Strain identifier
BacDive ID: 388
Type strain: 
Species: Candidimonas humi
Strain Designation: SC-092
Strain history: <- C. M. Manaia, Escola Superior de Biotecnol., Univ. Católica Portuguesa, Porto, Portugal; SC-092
NCBI tax ID(s): 683355 (species)
version 9.3 (current version)
General
@ref: 18005
BacDive-ID: 388
DSM-Number: 25336
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Candidimonas humi SC-092 is a mesophilic, Gram-negative bacterium that was isolated from sewage sludge compost.
NCBI tax id
- NCBI tax id: 683355
- Matching level: species
strain history
- @ref: 18005
- history: <- C. M. Manaia, Escola Superior de Biotecnol., Univ. Católica Portuguesa, Porto, Portugal; SC-092
doi: 10.13145/bacdive388.20250331.9.3
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Alcaligenaceae
- genus: Candidimonas
- species: Candidimonas humi
- full scientific name: Candidimonas humi Vaz-Moreira et al. 2011
@ref: 18005
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Alcaligenaceae
genus: Candidimonas
species: Candidimonas humi
full scientific name: Candidimonas humi Vaz-Moreira et al. 2011
strain designation: SC-092
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 125439 | negative | 97.9 |
| 125438 | negative | 95.056 |
Culture and growth conditions
culture medium
- @ref: 18005
- name: NUTRIENT AGAR (DSMZ Medium 1)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1
- composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
culture temp
- @ref: 18005
- growth: positive
- type: growth
- temperature: 28
Physiology and metabolism
spore formation
- @ref: 125439
- spore formation: no
- confidence: 98
fatty acid profile
fatty acids
@ref fatty acid percentage ECL 60743 C16:0 34.5 16 60743 C18:0 5.8 18 60743 C12:0 2OH 1.9 13.178 60743 C12:0 ALDE ? 0.6 10.915 60743 C14:0 3OH/C16:1 ISO I 7.2 15.485 60743 C16:0 2OH 1.4 17.233 60743 C16:1 2OH 0.9 17.047 60743 C16:1 ω7c 7.7 15.819 60743 C17:0 CYCLO 27.9 16.888 60743 C18:1 ω7c /12t/9t 6.9 17.824 60743 C18:2 ω6,9c/C18:0 ANTE 0.5 17.724 60743 C19:0 CYCLO ω8c 1.7 18.9 60743 Unidentified 3 18.135 - type of FA analysis: whole cell analysis
- method/protocol: CCUG
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | sampling date | geographic location |
|---|---|---|---|---|---|---|
| 18005 | sewage sludge compost | Portugal | PRT | Europe | ||
| 60743 | Sewage sludge compost | Portugal | PRT | Europe | 2005 | Porto ? |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Biodegradation | #Composting |
| #Engineered | #Waste | #Sewage sludge |
taxonmaps
- @ref: 69479
- File name: preview.99_20255.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_7;96_2229;97_12455;98_15319;99_20255&stattab=map
- Last taxonomy: Candidimonas
- 16S sequence: FN556192
- Sequence Identity:
- Total samples: 171
- soil counts: 62
- aquatic counts: 50
- animal counts: 42
- plant counts: 17
Safety information
risk assessment
- @ref: 18005
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 18005
- description: Candidimonas humi partial 16S rRNA gene, type strain SC-092T
- accession: FN556192
- length: 1411
- database: nuccore
- NCBI tax ID: 683355
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Candidimonas humi DSM 25336 | GCA_019166065 | contig | ncbi | 683355 |
| 66792 | Candidimonas humi strain DSM 25336 | 683355.3 | wgs | patric | 683355 |
Genome-based predictions
predictions
| @ref | model | trait | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 125438 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 95.056 | no |
| 125438 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 98.432 | no |
| 125438 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 87.576 | no |
| 125438 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 81.16 | no |
| 125438 | thermophile | thermophilic | Ability to grow at temperatures above or equal to 45°C | no | 96.481 | no |
| 125438 | motile2+ | flagellated | Ability to perform flagellated movement | no | 61.575 | no |
| 125439 | BacteriaNet | spore_formation | Ability to form endo- or exospores | no | 98 | |
| 125439 | BacteriaNet | motility | Ability to perform movement | yes | 84.3 | |
| 125439 | BacteriaNet | gram_stain | Reaction to gram-staining | negative | 97.9 | |
| 125439 | BacteriaNet | oxygen_tolerance | Oxygenic conditions needed for growth | facultative aerobe | 71.6 |
External links
@ref: 18005
culture collection no.: DSM 25336, CCUG 55807, LMG 24813
straininfo link
- @ref: 70068
- straininfo: 359549
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 20952543 | Candidimonas nitroreducens gen. nov., sp. nov. and Candidimonas humi sp. nov., isolated from sewage sludge compost. | Vaz-Moreira I, Figueira V, Lopes AR, De Brandt E, Vandamme P, Nunes OC, Manaia CM | Int J Syst Evol Microbiol | 10.1099/ijs.0.021188-0 | 2010 | Alcaligenaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Catalase/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/metabolism, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Sodium Chloride/metabolism, *Soil, Temperature | Metabolism |
| Phylogeny | 22039000 | Candidimonas bauzanensis sp. nov., isolated from soil, and emended description of the genus Candidimonas Vaz-Moreira et al. 2011. | Zhang DC, Busse HJ, Wieser C, Liu HC, Zhou YG, Schinner F, Margesin R | Int J Syst Evol Microbiol | 10.1099/ijs.0.036400-0 | 2011 | Alcaligenaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Italy, Molecular Sequence Data, Phenotype, Phospholipids/analysis, *Phylogeny, Polyamines/analysis, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil Microbiology | Genetics |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 18005 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25336) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-25336 | |
| 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 | |
| 60743 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 55807) | https://www.ccug.se/strain?id=55807 | |
| 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) | |
| 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 | |
| 70068 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID359549.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
| 125438 | Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann | 10.1101/2024.08.12.607695 | Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets | |
| 125439 | Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy | https://github.com/GenomeNet/deepG | deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 |