Strain identifier
BacDive ID: 14095
Type strain:
Species: Pseudopedobacter saltans
Strain Designation: 113
Strain history: CIP <- 1998, LMG <- P. Steyn: strain 113
NCBI tax ID(s): 762903 (strain), 151895 (species)
General
@ref: 4555
BacDive-ID: 14095
DSM-Number: 12145
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative
description: Pseudopedobacter saltans 113 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
762903 | strain |
151895 | species |
strain history
@ref | history |
---|---|
4555 | <- LMG |
67770 | IAM 15374 <-- NBRC 100064 <-- LMG 9526 <-- P. Steyn 113. |
122408 | CIP <- 1998, LMG <- P. Steyn: strain 113 |
doi: 10.13145/bacdive14095.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pseudopedobacter
- species: Pseudopedobacter saltans
- full scientific name: Pseudopedobacter saltans (Steyn et al. 1998) Cao et al. 2014
synonyms
- @ref: 20215
- synonym: Pedobacter saltans
@ref: 4555
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pseudopedobacter
species: Pseudopedobacter saltans
full scientific name: Pseudopedobacter saltans (Steyn et al. 1998) Cao et al. 2014 emend. Hahnke et al. 2016
strain designation: 113
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.999 | ||
122408 | negative | rod-shaped | no |
pigmentation
- @ref: 122408
- production: no
- name: Pyocyanin
multimedia
- @ref: 66793
- multimedia content: EM_DSM_12145_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4555 | OXOID NUTRIENT BROTH (DSMZ Medium 948) | yes | https://mediadive.dsmz.de/medium/948 | Name: OXOID NUTRIENT BROTH (DSMZ Medium 948) Composition: Nutrient broth 13.0 g/l Distilled water |
36468 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
122408 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4555 | positive | growth | 28 | mesophilic |
36468 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
122408 | positive | growth | 25-41 | |
122408 | no | growth | 5 | psychrophilic |
122408 | no | growth | 10 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 122408
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.994 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
122408 | NaCl | positive | growth | 0-4 % |
122408 | NaCl | no | growth | 6 % |
122408 | NaCl | no | growth | 8 % |
122408 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-7
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
122408 | 16947 | citrate | - | carbon source |
122408 | 4853 | esculin | + | hydrolysis |
122408 | 17632 | nitrate | - | reduction |
122408 | 16301 | nitrite | - | reduction |
122408 | 17632 | nitrate | - | respiration |
antibiotic resistance
- @ref: 122408
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
- @ref: 122408
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
122408 | oxidase | + | |
122408 | beta-galactosidase | + | 3.2.1.23 |
122408 | alcohol dehydrogenase | - | 1.1.1.1 |
122408 | gelatinase | - | |
122408 | amylase | - | |
122408 | DNase | - | |
122408 | caseinase | - | 3.4.21.50 |
122408 | catalase | + | 1.11.1.6 |
122408 | tween esterase | - | |
122408 | lecithinase | - | |
122408 | lipase | - | |
122408 | lysine decarboxylase | - | 4.1.1.18 |
122408 | ornithine decarboxylase | - | 4.1.1.17 |
122408 | tryptophan deaminase | - | |
122408 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122408 | - | + | + | + | - | + | - | - | - | - | + | + | - | + | - | + | + | + | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122408 | + | + | + | - | + | - | + | + | - | + | + | + | + | - | - | + | + | - | + | - | + | + | + | + | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
4555 | soil | Iceland | ISL | Europe |
54759 | Soil | Iceland | ISL | Europe |
67770 | Soil | Iceland | ISL | Europe |
122408 | Environment, Soil | Iceland | ISL | Europe |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_2492.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_328;96_1344;97_1595;98_1940;99_2492&stattab=map
- Last taxonomy: Pseudopedobacter saltans subclade
- 16S sequence: NR_074586
- Sequence Identity:
- Total samples: 1251
- soil counts: 448
- aquatic counts: 441
- animal counts: 283
- plant counts: 79
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
4555 | 1 | Risk group (German classification) |
122408 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pedobacter saltans strain LMG 10337 16S ribosomal RNA gene, partial sequence | AF329958 | 680 | ena | 762903 |
20218 | Pedobacter saltans partial 16S rRNA gene, strain DSM 12145T | AJ438173 | 1479 | ena | 762903 |
4555 | Pseudopedobacter saltans DSM 12145 16S ribosomal RNA, partial sequence | NR_074586 | 1517 | nuccore | 762903 |
67770 | Pedobacter saltans gene for 16S rRNA, partial sequence, strain: NBRC 100064 | AB681143 | 1454 | ena | 151895 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudopedobacter saltans DSM 12145 | GCA_000190735 | complete | ncbi | 762903 |
66792 | Pedobacter saltans DSM 12145 | 762903.4 | complete | patric | 762903 |
66792 | Pseudopedobacter saltans DSM 12145 | 649633082 | complete | img | 762903 |
GC content
@ref | GC-content | method |
---|---|---|
4555 | 37.0 | |
4555 | 36.6 | sequence analysis |
67770 | 37 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 91.832 | no |
flagellated | no | 96.952 | no |
gram-positive | no | 98.3 | no |
anaerobic | no | 98.395 | no |
aerobic | yes | 87.399 | no |
halophile | no | 93.507 | no |
spore-forming | no | 94.004 | no |
glucose-util | yes | 89.58 | no |
thermophile | no | 97.35 | yes |
glucose-ferment | no | 85.131 | no |
External links
@ref: 4555
culture collection no.: DSM 12145, CCUG 39354, CIP 105500, JCM 21818, LMG 10337, MCCC 1A06472, NBRC 100064, ATCC 51119, IAM 15374, LMG 9526, NCIMB 13643
straininfo link
- @ref: 83263
- straininfo: 11927
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17551054 | Parapedobacter koreensis gen. nov., sp. nov. | Kim MK, Na JR, Cho DH, Soung NK, Yang DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.64677-0 | 2007 | Bacterial Typing Techniques, Bacteroidetes/chemistry/*classification/genetics/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Korea, Locomotion, Molecular Sequence Data, Oryza/*microbiology, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, Bacterial | Genetics |
Phylogeny | 24573160 | Pseudopedobacter beijingensis gen. nov., sp. nov., isolated from coking wastewater activated sludge, and reclassification of Pedobacter saltans as Pseudopedobacter saltans comb. nov. | Cao J, Lai Q, Li G, Shao Z | Int J Syst Evol Microbiol | 10.1099/ijs.0.053991-0 | 2014 | Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, China, *Coke, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Pedobacter/classification, Phosphatidylethanolamines/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/microbiology, Vitamin K 2/analogs & derivatives/chemistry, Waste Water/*microbiology | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4555 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12145) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12145 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
36468 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17526 | ||||
54759 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 39354) | https://www.ccug.se/strain?id=39354 | |||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
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 | |||
83263 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID11927.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122408 | Curators of the CIP | Collection of Institut Pasteur (CIP 105500) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105500 |