
| #Host Body-Site | #Gastrointestinal tract | #Stomach |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Endomicrobium proavitum Rsa215 | GCA_001027545 | complete | ncbi | 1408281 |
| 66792 | Endomicrobium proavitum strain Rsa215 | 1408281.4 | complete | patric | 1408281 |
| 66792 | Endomicrobium proavitum Rsa215 | 2639763091 | complete | img | 1408281 |
GC content
- @ref: 24440
- GC-content: 39.3
- method: sequence analysis
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 93.423 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | yes | 93.222 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | no | 95.92 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 93.185 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 82.992 | yes |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 78.95 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 96.4 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | no | 72 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 72.3 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | obligate anaerobe | 80 |
External links
@ref: 24440
culture collection no.: DSM 29378, JCM 30189, JCM 32103
straininfo link
- @ref: 90964
- straininfo: 405635
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26119974 | Endomicrobium proavitum, the first isolate of Endomicrobia class. nov. (phylum Elusimicrobia)--an ultramicrobacterium with an unusual cell cycle that fixes nitrogen with a Group IV nitrogenase. | Zheng H, Dietrich C, Radek R, Brune A | Environ Microbiol | 10.1111/1462-2920.12960 | 2015 | Acetylene/metabolism, Animals, Bacteria/*classification/*genetics/isolation & purification/metabolism, Cell Cycle/genetics, Isoptera/*microbiology, Nitrogen/metabolism, Nitrogen Fixation/*genetics, Nitrogenase/*genetics/metabolism, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Symbiosis/genetics | Metabolism |
| Genetics | 26184928 | Complete Genome Sequence of Endomicrobium proavitum, a Free-Living Relative of the Intracellular Symbionts of Termite Gut Flagellates (Phylum Elusimicrobia). | Zheng H, Brune A | Genome Announc | 10.1128/genomeA.00679-15 | 2015 |
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 | |||
| 24440 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29378 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29378) | |||
| 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 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 90964 | 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-ID405635.1 | |||
| 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 |