Strain identifier
BacDive ID: 132633
Type strain: 
Species: Herbihabitans rhizosphaerae
Strain history: <- Zhang Y. Q., Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, CPCC 204279 <- Zhang Ch.F
NCBI tax ID(s): 1872711 (species)
version 8.1 (current version)
General
@ref: 24422
BacDive-ID: 132633
DSM-Number: 101727
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, Gram-positive, rod-shaped
description: Herbihabitans rhizosphaerae DSM 101727 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from rhizosphere soil of the herb Limonium sinense .
NCBI tax id
- NCBI tax id: 1872711
- Matching level: species
strain history
- @ref: 24422
- history: <- Zhang Y. Q., Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, CPCC 204279 <- Zhang Ch.F
doi: 10.13145/bacdive132633.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Pseudonocardiales
- family: Pseudonocardiaceae
- genus: Herbihabitans
- species: Herbihabitans rhizosphaerae
- full scientific name: Herbihabitans rhizosphaerae Zhang et al. 2016
@ref: 24422
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Pseudonocardiaceae
genus: Herbihabitans
species: Herbihabitans rhizosphaerae
full scientific name: Herbihabitans rhizosphaerae Zhang et al. 2016
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell shape | motility | confidence |
|---|---|---|---|---|
| 24899 | positive | rod-shaped | no | |
| 69480 | positive | 100 |
pigmentation
- @ref: 24899
- production: no
- name: no pigments
Culture and growth conditions
culture medium
- @ref: 24422
- name: GPHF-MEDIUM (DSMZ Medium 553)
- growth: yes
- link: https://mediadive.dsmz.de/medium/553
- composition: Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 24899 | positive | growth | 20-40 | |
| 24899 | positive | optimum | 28 | mesophilic |
| 24422 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 24899 | positive | growth | 5.0-9.0 | alkaliphile |
| 24899 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 24899
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 99.447 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 24899 | NaCl | positive | growth | 0-3 %(w/v) |
| 24899 | NaCl | positive | optimum | 1 %(w/v) |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 24899 | 28017 | starch | - | hydrolysis |
| 24899 | 16199 | urea | - | hydrolysis |
| 24899 | 17925 | alpha-D-glucose | + | carbon source |
| 24899 | 17057 | cellobiose | + | carbon source |
| 24899 | 17057 | cellobiose | + | builds acid from |
| 24899 | 17108 | D-arabinose | + | carbon source |
| 24899 | 17108 | D-arabinose | + | builds acid from |
| 24899 | 28847 | D-fucose | + | carbon source |
| 24899 | 12936 | D-galactose | + | carbon source |
| 24899 | 8391 | D-gluconate | + | carbon source |
| 24899 | 15748 | D-glucuronate | + | carbon source |
| 24899 | 16899 | D-mannitol | + | carbon source |
| 24899 | 16024 | D-mannose | + | carbon source |
| 24899 | 23652 | dextrin | + | carbon source |
| 24899 | 5291 | gelatin | + | hydrolysis |
| 24899 | 32323 | glucuronamide | + | carbon source |
| 24899 | 17754 | glycerol | + | carbon source |
| 24899 | 17754 | glycerol | + | builds acid from |
| 24899 | 18287 | L-fucose | + | carbon source |
| 24899 | 17632 | nitrate | + | reduction |
| 24899 | 17814 | salicin | + | carbon source |
| 24899 | 27897 | tryptophan | + | energy source |
| 24899 | 32528 | turanose | + | carbon source |
| 24899 | 53423 | tween 40 | + | hydrolysis |
metabolite production
- @ref: 24899
- Chebi-ID: 35581
- metabolite: indole
- production: yes
metabolite tests
- @ref: 24899
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 24899 | alkaline phosphatase | + | 3.1.3.1 |
| 24899 | beta-glucosidase | + | 3.2.1.21 |
| 24899 | catalase | + | 1.11.1.6 |
| 24899 | chymotrypsin | + | 3.4.4.5 |
| 24899 | cystine arylamidase | + | 3.4.11.3 |
| 24899 | cytochrome oxidase | + | 1.9.3.1 |
| 24899 | esterase (C 4) | + | |
| 24899 | esterase lipase (C 8) | + | |
| 24899 | lipase (C 14) | + | |
| 24899 | tryptophan deaminase | + | 4.1.99.1 |
Isolation, sampling and environmental information
isolation
- @ref: 24422
- sample type: rhizosphere soil of the herb Limonium sinense (Girard)
- host species: Limonium sinense
- geographic location: Xinjiang Province, Yili Valley (42° 34' 16.11'' N 81° 13' 14.07'' E, 1323 m H)
- country: China
- origin.country: CHN
- continent: Asia
- latitude: 42.5711
- longitude: 81.2206
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Rhizosphere |
taxonmaps
- @ref: 69479
- File name: preview.99_32497.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_15716;97_19257;98_24046;99_32497&stattab=map
- Last taxonomy: Herbihabitans rhizosphaerae subclade
- 16S sequence: KX128908
- Sequence Identity:
- Total samples: 1097
- soil counts: 714
- aquatic counts: 34
- animal counts: 74
- plant counts: 275
Safety information
risk assessment
- @ref: 24422
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24422
- description: Herbihabitans rhizosphaerae strain CPCC 204279 16S ribosomal RNA gene, partial sequence
- accession: KX128908
- length: 1496
- database: ena
- NCBI tax ID: 1872711
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Herbihabitans rhizosphaerae DSM 101727 | GCA_004216555 | scaffold | ncbi | 1872711 |
| 66792 | Herbihabitans rhizosphaerae strain DSM 101727 | 1872711.3 | wgs | patric | 1872711 |
| 66792 | Herbihabitans rhizosphaerae DSM 101727 | 2795385472 | draft | img | 1872711 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 24899 | 73.2 | Thermal denaturation, fluorometry |
| 24422 | 73.2 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 95.327 | yes |
| flagellated | no | 96.903 | yes |
| gram-positive | yes | 88.15 | yes |
| anaerobic | no | 98.94 | no |
| aerobic | yes | 93.604 | yes |
| halophile | no | 85.851 | no |
| spore-forming | yes | 88.743 | no |
| glucose-util | yes | 89.613 | yes |
| thermophile | no | 91.888 | yes |
| glucose-ferment | no | 91.953 | no |
External links
@ref: 24422
culture collection no.: DSM 101727, NBRC 111774, CPCC 204279
straininfo link
- @ref: 90947
- straininfo: 405701
literature
- topic: Phylogeny
- Pubmed-ID: 27470940
- title: Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard).
- authors: Zhang CF, Ai MJ, Wang JX, Liu SW, Zhao LL, Su J, Sun CH, Yu LY, Zhang YQ
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001325
- year: 2016
- mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Muramic Acids/chemistry, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plumbaginaceae/*microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry
- topic2: Transcriptome
Reference
| @id | authors | title | doi/url | catalogue | 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 | |||
| 24422 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-101727 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101727) | |||
| 24899 | C.-F. A. Zhang, Meng-Jie,Wang, Ju-Xian,Liu, Shao-Wei,Zhao, Li-Li,Su, Jing,Sun, Cheng-Hang,Yu, Li-Yan,Zhang, Yu-Qin | Herbihabitans rhizosphaerae gen. nov., sp. nov., a member of the family Pseudonocardiaceae isolated from rhizosphere soil of the herb Limonium sinense (Girard) | 10.1099/ijsem.0.001325 | IJSEM 66: 4156-4161 2016 | 27470940 | |
| 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 | |||
| 90947 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID405701.1 |