Strain identifier
BacDive ID: 140674
Type strain:
Species: Pedobacter psychrophilus
Strain Designation: P4487A
NCBI tax ID(s): 1826909 (species)
version 8.1 (current version)
General
@ref: 43438
BacDive-ID: 140674
keywords: genome sequence, 16S sequence, Bacteria, aerobe, Gram-negative, rod-shaped, colony-forming
description: Pedobacter psychrophilus P4487A is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from fragmentary rock.
NCBI tax id
- NCBI tax id: 1826909
- Matching level: species
doi: 10.13145/bacdive140674.20230509.8.1
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 psychrophilus
- full scientific name: Pedobacter psychrophilus Švec et al. 2017
@ref: 43438
domain: Bacteria
phylum: Bacteroidetes
class: Sphingobacteriia
order: Sphingobacteriales
family: Sphingobacteriaceae
genus: Pedobacter
species: Pedobacter psychrophilus
strain designation: P4487A
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell shape | motility | confidence |
---|---|---|---|---|
43438 | negative | rod-shaped | no | |
69480 | no | 94.879 | ||
69480 | negative | 99.996 |
colony morphology
- @ref: 43438
- colony size: 1 mm
- colony color: pink
- colony shape: circular
- incubation period: 5 days
- medium used: R2A agar
pigmentation
@ref | production | color | name |
---|---|---|---|
43438 | yes | Pink | |
43438 | yes | Carotenoid | |
43438 | no | Flexirubin |
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
43438 | Brain heart infusion agar | no |
43438 | Columbia blood agar | no |
43438 | MacConkey agar | no |
43438 | Nutrient agar (NA) | no |
43438 | Reasoner's 2A agar (R2A) | yes |
43438 | Trypticase Soy Agar (TSA) | no |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43438 | positive | growth | 5-25 | |
43438 | no | growth | 1 | psychrophilic |
43438 | no | growth | 30 | mesophilic |
43438 | no | growth | 35 | mesophilic |
43438 | positive | optimum | 20 | psychrophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43438 | positive | growth | 6-9 | alkaliphile |
43438 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
- @ref: 43438
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
43438 | no | |
69481 | no | 100 |
69480 | no | 99.996 |
halophily
@ref | salt | growth | tested relation | concentration | halophily level |
---|---|---|---|---|---|
43438 | NaCl | positive | growth | 2 %(w/v) | |
43438 | NaCl | positive | optimum | 0 %(w/v) | non-halophilic |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43438 | 28757 | fructose | - | builds acid from |
43438 | 29864 | mannitol | - | builds acid from |
43438 | casein | - | hydrolysis | |
43438 | 5291 | gelatin | - | hydrolysis |
43438 | 61995 | lecithin | - | hydrolysis |
43438 | 53426 | tween 80 | - | hydrolysis |
43438 | 18186 | tyrosine | - | hydrolysis |
43438 | 17632 | nitrate | - | reduction |
43438 | 16301 | nitrite | - | reduction |
43438 | 64552 | 2-hydroxybutyrate | - | respiration |
43438 | 30916 | 2-oxoglutarate | - | respiration |
43438 | 28644 | 2-oxopentanoate | - | respiration |
43438 | 62064 | 2,3-butanediol | - | respiration |
43438 | 37054 | 3-hydroxybutyrate | - | respiration |
43438 | 16724 | 4-hydroxybutyrate | - | respiration |
43438 | 18101 | 4-hydroxyphenylacetic acid | - | respiration |
43438 | 15963 | ribitol | - | respiration |
43438 | 73706 | bromosuccinate | - | respiration |
43438 | 16383 | cis-aconitate | - | respiration |
43438 | 16947 | citrate | - | respiration |
43438 | 15570 | D-alanine | - | respiration |
43438 | 18333 | D-arabitol | - | respiration |
43438 | 15824 | D-fructose | - | respiration |
43438 | 15895 | D-galactonic acid lactone | - | respiration |
43438 | 12936 | D-galactose | - | respiration |
43438 | 18024 | D-galacturonic acid | - | respiration |
43438 | 8391 | D-gluconate | - | respiration |
43438 | 17784 | D-glucosaminic acid | - | respiration |
43438 | 14314 | D-glucose 6-phosphate | - | respiration |
43438 | 15748 | D-glucuronate | - | respiration |
43438 | 16899 | D-mannitol | - | respiration |
43438 | 16024 | D-mannose | - | respiration |
43438 | 27605 | D-psicose | - | respiration |
43438 | 33801 | D-saccharate | - | respiration |
43438 | 16523 | D-serine | - | respiration |
43438 | 17924 | D-sorbitol | - | respiration |
43438 | 17126 | DL-carnitine | - | respiration |
43438 | 17113 | erythritol | - | respiration |
43438 | 16000 | ethanolamine | - | respiration |
43438 | 15740 | formate | - | respiration |
43438 | 16865 | gamma-aminobutyric acid | - | respiration |
43438 | 29042 | glucose 1-phosphate | - | respiration |
43438 | 32323 | glucuronamide | - | respiration |
43438 | 14336 | glycerol 1-phosphate | - | respiration |
43438 | 73804 | glycyl L-aspartic acid | - | respiration |
43438 | 24741 | hydroxyproline | - | respiration |
43438 | 16411 | indole-3-acetic acid | - | respiration |
43438 | 17596 | inosine | - | respiration |
43438 | 17240 | itaconate | - | respiration |
43438 | 21217 | L-alaninamide | - | respiration |
43438 | 16977 | L-alanine | - | respiration |
43438 | 73786 | L-alanylglycine | - | respiration |
43438 | 30849 | L-arabinose | - | respiration |
43438 | 17196 | L-asparagine | - | respiration |
43438 | 29991 | L-aspartate | - | respiration |
43438 | 18287 | L-fucose | - | respiration |
43438 | 15971 | L-histidine | - | respiration |
43438 | 15603 | L-leucine | - | respiration |
43438 | 15729 | L-ornithine | - | respiration |
43438 | 17295 | L-phenylalanine | - | respiration |
43438 | 17203 | L-proline | - | respiration |
43438 | 18183 | L-pyroglutamic acid | - | respiration |
43438 | 62345 | L-rhamnose | - | respiration |
43438 | 17115 | L-serine | - | respiration |
43438 | 16857 | L-threonine | - | respiration |
43438 | 24996 | lactate | - | respiration |
43438 | 6359 | lactulose | - | respiration |
43438 | 15792 | malonate | - | respiration |
43438 | 37657 | methyl D-glucoside | - | respiration |
43438 | 51850 | methyl pyruvate | - | respiration |
43438 | 75146 | monomethyl succinate | - | respiration |
43438 | 17268 | myo-inositol | - | respiration |
43438 | 28037 | N-acetylgalactosamine | - | respiration |
43438 | 50048 | phenylethylamine | - | respiration |
43438 | 17272 | propionate | - | respiration |
43438 | 17148 | putrescine | - | respiration |
43438 | 26490 | quinate | - | respiration |
43438 | 16634 | raffinose | - | respiration |
43438 | 41865 | sebacic acid | - | respiration |
43438 | 143136 | succinamate | - | respiration |
43438 | 30031 | succinate | - | respiration |
43438 | 17992 | sucrose | - | respiration |
43438 | 17748 | thymidine | - | respiration |
43438 | 27082 | trehalose | - | respiration |
43438 | 53423 | tween 40 | - | respiration |
43438 | 53426 | tween 80 | - | respiration |
43438 | 16704 | uridine | - | respiration |
43438 | 27248 | urocanic acid | - | respiration |
43438 | 17151 | xylitol | - | respiration |
43438 | 17306 | maltose | + | builds acid from |
43438 | 18222 | xylose | + | builds acid from |
43438 | 4853 | esculin | + | hydrolysis |
43438 | 28017 | starch | + | hydrolysis |
43438 | 64552 | 2-hydroxybutyrate | + | respiration |
43438 | 40585 | alpha-cyclodextrin | + | respiration |
43438 | 17925 | alpha-D-glucose | + | respiration |
43438 | 17057 | cellobiose | + | respiration |
43438 | 23652 | dextrin | + | respiration |
43438 | 28066 | gentiobiose | + | respiration |
43438 | 28087 | glycogen | + | respiration |
43438 | 29985 | L-glutamate | + | respiration |
43438 | 17716 | lactose | + | respiration |
43438 | 17306 | maltose | + | respiration |
43438 | 28053 | melibiose | + | respiration |
43438 | 506227 | N-acetylglucosamine | + | respiration |
43438 | 73784 | glycyl-l-glutamate | + | respiration |
43438 | 32528 | turanose | + | respiration |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | group ID | is resistant | resistance conc. |
---|---|---|---|---|---|---|---|---|
43438 | 28971 | ampicillin | yes | yes | 10 µg (disc) | |||
43438 | 3393 | carbenicillin | yes | yes | 100 µg (disc) | |||
43438 | 3508 | ceftazidime | yes | yes | 10 µg (disc) | |||
43438 | 3542 | cephalothin | yes | yes | 30 µg (disc) | |||
43438 | 100241 | ciprofloxacin | yes | yes | 5 µg (disc) | |||
43438 | 17833 | gentamicin | yes | yes | 10 µg (disc) | |||
43438 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) | |||
43438 | 471744 | imipenem | yes | yes | 10 µg (disc) | |||
43438 | 6104 | kanamycin | yes | yes | 30 µg (disc) | |||
43438 | 8232 | piperacillin | yes | yes | 30 µg (disc) | |||
43438 | 8309 | polymyxin b | yes | yes | 300 Unit (disc) | |||
43438 | 17076 | streptomycin | yes | yes | 10 µg (disc) | |||
43438 | 27902 | tetracycline | yes | yes | 30 µg (disc) | |||
43438 | 45924 | trimethoprim | yes | yes | 25 µg (disc) | 26 | ||
43438 | 9332 | sulfamethoxazole | yes | yes | 25 µg (disc) | 26 | ||
43438 | 161680 | aztreonam | yes | yes | 30 µg (disc) | |||
43438 | 472657 | cefixime | yes | yes | 5 µg (disc) |
metabolite production
- @ref: 43438
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
43438 | catalase | + | 1.11.1.6 |
43438 | cytochrome oxidase | +/- | 1.9.3.1 |
43438 | DNase | + | |
43438 | esterase (C 4) | + | |
43438 | esterase Lipase (C 8) | +/- | |
43438 | leucine arylamidase | + | 3.4.11.1 |
43438 | valine arylamidase | + | |
43438 | naphthol-AS-BI-phosphohydrolase | + | |
43438 | beta-galactosidase | + | 3.2.1.23 |
43438 | alpha-glucosidase | + | 3.2.1.20 |
43438 | alkaline phosphatase | + | 3.1.3.1 |
43438 | acid phosphatase | + | 3.1.3.2 |
43438 | urease | - | 3.5.1.5 |
43438 | arginine dihydrolase | - | 3.5.3.6 |
43438 | lysine decarboxylase | - | 4.1.1.18 |
43438 | ornithine decarboxylase | - | 4.1.1.17 |
43438 | lipase (C 14) | - | |
43438 | cystine arylamidase | - | 3.4.11.3 |
43438 | trypsin | - | 3.4.21.4 |
43438 | chymotrypsin | - | 3.4.4.5 |
43438 | beta-glucuronidase | - | 3.2.1.31 |
43438 | beta-glucosidase | - | 3.2.1.21 |
43438 | alpha-galactosidase | - | 3.2.1.22 |
43438 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43438 | alpha-mannosidase | - | 3.2.1.24 |
43438 | alpha-fucosidase | - | 3.2.1.51 |
Isolation, sampling and environmental information
isolation
- @ref: 43438
- sample type: fragmentary rock
- geographic location: James Ross Island, Antarctica
- country: Antarctica
- origin.country: ATA
- continent: Australia and Oceania
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Geologic
taxonmaps
- @ref: 69479
- File name: preview.99_3021.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_115;96_1588;97_1895;98_2325;99_3021&stattab=map
- Last taxonomy: Pedobacter psychrophilus subclade
- 16S sequence: KX113374
- Sequence Identity:
- Total samples: 595
- soil counts: 70
- aquatic counts: 250
- animal counts: 245
- plant counts: 30
Sequence information
16S sequences
- @ref: 43438
- description: 16S rRNA gene sequence
- accession: KX113374
- database: nuccore
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pedobacter psychrophilus CCM 8644 | GCA_001652725 | contig | ncbi | 1826909 |
66792 | Pedobacter sp. CCM 8644 | 1826909.3 | wgs | patric | 1826909 |
66792 | Pedobacter psychrophilus CCM 8644 | 2744054859 | draft | img | 1826909 |
GC content
- @ref: 43438
- GC-content: 46.3
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 91.102 | no |
gram-positive | no | 97.796 | yes |
anaerobic | no | 97.427 | no |
aerobic | yes | 87.682 | yes |
halophile | no | 94.802 | yes |
spore-forming | no | 95.675 | yes |
glucose-util | yes | 87.227 | yes |
flagellated | no | 97.591 | yes |
glucose-ferment | no | 90.418 | no |
thermophile | no | 98.765 | no |
External links
@ref: 43438
culture collection no.: CCM 8644, LMG 29436
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 28771123 | Pedobacter psychrophilus sp. nov., isolated from fragmentary rock. | Svec P, Kralova S, Busse HJ, Kleinhagauer T, Kyrova K, Pantucek R, Maslanova I, Stankova E, Nemec M, Holochova P, Bartak M, Sedlacek I | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001962 | 2017 | Antarctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Pedobacter/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Spermidine/analogs & derivatives/chemistry, Sphingolipids/chemistry, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 35059849 | Pedobacter segetis sp. nov., a Novel Bacterium Isolated from Soil. | Ten LN, Li W, Hong SM, Kim MK, Lee SY, Jung HY | Curr Microbiol | 10.1007/s00284-021-02753-w | 2022 | DNA, Bacterial/genetics, *Pedobacter/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil, Soil Microbiology |
Reference
@id | authors | title | doi/url | journal | pubmed |
---|---|---|---|---|---|
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 | ||
43438 | Pavel Švec, Stanislava Kralova, Hans-Juergen Busse, Tanita Kleinhagauer, Kamila Kýrova, Roman Pantucek, Ivana Mašlanova, Eva Stankova, Miroslav Nemec, Pavla Holochova, Miloš Bartak, Ivo Sedlacek | Pedobacter psychrophilus sp. nov., isolated from fragmentary rock | 10.1099/ijsem.0.001962 | IJSEM 67: 2538-2543 2017 | 28771123 |
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 | ||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 |
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 |