Strain identifier
BacDive ID: 130603
Type strain: 
Species: Falsigemmobacter intermedius
Strain Designation: 119/4
Strain history: CIP <- 2014, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 119/4
NCBI tax ID(s): 1553448 (species)
version 9.1 (current version)
General
@ref: 21597
BacDive-ID: 130603
DSM-Number: 28642
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, rod-shaped
description: Falsigemmobacter intermedius 119/4 is a Gram-negative, rod-shaped bacterium that was isolated from choana swab of a white stork nestling .
NCBI tax id
- NCBI tax id: 1553448
- Matching level: species
strain history
| @ref | history |
|---|---|
| 35292 | 2014, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 119/4 |
| 21597 | <- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; 119/4 <- R. K. J. Wilharm, Robert-Koch-Institut, Wernigerode, Germany |
| 115973 | CIP <- 2014, P. Kämpfer, Giessen Univ., Giessen, Germany: strain 119/4 |
doi: 10.13145/bacdive130603.20240916.9.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Paracoccaceae
- genus: Falsigemmobacter
- species: Falsigemmobacter intermedius
- full scientific name: Falsigemmobacter intermedius (Kämpfer et al. 2015) Li et al. 2023
synonyms
- @ref: 20215
- synonym: Gemmobacter intermedius
@ref: 21597
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Gemmobacter
species: Gemmobacter intermedius
full scientific name: Gemmobacter intermedius Kämpfer et al. 2015
strain designation: 119/4
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 115973 | negative | rod-shaped | no | |
| 69480 | negative | 97.333 |
Culture and growth conditions
culture medium
| @ref | name | growth | composition | link |
|---|---|---|---|---|
| 35292 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
| 21597 | LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) | yes | 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 | https://mediadive.dsmz.de/medium/381 |
| 115973 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
| @ref | growth | type | temperature |
|---|---|---|---|
| 35292 | positive | growth | 30 |
| 21597 | positive | growth | 37 |
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 99
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | country | origin.country | continent |
|---|---|---|---|---|---|
| 21597 | choana swab of a white stork nestling (Ciconia ciconia) | Ciconia ciconia | Poland | POL | Europe |
| 115973 | Animal, Stork | Poland | POL | Europe |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Patient | #Swab |
| #Host | #Birds | |
| #Host Body-Site | #Oral cavity and airways | #Airways |
taxonmaps
- @ref: 69479
- File name: preview.99_59545.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_8322;97_32983;98_42329;99_59545&stattab=map
- Last taxonomy: Poaceae
- 16S sequence: KM407667
- Sequence Identity:
- Total samples: 1231
- soil counts: 80
- aquatic counts: 547
- animal counts: 520
- plant counts: 84
Safety information
risk assessment
| @ref | biosafety level | biosafety level comment |
|---|---|---|
| 21597 | 1 | Risk group (German classification) |
| 115973 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 21597
- description: Falsigemmobacter intermedius strain 119/4 16S ribosomal RNA gene, partial sequence
- accession: KM407667
- length: 1344
- database: nuccore
- NCBI tax ID: 1553448
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Gemmobacter intermedius 119/4 | GCA_004054105 | scaffold | ncbi | 1553448 |
| 66792 | Gemmobacter intermedius 119/4 | 2891541355 | draft | img | 1553448 |
GC content
- @ref: 21597
- GC-content: 64
- method: fluorimetric
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 99 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.333 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 94.226 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 82.95 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.361 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 93.333 | yes |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | no | 54.394 | no |
External links
@ref: 21597
culture collection no.: DSM 28642, CCM 8510, CIP 110795, LMG 28215
straininfo link
- @ref: 89117
- straininfo: 399541
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25479954 | Gemmobacter intermedius sp. nov., isolated from a white stork (Ciconia ciconia). | Kampfer P, Jerzak L, Wilharm G, Golke J, Busse HJ, Glaeser SP | Int J Syst Evol Microbiol | 10.1099/ijs.0.000012 | 2014 | Animals, Bacterial Typing Techniques, Base Composition, Birds/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, Poland, Putrescine/chemistry, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Spermidine/chemistry, Ubiquinone/chemistry | Genetics |
| Phylogeny | 32686033 | Falsigemmobacter faecalis gen. nov. sp. nov., isolated from faeces of Rhinopithecus roxellanae, and reclassification of Gemmobacter intermedius as Falsigemmobacter intermedius comb. nov. | Li G, Jiang Y, Li Q, Chen X, Jiang L, Zhang K, An D, Lang L, Han L, Huang X, Jiang C | Arch Microbiol | 10.1007/s00203-020-01978-w | 2020 | Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Feces/microbiology, Phosphatidylethanolamines, *Phylogeny, Presbytini/*microbiology, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Species Specificity | Enzymology |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 21597 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28642 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28642) | |
| 35292 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/30608 | ||
| 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 | |
| 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/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 89117 | 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-ID399541.1 | |
| 115973 | Curators of the CIP | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110795 | Collection of Institut Pasteur (CIP 110795) |