Strain identifier
BacDive ID: 16485
Type strain:
Species: Streptomyces indicus
Strain Designation: IH32-1
Strain history: CGMCC 4.5727 <-- Y. Luo et al. IH32-1.
NCBI tax ID(s): 417292 (species)
General
@ref: 16602
BacDive-ID: 16485
DSM-Number: 42001
keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic, Gram-positive
description: Streptomyces indicus IH32-1 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from deep-sea sediment sample.
NCBI tax id
- NCBI tax id: 417292
- Matching level: species
strain history
@ref | history |
---|---|
16602 | <- J. Xu, Marine Biogenetic Resources, Third Inst. Oceanography, SOA, China; IH32-1 <- J. Xu and Y. Luo |
67770 | CGMCC 4.5727 <-- Y. Luo et al. IH32-1. |
doi: 10.13145/bacdive16485.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Kitasatosporales
- family: Streptomycetaceae
- genus: Streptomyces
- species: Streptomyces indicus
- full scientific name: Streptomyces indicus Luo et al. 2011
@ref: 16602
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Streptomycetaceae
genus: Streptomyces
species: Streptomyces indicus
full scientific name: Streptomyces indicus Luo et al. 2011
strain designation: IH32-1
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
@ref | colony color | medium used |
---|---|---|
69319 | Beige (1001) | suter with tyrosine |
69319 | Ivory (1014) | ISP 5 |
69319 | Ivory (1014) | ISP 7 |
69319 | Light ivory (1015) | ISP 3 |
69319 | Light ivory (1015) | suter without tyrosine |
69319 | Sand yellow (1002) | ISP 4 |
69319 | Sand yellow (1002) | ISP 6 |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
69319 | yes | Aerial mycelium | Pure white (9010) | ISP 2 |
69319 | yes | Aerial mycelium | Pure white (9010) | ISP 3 |
69319 | yes | Aerial mycelium | Pure white (9010) | ISP 4 |
69319 | yes | Aerial mycelium | Signal white (9003) | ISP 5 |
69319 | no | Aerial mycelium | ISP 6 | |
69319 | yes | Aerial mycelium | Light ivory (1015) | ISP 7 |
69319 | no | Aerial mycelium | suter with tyrosine | |
69319 | no | Aerial mycelium | suter without tyrosine |
pigmentation
@ref | production | name | color |
---|---|---|---|
69319 | no | Melanin | |
69319 | yes | soluble pigment | Sand yellow (1002), ivory (1014) |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
69319 | DSM_42001_image3.jpeg | Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
69319 | DSM_42001_image4.jpeg | Plates (65, ISP2, ISP3, ISP4, ISP5, ISP7) | Helmholtz-Zentrum für Infektionsforschung GmbH |
Culture and growth conditions
culture temp
- @ref: 67770
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 100 |
69480 | yes | 100 |
halophily
- @ref: 69319
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-7.5 %
observation
- @ref: 67770
- observation: quinones: MK-9(H6), MK-9(H4), MK-9(H8)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
69319 | 22599 | arabinose | + | growth |
69319 | 62968 | cellulose | - | growth |
69319 | 28757 | fructose | + | growth |
69319 | 17234 | glucose | - | growth |
69319 | 17268 | inositol | + | growth |
69319 | 37684 | mannose | - | growth |
69319 | 16634 | raffinose | +/- | growth |
69319 | 26546 | rhamnose | +/- | growth |
69319 | 17992 | sucrose | + | growth |
69319 | 18222 | xylose | + | growth |
68379 | 17632 | nitrate | + | reduction |
68379 | 4853 | esculin | + | hydrolysis |
68379 | 16199 | urea | + | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17634 | D-glucose | + | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68379 | gelatinase | + | |
68379 | urease | + | 3.5.1.5 |
68379 | beta-glucosidase | + | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | + | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
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 coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69319 | + | - | - | + | - | + | + | + | + | + | + | + | - | - | - | - | - | - | - |
API zym
@ref | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
69319 | + | + | +/- | - | + | + | - | +/- | - | + | + | + | + | - | + | + | + | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
16602 | deep-sea (2434 m) sediment sample | Indian Ocean (25.3206° S, 70.0402° E) | India | IND | Asia | -25.3206 | 70.0402 |
67770 | Deep-sea sediment from the Indian Ocean |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
- @ref: 16602
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16602
- description: Streptomyces indicus strain IH32-1 16S ribosomal RNA gene, partial sequence
- accession: EF157833
- length: 1488
- database: ena
- NCBI tax ID: 417292
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Streptomyces indicus strain CGMCC 4.5727 | 417292.4 | wgs | patric | 417292 |
66792 | Streptomyces indicus CGMCC 4.5727 | 2675903130 | draft | img | 417292 |
67770 | Streptomyces indicus CGMCC 4.5727 | GCA_900100315 | scaffold | ncbi | 417292 |
GC content
@ref | GC-content | method |
---|---|---|
16602 | 71.3 | high performance liquid chromatography (HPLC) |
67770 | 71.4 | genome sequence analysis |
67770 | 70.3-72.3 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 100 | no |
gram-positive | yes | 88.807 | no |
anaerobic | no | 99.385 | no |
halophile | no | 91.364 | no |
spore-forming | yes | 94.89 | no |
glucose-util | yes | 87.052 | yes |
aerobic | yes | 90.484 | no |
flagellated | no | 97.439 | no |
motile | no | 90.034 | no |
thermophile | no | 98.814 | yes |
glucose-ferment | no | 80.203 | yes |
External links
@ref: 16602
culture collection no.: DSM 42001, CGMCC 4.5727, MCCC IA03308, JCM 18323
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21169463 | Streptomyces indicus sp. nov., an actinomycete isolated from deep-sea sediment. | Luo Y, Xiao J, Wang Y, Xu J, Xie S, Xu J | Int J Syst Evol Microbiol | 10.1099/ijs.0.029389-0 | 2010 | DNA, Bacterial/genetics, Fatty Acids/metabolism, Geologic Sediments/*microbiology, Indian Ocean, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Streptomyces/*classification/genetics/*isolation & purification/metabolism | Metabolism |
Phylogeny | 33666547 | Streptomyces ureilyticus sp. nov. and Streptomyces mesophilus sp. nov., two novel Actinobacteria with antimicrobial activity isolated from lake sediment. | Tokatli A, Idil O, Saygin H, Sahin N | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004738 | 2021 | ||
Phylogeny | 33738648 | Streptomyces polyasparticus sp. nov. isolated from cotton field soil by a medium applied with polyaspartic acid. | Liu W, Zeng H, Xia Z, Luo X, Zhang L, Wan C | Antonie Van Leeuwenhoek | 10.1007/s10482-021-01557-z | 2021 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Peptides, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil, Soil Microbiology, *Streptomyces/genetics | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16602 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 42001) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-42001 | |||
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 | |||
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/ | ||||
68379 | Automatically annotated from API Coryne | |||||
68382 | Automatically annotated from API zym | |||||
69319 | Wink, J. | https://cdn.dsmz.de/wink/DSM%2042001.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | |||
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 |