Strain identifier
BacDive ID: 14094
Type strain:
Species: Pedobacter africanus
Strain Designation: K1/K2
Strain history: CIP <- 1998, LMG <- P. Steyn: strain K1/K2
NCBI tax ID(s): 151894 (species)
General
@ref: 4608
BacDive-ID: 14094
DSM-Number: 12126
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative
description: Pedobacter africanus K1/K2 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.
NCBI tax id
- NCBI tax id: 151894
- Matching level: species
strain history
@ref | history |
---|---|
4608 | <- LMG |
116124 | CIP <- 1998, LMG <- P. Steyn: strain K1/K2 |
doi: 10.13145/bacdive14094.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Sphingobacteriia
- order: Sphingobacteriales
- family: Sphingobacteriaceae
- genus: Pedobacter
- species: Pedobacter africanus
- full scientific name: Pedobacter africanus Steyn et al. 1998
@ref: 4608
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter africanus
full scientific name: Pedobacter africanus Steyn et al. 1998
strain designation: K1/K2
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.998 | ||
116124 | negative | rod-shaped | no |
pigmentation
- @ref: 116124
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
4608 | NUTRIENT AGAR (DSMZ Medium 1) | yes | https://mediadive.dsmz.de/medium/1 | 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 |
39305 | MEDIUM 3 - Columbia agar | yes | Columbia agar (39.000 g);distilled water (1000.000 ml) | |
116124 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
4608 | positive | growth | 28 | mesophilic |
39305 | positive | growth | 25 | mesophilic |
116124 | positive | growth | 25-37 | mesophilic |
116124 | no | growth | 5 | psychrophilic |
116124 | no | growth | 10 | psychrophilic |
116124 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 116124
- oxygen tolerance: obligate aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.952 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116124 | NaCl | positive | growth | 0-8 % |
116124 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | + | builds acid from | 32528 |
68371 | gentiobiose | + | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | - | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | + | builds acid from | 27082 |
68371 | sucrose | + | builds acid from | 17992 |
68371 | melibiose | + | builds acid from | 28053 |
68371 | lactose | + | builds acid from | 17716 |
68371 | maltose | + | builds acid from | 17306 |
68371 | cellobiose | + | builds acid from | 17057 |
68371 | salicin | + | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | + | builds acid from | 18305 |
68371 | amygdalin | + | builds acid from | 27613 |
68371 | N-acetylglucosamine | + | builds acid from | 59640 |
68371 | methyl alpha-D-mannoside | + | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-mannose | + | builds acid from | 16024 |
68371 | D-fructose | + | builds acid from | 15824 |
68371 | D-glucose | + | builds acid from | 17634 |
68371 | D-galactose | + | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | D-arabinose | + | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
116124 | esculin | + | hydrolysis | 4853 |
116124 | nitrate | + | reduction | 17632 |
116124 | nitrite | - | reduction | 16301 |
116124 | nitrate | - | respiration | 17632 |
antibiotic resistance
- @ref: 116124
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: yes
- is resistant: no
metabolite production
- @ref: 116124
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
116124 | oxidase | + | |
116124 | beta-galactosidase | + | 3.2.1.23 |
116124 | alcohol dehydrogenase | - | 1.1.1.1 |
116124 | gelatinase | - | |
116124 | amylase | - | |
116124 | DNase | - | |
116124 | caseinase | - | 3.4.21.50 |
116124 | catalase | + | 1.11.1.6 |
116124 | tween esterase | - | |
116124 | lecithinase | - | |
116124 | lipase | - | |
116124 | lysine decarboxylase | - | 4.1.1.18 |
116124 | ornithine decarboxylase | - | 4.1.1.17 |
116124 | tryptophan deaminase | - | |
116124 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116124 | - | + | + | + | - | + | + | - | - | - | + | + | - | + | - | + | + | + | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116124 | - | - | + | +/- | +/- | - | - | - | - | + | + | + | + | - | +/- | - | - | - | - | + | +/- | + | + | + | + | + | + | + | + | + | + | + | - | +/- | +/- | - | - | - | + | + | - | - | - | +/- | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116124 | + | - | + | + | + | - | + | + | + | + | + | + | + | + | + | + | + | + | + | - | + | + | + | + | - | - | - | - | - | - | - | - | - | - | + | + | - | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | - | - | - | + | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
4608 | soil | Eastern Transvaal, Belfast | South Africa | ZAF | Africa |
54758 | Soil | Eastern Transvaal,Belfast, | Africa | ||
116124 | Environment, Soil | South Africa | ZAF | Africa |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Soil
taxonmaps
- @ref: 69479
- File name: preview.99_5331.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_319;97_404;98_3973;99_5331&stattab=map
- Last taxonomy: Pedobacter africanus
- 16S sequence: AB681144
- Sequence Identity:
- Total samples: 307
- soil counts: 66
- aquatic counts: 150
- animal counts: 39
- plant counts: 52
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
4608 | 1 | Risk group (German classification) |
116124 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pedobacter africanus partial 16S rRNA gene, strain DSM 12126T | AJ438171 | 1490 | ena | 151894 |
20218 | Pedobacter africanus strain LMG 10353 16S ribosomal RNA gene, partial sequence | AF329953 | 681 | ena | 151894 |
20218 | Pedobacter africanus gene for 16S rRNA, partial sequence, strain: NBRC 100065 | AB681144 | 1447 | ena | 151894 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pedobacter africanus DSM 12126 | GCA_900176535 | contig | ncbi | 151894 |
66792 | Pedobacter africanus strain DSM 12126 | 151894.4 | wgs | patric | 151894 |
66792 | Pedobacter africanus DSM 12126 | 2622736459 | draft | img | 151894 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 86.573 | no |
gram-positive | no | 98.268 | no |
anaerobic | no | 98.83 | no |
aerobic | yes | 82.52 | no |
halophile | no | 94.549 | no |
spore-forming | no | 94.134 | no |
glucose-util | yes | 92.03 | no |
flagellated | no | 95.722 | no |
glucose-ferment | no | 88.327 | no |
thermophile | no | 98.597 | no |
External links
@ref: 4608
culture collection no.: DSM 12126, LMG 10353, CCUG 39353, CIP 105499
straininfo link
- @ref: 83262
- straininfo: 11921
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17082391 | Pedobacter ginsengisoli sp. nov., a DNase-producing bacterium isolated from soil of a ginseng field in South Korea. | Ten LN, Liu QM, Im WT, Lee M, Yang DC, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.64414-0 | 2006 | Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deoxyribonucleases/*biosynthesis, Fatty Acids/analysis/chemistry, Genes, rRNA, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, *Panax, Phylogeny, Quinones/analysis/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology | Genetics |
Phylogeny | 17267983 | Pedobacter panaciterrae sp. nov., isolated from soil in South Korea. | Yoon MH, Ten LN, Im WT, Lee ST | Int J Syst Evol Microbiol | 10.1099/ijs.0.64693-0 | 2007 | Anaerobiosis, Bacterial Typing Techniques, Bacteroidetes/*classification/cytology/*isolation & purification/physiology, Carbohydrate Metabolism, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Gelatinases/analysis, Genes, rRNA, Hydrogen Sulfide/metabolism, Indoles/metabolism, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phylogeny, Quinones/analysis/chemistry, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, *Soil Microbiology | Metabolism |
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 | 24425748 | Pedobacter nutrimenti sp. nov., isolated from chilled food. | Derichs J, Kampfer P, Lipski A | Int J Syst Evol Microbiol | 10.1099/ijs.0.058677-0 | 2014 | Animals, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Meat/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Pedobacter/*classification/genetics/isolation & purification, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Swine, Vitamin K 2/analogs & derivatives/chemistry | Biotechnology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
4608 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12126) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-12126 | |||
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 | |
39305 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17525 | ||||
54758 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 39353) | https://www.ccug.se/strain?id=39353 | |||
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) | |||
68371 | Automatically annotated from API 50CH acid | |||||
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 | |||
83262 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID11921.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
116124 | Curators of the CIP | Collection of Institut Pasteur (CIP 105499) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105499 |