Strain identifier
BacDive ID: 14137
Type strain: 
Species: Parapedobacter luteus
Strain Designation: 4M29
Strain history: S.-W. Kwon 4M29.
NCBI tax ID(s): 623280 (species)
version 8.1 (current version)
General
@ref: 16610
BacDive-ID: 14137
DSM-Number: 22899
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Parapedobacter luteus 4M29 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from cotton waste compost.
NCBI tax id
- NCBI tax id: 623280
- Matching level: species
strain history
| @ref | history |
|---|---|
| 16610 | <- S.-W. Kwon, KACC; 4M29 <- H.-Y. Weon |
| 67770 | S.-W. Kwon 4M29. |
doi: 10.13145/bacdive14137.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Parapedobacter
- species: Parapedobacter luteus
- full scientific name: Parapedobacter luteus Kim et al. 2010
@ref: 16610
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Parapedobacter
species: Parapedobacter luteus
full scientific name: Parapedobacter luteus Kim et al. 2010
strain designation: 4M29
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29451 | negative | 1.3-2.5 µm | 0.5 µm | rod-shaped | no | |
| 69480 | negative | 99.994 |
pigmentation
- @ref: 29451
- production: yes
Culture and growth conditions
culture medium
- @ref: 16610
- name: R2A MEDIUM (DSMZ Medium 830)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830
- composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16610 | positive | growth | 28 | mesophilic |
| 29451 | positive | growth | 15-45 | |
| 29451 | positive | optimum | 30 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29451 | positive | growth | 06-08 |
| 29451 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 29451
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29451 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.995 |
halophily
- @ref: 29451
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-5 %
observation
| @ref | observation |
|---|---|
| 29451 | aggregates in chains |
| 67770 | quinones: MK-7 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29451 | 22599 | arabinose | + | carbon source |
| 29451 | 17234 | glucose | + | carbon source |
| 29451 | 28087 | glycogen | + | carbon source |
| 29451 | 17306 | maltose | + | carbon source |
| 29451 | 37684 | mannose | + | carbon source |
| 29451 | 28053 | melibiose | + | carbon source |
| 29451 | 26271 | proline | + | carbon source |
| 29451 | 26546 | rhamnose | + | carbon source |
| 29451 | 17992 | sucrose | + | carbon source |
| 29451 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29451 | catalase | + | 1.11.1.6 |
| 29451 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 16610 | cotton waste compost | Suwon | Republic of Korea | KOR | Asia |
| 67770 | Cotton waste compost | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Agriculture | |
| #Engineered | #Biodegradation | #Composting |
| #Engineered | #Waste | #Solid plant waste |
| #Host | #Plants | #Shrub (Scrub) |
taxonmaps
- @ref: 69479
- File name: preview.99_4811.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15793;96_2374;97_2890;98_3601;99_4811&stattab=map
- Last taxonomy: Parapedobacter luteus subclade
- 16S sequence: FJ754320
- Sequence Identity:
- Total samples: 509
- soil counts: 136
- aquatic counts: 103
- animal counts: 230
- plant counts: 40
Safety information
risk assessment
- @ref: 16610
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16610
- description: Parapedobacter luteus strain 4M29 16S ribosomal RNA gene, partial sequence
- accession: FJ754320
- length: 1463
- database: ena
- NCBI tax ID: 623280
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Parapedobacter luteus strain DSM 22899 | 623280.3 | wgs | patric | 623280 |
| 66792 | Parapedobacter luteus DSM 22899 | 2595698205 | draft | img | 623280 |
| 67770 | Parapedobacter luteus DSM 22899 | GCA_900168055 | scaffold | ncbi | 623280 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16610 | 47.6 | high performance liquid chromatography (HPLC) |
| 29451 | 47.6 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.514 | yes |
| anaerobic | no | 99.11 | yes |
| halophile | no | 90.2 | no |
| spore-forming | no | 94.602 | no |
| glucose-util | yes | 92.154 | yes |
| flagellated | no | 97.816 | yes |
| aerobic | yes | 85.229 | yes |
| thermophile | no | 97.858 | no |
| motile | no | 92.81 | no |
| glucose-ferment | no | 87.686 | no |
External links
@ref: 16610
culture collection no.: DSM 22899, JCM 15977, KACC 10955
straininfo link
- @ref: 83302
- straininfo: 400418
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 19767359 | Parapedobacter luteus sp. nov. and Parapedobacter composti sp. nov., isolated from cotton waste compost. | Kim SJ, Weon HY, Kim YS, Yoo SH, Kim BY, Anandham R, Kwon SW | Int J Syst Evol Microbiol | 10.1099/ijs.0.013318-0 | 2009 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Gossypium/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sphingobacterium/*classification/genetics/*isolation & purification/metabolism, Waste Products/*analysis | Metabolism |
| Phylogeny | 33013721 | Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae. | Nagar S, Talwar C, Haider S, Puri A, Ponnusamy K, Gupta M, Sood U, Bajaj A, Lal R, Kumar R | Front Microbiol | 10.3389/fmicb.2020.01725 | 2020 |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 16610 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22899) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22899 | ||||
| 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 | ||||
| 29451 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25856 | 28776041 | ||
| 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) | ||||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
| 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) | ||||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
| 83302 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400418.1 | StrainInfo: A central database for resolving microbial strain identifiers |