Strain identifier
BacDive ID: 158323
Type strain:
Species: Nocardia rhizosphaerihabitans
Strain history: <- S. Qin, Jangsu Normal University, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province; KLBMP S0039
NCBI tax ID(s): 1691570 (species)
General
@ref: 64999
BacDive-ID: 158323
DSM-Number: 101726
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive
description: Nocardia rhizosphaerihabitans DSM 101726 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from coastal soil.
NCBI tax id
- NCBI tax id: 1691570
- Matching level: species
strain history
- @ref: 64999
- history: <- S. Qin, Jangsu Normal University, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province; KLBMP S0039
doi: 10.13145/bacdive158323.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Nocardiaceae
- genus: Nocardia
- species: Nocardia rhizosphaerihabitans
- full scientific name: Nocardia rhizosphaerihabitans Ding et al. 2018
@ref: 64999
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiaceae
genus: Nocardia
species: Nocardia rhizosphaerihabitans
full scientific name: Nocardia rhizosphaerihabitans Ding et al. 2018
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence |
---|---|---|---|
65296 | positive | no | |
69480 | no | 90.694 | |
69480 | positive | 100 |
multicellular morphology
- @ref: 65296
- forms multicellular complex: yes
- complex color: yellowish white to white
- further description: forms extensively branched, yellowish white to white substrate mycelium and white to gray–white aerial mycelium that fragments into short to elongated rod-like elements on tested media
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
64999 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
65296 | ISP2 | yes | ||
65296 | ISP5 | yes | ||
65296 | ISP6 | yes | ||
65296 | tryptic soy agar | yes | ||
65296 | potato-dextrose agar | yes | ||
65296 | ISP3 | yes | ||
65296 | ISP4 | yes | ||
65296 | ISP7 | yes | ||
65296 | Czapek's agar | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
64999 | positive | growth | 28 | mesophilic |
65296 | positive | growth | 10-37 | |
65296 | positive | optimum | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
65296 | positive | growth | 5-10 | alkaliphile |
65296 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 65296
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69480 | no | 94.013 |
69481 | yes | 96 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
65296 | NaCl | positive | growth | 0-5 %(w/v) |
65296 | NaCl | positive | optimum | 1-3 %(w/v) |
observation
- @ref: 65296
- observation: weakly acid-alcohol-fast
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
65296 | 16708 | adenine | - | hydrolysis |
65296 | 27613 | amygdalin | + | builds acid from |
65296 | casein | - | hydrolysis | |
65296 | 17057 | cellobiose | - | carbon source |
65296 | 62968 | cellulose | - | hydrolysis |
65296 | 15824 | D-fructose | + | carbon source |
65296 | 12936 | D-galactose | - | carbon source |
65296 | 17634 | D-glucose | + | carbon source |
65296 | 16024 | D-mannose | + | carbon source |
65296 | 16988 | D-ribose | - | carbon source |
65296 | 23652 | dextrin | + | carbon source |
65296 | 33946 | erythrose | - | carbon source |
65296 | 5291 | gelatin | - | hydrolysis |
65296 | 15428 | glycine | + | nitrogen source |
65296 | 28087 | glycogen | + | builds acid from |
65296 | 17368 | hypoxanthine | - | hydrolysis |
65296 | 17268 | myo-inositol | - | carbon source |
65296 | 16977 | L-alanine | + | nitrogen source |
65296 | 30849 | L-arabinose | + | builds acid from |
65296 | 30849 | L-arabinose | + | carbon source |
65296 | 16467 | L-arginine | + | nitrogen source |
65296 | 15971 | L-histidine | + | nitrogen source |
65296 | 18019 | L-lysine | + | nitrogen source |
65296 | 17203 | L-proline | + | nitrogen source |
65296 | 17115 | L-serine | + | nitrogen source |
65296 | 17716 | lactose | - | carbon source |
65296 | 17306 | maltose | + | carbon source |
65296 | 37684 | mannose | + | builds acid from |
65296 | 74863 | methyl beta-D-xylopyranoside | + | builds acid from |
65296 | milk | + | assimilation | |
65296 | 16634 | raffinose | - | carbon source |
65296 | 26546 | rhamnose | + | carbon source |
65296 | 28017 | starch | - | hydrolysis |
65296 | 17992 | sucrose | + | builds acid from |
65296 | 27082 | trehalose | + | builds acid from |
65296 | 27082 | trehalose | + | carbon source |
65296 | 53424 | tween 20 | - | hydrolysis |
65296 | 53423 | tween 40 | - | hydrolysis |
65296 | 53426 | tween 80 | - | hydrolysis |
65296 | 18222 | xylose | - | carbon source |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. | is resistant | resistance conc. | group ID |
---|---|---|---|---|---|---|---|---|
65296 | 7809 | oxacillin | yes | yes | 1 µg (disc) | |||
65296 | 3745 | clindamycin | yes | yes | 2 µg (disc) | |||
65296 | 100241 | ciprofloxacin | yes | yes | 5 µg (disc) | |||
65296 | 100246 | norfloxacin | yes | yes | 10 µg (disc) | |||
65296 | 48923 | erythromycin | yes | yes | 15 µg (disc) | |||
65296 | 63598 | levofloxacin | yes | yes | 5 µg (disc) | |||
65296 | 17334 | penicillin | yes | yes | 10 µg (disc) | |||
65296 | 3732 | clarithromycin | yes | yes | 15 µg (disc) | |||
65296 | 50694 | minocycline | yes | yes | 30 µg (disc) | |||
65296 | 8309 | polymyxin b | yes | yes | 30 µg (disc) | |||
65296 | 28001 | vancomycin | yes | yes | 30 µg (disc) | |||
65296 | 9215 | spectinomycin | yes | yes | 100 µg (disc) | |||
65296 | 45924 | trimethoprim | yes | yes | 1.25 µg (disc) | 26 | ||
65296 | 9332 | sulfamethoxazole | yes | yes | 23.75 µg (disc) | 26 |
metabolite production
- @ref: 65296
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: yes
enzymes
@ref | value | activity | ec |
---|---|---|---|
65296 | urease | + | 3.5.1.5 |
65296 | catalase | + | 1.11.1.6 |
fatty acid profile
fatty acids
@ref fatty acid percentage 65296 C14:0 0.4 65296 C16:0 28.2 65296 C17:0 0.5 65296 C18:0 31.1 65296 C18:0 10-methyl, TBSA 17.7 65296 C18:1ω9c 12.2 65296 C20:0 0.3 65296 C16:1ω7c and/or C16:1ω6c 7.9 65296 C19:1ω11c and/or C19:1ω9c 0.5 - type of FA analysis: whole cell analysis
- incubation medium: tryptic soy broth
- agar/liquid: liquid
- incubation temperature: 28
- incubation time: 5
- software version: Sherlock 6.0
- library/peak naming table: TSBA6
- system: MIS MIDI
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude | enrichment culture | enrichment culture composition | enrichment culture duration | enrichment culture temperature |
---|---|---|---|---|---|---|---|---|---|---|---|
64999 | coastal soil | Jiangsu Province, Lianyungang region (34° 20' 29.4'' N, 119° 8' 25.4 E) | China | CHN | Asia | 34.3415 | 119.14 | ||||
65296 | rhizosphere soil of Lycium Linn | coastal region in Lianyungang, Jiangsu Province | China | CHN | Asia | starch-arginine agar | 5.0 g glucose, 5.0 g soluble starch, 1.0 g yeast extract, 2.0 g hydrolyzed casein, 2.0 g CaCO3, 15.0 g agar, 1000 ml H2O, pH 7.2] supplemented with 3 % (w/v) NaCl and nystatin and nalidixic acid | 21 days | 28 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host Body-Site | #Plant | #Rhizosphere |
#Environmental | #Terrestrial | #Soil |
#Host | #Plants | #Tree |
taxonmaps
- @ref: 69479
- File name: preview.99_825.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_243;97_280;98_507;99_825&stattab=map
- Last taxonomy: Nocardia
- 16S sequence: KP972636
- Sequence Identity:
- Total samples: 542
- soil counts: 198
- aquatic counts: 84
- animal counts: 206
- plant counts: 54
Safety information
risk assessment
- @ref: 64999
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | database | length | NCBI tax ID |
---|---|---|---|---|---|
65296 | 16S rRNA gene sequence | KP972636 | nuccore | ||
64999 | Nocardia rhizosphaerihabitans strain KLBMP S0039 16S ribosomal RNA gene, partial sequence | KP972636.3 | ena | 1407 | 1691570 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Nocardia rhizosphaerihabitans CGMCC 4.7329 | GCA_014646295 | scaffold | ncbi | 1691570 |
66792 | Nocardia rhizosphaerihabitans strain CGMCC 4.7329 | 1691570.3 | wgs | patric | 1691570 |
GC content
- @ref: 65296
- GC-content: 68.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 96 | no |
flagellated | no | 97.435 | yes |
gram-positive | yes | 85.059 | yes |
anaerobic | no | 99.151 | no |
aerobic | yes | 88.548 | yes |
halophile | no | 91.39 | no |
spore-forming | yes | 81 | no |
thermophile | no | 99.209 | no |
glucose-util | yes | 88.441 | no |
motile | no | 93.214 | no |
glucose-ferment | no | 90.65 | no |
External links
@ref: 64999
culture collection no.: DSM 101726, CGMCC 4.7329, KCTC 39693, KLBMP S0039
straininfo link
- @ref: 111133
- straininfo: 408094
literature
- topic: Phylogeny
- Pubmed-ID: 29125460
- title: Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil.
- authors: Ding P, Bai JL, Wang TT, Sun Y, Cao CL, Jiang JH, Qin S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.002481
- year: 2017
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lycium/*microbiology, Nocardia/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, 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 | |||
64999 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-101726 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 101726) | |||
65296 | Peng Ding, Juan-Luan Bai, Tian-Tian Wang, Yong Sun, Cheng-Liang Cao, Ji-Hong Jiang, Sheng Qin | Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil | 10.1099/ijsem.0.002481 | IJSEM 68: 192-197 2018 | 29125460 | |
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 | |||
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 | |||
111133 | 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-ID408094.1 |