Strain identifier
BacDive ID: 13071
Type strain:
Species: Pseudomonas indica
Strain history: CIP <- 2002, DSMZ <- T. Chakrabarti, MTCC, Chandigarh, India
NCBI tax ID(s): 1215103 (strain), 137658 (species)
General
@ref: 5220
BacDive-ID: 13071
DSM-Number: 14015
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Pseudomonas indica DSM 14015 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from oil field soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1215103 | strain |
137658 | species |
strain history
@ref | history |
---|---|
5220 | <- T. Chakrabarti, MTCC, Chandigarh, India |
67770 | IAM 15083 <-- MTCC 3713 <-- T. Chakrabarti IMT37. |
120076 | CIP <- 2002, DSMZ <- T. Chakrabarti, MTCC, Chandigarh, India |
doi: 10.13145/bacdive13071.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas indica
- full scientific name: Pseudomonas indica Pandey et al. 2002
@ref: 5220
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas indica
full scientific name: Pseudomonas indica Pandey et al. 2002
type strain: yes
Morphology
cell morphology
- @ref: 120076
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
pigmentation
- @ref: 120076
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5220 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water |
39930 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
120076 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5220 | positive | growth | 30 | mesophilic |
39930 | positive | growth | 30 | mesophilic |
59221 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
120076 | positive | growth | 25-41 | |
120076 | no | growth | 5 | psychrophilic |
120076 | no | growth | 10 | psychrophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
59221 | aerobe |
120076 | obligate aerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120076 | NaCl | positive | growth | 0-4 % |
120076 | NaCl | no | growth | 6 % |
120076 | NaCl | no | growth | 8 % |
120076 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
120076 | 16947 | citrate | + | carbon source |
120076 | 4853 | esculin | - | hydrolysis |
120076 | 17632 | nitrate | + | reduction |
120076 | 16301 | nitrite | + | reduction |
120076 | 17632 | nitrate | + | respiration |
antibiotic resistance
- @ref: 120076
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 120076
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
120076 | oxidase | + | |
120076 | beta-galactosidase | - | 3.2.1.23 |
120076 | alcohol dehydrogenase | - | 1.1.1.1 |
120076 | gelatinase | + | |
120076 | amylase | + | |
120076 | caseinase | - | 3.4.21.50 |
120076 | catalase | + | 1.11.1.6 |
120076 | tween esterase | - | |
120076 | lecithinase | - | |
120076 | lipase | - | |
120076 | lysine decarboxylase | - | 4.1.1.18 |
120076 | ornithine decarboxylase | - | 4.1.1.17 |
120076 | protease | - | |
120076 | tryptophan deaminase | - | |
120076 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120076 | - | + | + | + | + | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120076 | + | + | + | - | - | - | - | + | - | + | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | + | - | + | - | - | - | - | - | - | - | - | - | + | + | - | - | - | + | + | + | - | - | + | + | + | - | - | - | - | + | - | + | + | + | - | - | - | - | - | - | + | + | + | - | + | + | + | + | + | + | + | - | + | - | - | - | + | + | + | + | + | + | + | + | + | + | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5220 | oil field soil | Gujarat | India | IND | Asia |
59221 | Soil,oil field | India | IND | Asia | |
67770 | Soil sample of oil field in Gujarat | ||||
120076 | Environment, Soil, oil field | Gujarat | India | IND | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Industrial | #Oil reservoir |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_5211.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_36;97_3093;98_3884;99_5211&stattab=map
- Last taxonomy: Pseudomonas indica subclade
- 16S sequence: AF302795
- Sequence Identity:
- Total samples: 1371
- soil counts: 241
- aquatic counts: 578
- animal counts: 409
- plant counts: 143
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
5220 | 1 | Risk group (German classification) |
120076 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 5220
- description: Pseudomonas sp. IMT37 16S ribosomal RNA gene, partial sequence
- accession: AF302795
- length: 1509
- database: ena
- NCBI tax ID: 137658
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas indica NBRC 103045 strain NBRC 103045 | 1215103.3 | wgs | patric | 1215103 |
66792 | Pseudomonas indica strain JCM 21544 | 137658.3 | wgs | patric | 137658 |
66792 | Pseudomonas indica JCM 21544 | 2663762782 | draft | img | 137658 |
67770 | Pseudomonas indica NBRC 103045 | GCA_002091635 | contig | ncbi | 1215103 |
67770 | Pseudomonas indica JCM 21544 | GCA_900100285 | scaffold | ncbi | 137658 |
GC content
@ref | GC-content | method |
---|---|---|
5220 | 72 | |
67770 | 72 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 88.406 | no |
gram-positive | no | 98.798 | no |
anaerobic | no | 97.882 | no |
aerobic | yes | 87.847 | yes |
halophile | no | 84.702 | no |
spore-forming | no | 94.487 | no |
thermophile | no | 99.623 | yes |
glucose-util | yes | 94.502 | no |
glucose-ferment | no | 90.255 | no |
flagellated | yes | 75.77 | no |
External links
@ref: 5220
culture collection no.: DSM 14015, CIP 107714, MTCC 3713, CCUG 51511, IMT 37, JCM 21544, DSM 23066, IAM 15083, NBRC 103045, TBRC 7233
straininfo link
- @ref: 82281
- straininfo: 100888
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12361258 | Pseudomonas indica sp. nov., a novel butane-utilizing species. | Pandey KK, Mayilraj S, Chakrabarti T | Int J Syst Evol Microbiol | 10.1099/00207713-52-5-1559 | 2002 | Base Sequence, Butanes/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry, Genome, Bacterial, Microscopy, Electron, Molecular Sequence Data, Phylogeny, Pseudomonas/*classification/genetics/*metabolism/ultrastructure, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as Topic | Genetics |
Phylogeny | 28984556 | Pseudomonas tarimensis sp. nov., an endophytic bacteria isolated from Populus euphratica. | Anwar N, Rozahon M, Zayadan B, Mamtimin H, Abdurahman M, Kurban M, Abdurusul M, Mamtimin T, Abdukerim M, Rahman E | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002295 | 2017 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Stems/*microbiology, Populus/*microbiology, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Phylogeny | 30950783 | Pseudomonas urumqiensis sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia. | Zou Y, He S, Sun Y, Zhang X, Liu Y, Cheng Q | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003390 | 2019 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fabaceae/*microbiology, Fatty Acids/chemistry, Genes, Bacterial, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology | Transcriptome |
Phylogeny | 31429815 | Pseudomonas mangiferae sp. nov., isolated from bark of mango tree in Thailand. | Anurat P, Duangmal K, Srisuk N | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003657 | 2019 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Mangifera/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Bark/*microbiology, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5220 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14015) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14015 | |||
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 | |||
39930 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5180 | ||||
59221 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 51511) | https://www.ccug.se/strain?id=51511 | |||
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 | 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 | |||
82281 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100888.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120076 | Curators of the CIP | Collection of Institut Pasteur (CIP 107714) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107714 |