Strain identifier
BacDive ID: 141046
Type strain:
Species: Propioniciclava sinopodophylli
Strain Designation: TEYR-7
Strain history: <- Lei Zhang, Northwest A&F Univ., Yangling, Shannxi
NCBI tax ID(s): 1837344 (species)
General
@ref: 43926
BacDive-ID: 141046
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive, rod-shaped, colony-forming
description: Propioniciclava sinopodophylli TEYR-7 is a facultative anaerobe, Gram-positive, rod-shaped bacterium that forms circular colonies and was isolated from surface-sterilized leaves of Sinopodophyllum hexandrum collected from the Qinling Mountains in Shaanxi Province, northwest China.
NCBI tax id
- NCBI tax id: 1837344
- Matching level: species
strain history
- @ref: 67771
- history: <- Lei Zhang, Northwest A&F Univ., Yangling, Shannxi
doi: 10.13145/bacdive141046.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Propionibacteriales
- family: Propionibacteriaceae
- genus: Propioniciclava
- species: Propioniciclava sinopodophylli
- full scientific name: Propioniciclava sinopodophylli Zhang et al. 2017
synonyms
@ref synonym 20215 Brevilactibacter sinopodophylli 20215 Propioniciclava sinopodophylli
@ref: 43926
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Propionibacteriales
family: Propionibacteriaceae
genus: Propioniciclava
species: Propioniciclava sinopodophylli
strain designation: TEYR-7
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
43926 | positive | 1.1-1.5 µm | 0.6-0.7 µm | rod-shaped | no | |
69480 | no | 92.481 | ||||
69480 | positive | 100 |
colony morphology
- @ref: 43926
- colony size: 2-3 mm
- colony color: pale yellow
- colony shape: circular
- incubation period: 2 days
- medium used: R2A agar
Culture and growth conditions
culture medium
@ref | name | growth |
---|---|---|
43926 | MacConkey agar | no |
43926 | Reasoner's 2A agar (R2A) | yes |
43926 | Tryptic soy agar | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43926 | positive | growth | 15-37 | |
43926 | positive | optimum | 28-30 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43926 | positive | growth | 6.0-9.0 | alkaliphile |
43926 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
43926 | facultative anaerobe |
67771 | facultative anaerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.995 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43926 | NaCl | positive | growth | 0-3 %(w/v) |
43926 | NaCl | positive | optimum | 0-1 %(w/v) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43926 | 17128 | adipate | - | assimilation |
43926 | 27689 | decanoate | - | assimilation |
43926 | 17634 | D-glucose | - | assimilation |
43926 | 16899 | D-mannitol | - | assimilation |
43926 | 16024 | D-mannose | - | assimilation |
43926 | 30849 | L-arabinose | - | assimilation |
43926 | 17306 | maltose | - | assimilation |
43926 | 506227 | N-acetylglucosamine | - | assimilation |
43926 | 18401 | phenylacetate | - | assimilation |
43926 | 32032 | potassium gluconate | - | assimilation |
43926 | 53258 | sodium citrate | - | assimilation |
43926 | 27613 | amygdalin | - | builds acid from |
43926 | 15963 | ribitol | - | builds acid from |
43926 | 17108 | D-arabinose | - | builds acid from |
43926 | 18333 | D-arabitol | - | builds acid from |
43926 | 28847 | D-fucose | - | builds acid from |
43926 | 12936 | D-galactose | - | builds acid from |
43926 | 62318 | D-lyxose | - | builds acid from |
43926 | 16899 | D-mannitol | - | builds acid from |
43926 | 6731 | melezitose | - | builds acid from |
43926 | 28053 | melibiose | - | builds acid from |
43926 | 16634 | raffinose | - | builds acid from |
43926 | 16988 | D-ribose | - | builds acid from |
43926 | 17924 | D-sorbitol | - | builds acid from |
43926 | 16443 | D-tagatose | - | builds acid from |
43926 | 16551 | D-trehalose | - | builds acid from |
43926 | 32528 | turanose | - | builds acid from |
43926 | 65327 | D-xylose | - | builds acid from |
43926 | 16813 | galactitol | - | builds acid from |
43926 | 17113 | erythritol | - | builds acid from |
43926 | 28066 | gentiobiose | - | builds acid from |
43926 | 17268 | myo-inositol | - | builds acid from |
43926 | 15443 | inulin | - | builds acid from |
43926 | 30849 | L-arabinose | - | builds acid from |
43926 | 18403 | L-arabitol | - | builds acid from |
43926 | 18287 | L-fucose | - | builds acid from |
43926 | 62345 | L-rhamnose | - | builds acid from |
43926 | 17266 | L-sorbose | - | builds acid from |
43926 | 65328 | L-xylose | - | builds acid from |
43926 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
43926 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
43926 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
43926 | 506227 | N-acetylglucosamine | - | builds acid from |
43926 | potassium 2-dehydro-D-gluconate | - | builds acid from | |
43926 | potassium 5-dehydro-D-gluconate | - | builds acid from | |
43926 | 32032 | potassium gluconate | - | builds acid from |
43926 | 17151 | xylitol | - | builds acid from |
43926 | 85146 | carboxymethylcellulose | - | hydrolysis |
43926 | casein | - | hydrolysis | |
43926 | 17895 | L-tyrosine | - | hydrolysis |
43926 | 25115 | malate | + | assimilation |
43926 | 17057 | cellobiose | + | builds acid from |
43926 | 15824 | D-fructose | + | builds acid from |
43926 | 17634 | D-glucose | + | builds acid from |
43926 | 17306 | maltose | + | builds acid from |
43926 | 16024 | D-mannose | + | builds acid from |
43926 | 4853 | esculin | + | builds acid from |
43926 | 15978 | glycerol 3-phosphate | + | builds acid from |
43926 | 17992 | sucrose | + | builds acid from |
43926 | 4853 | esculin | + | hydrolysis |
43926 | 5291 | gelatin | + | hydrolysis |
43926 | O-nitrophenyl-beta-D-galactopyranosid | + | hydrolysis | |
43926 | 28017 | starch | + | hydrolysis |
43926 | 17632 | nitrate | + | reduction |
43926 | 16004 | (R)-lactate | +/- | builds acid from |
43926 | 18305 | arbutin | +/- | builds acid from |
43926 | 28087 | glycogen | +/- | builds acid from |
43926 | 17814 | salicin | +/- | builds acid from |
43926 | 28017 | starch | +/- | builds acid from |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43926 | 16136 | hydrogen sulfide | no |
43926 | 35581 | indole | no |
43926 | 30089 | acetate | yes |
43926 | 17272 | propionate | yes |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43926 | cytochrome oxidase | + | 1.9.3.1 |
43926 | catalase | + | 1.11.1.6 |
43926 | urease | + | 3.5.1.5 |
43926 | arginine dihydrolase | - | 3.5.3.6 |
43926 | lysine decarboxylase | - | 4.1.1.18 |
43926 | ornithine decarboxylase | - | 4.1.1.17 |
43926 | acid phosphatase | + | 3.1.3.2 |
43926 | esterase (C 4) | + | |
43926 | esterase Lipase (C 8) | + | |
43926 | alpha-glucosidase | + | 3.2.1.20 |
43926 | beta-galactosidase | + | 3.2.1.23 |
43926 | beta-glucosidase | + | 3.2.1.21 |
43926 | leucine arylamidase | + | 3.4.11.1 |
43926 | naphthol-AS-BI-phosphohydrolase | + | |
43926 | alpha-chymotrypsin | +/- | 3.4.21.1 |
43926 | alpha-galactosidase | +/- | 3.2.1.22 |
43926 | valine arylamidase | +/- | |
43926 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
43926 | alkaline phosphatase | - | 3.1.3.1 |
43926 | cystine arylamidase | - | 3.4.11.3 |
43926 | alpha-fucosidase | - | 3.2.1.51 |
43926 | beta-glucuronidase | - | 3.2.1.31 |
43926 | lipase (C 14) | - | |
43926 | alpha-mannosidase | - | 3.2.1.24 |
43926 | trypsin | - | 3.4.21.4 |
fatty acid profile
fatty acids
@ref fatty acid percentage 43926 C15:0 anteiso 33.8 43926 C17:0 anteiso 1.5 43926 anteiso-C17:1B / iso-C17:1 I 7.6 43926 anteiso-C17:1ω9c1c 0.8 43926 C12:0 aldehyde / unknown 10.928 / iso-C16:1 I / C1 2.1 43926 C14:0 3.1 43926 C16:0 13.9 43926 C16:1ω7c / C16:1ω6c 6.1 43926 C16:1ω9c 1.3 43926 C17:0 2.6 43926 C17:1ω6c1c 1 43926 C17:1ω8c1c 1.2 43926 C18:0 1.5 43926 C18:1ω6c1c 1.7 43926 C18:1ω7c1c / C18:1ω6c1c 2 43926 C18:1ω9c1c 2.5 43926 C18:2ω6c, ω9c and/or anteiso-C 18 : 0 2 43926 C14:0 iso 9 43926 C15:0 iso 1.4 43926 C16:0 iso 4.1 43926 C18:1 iso H 0.8 - type of FA analysis: whole cell analysis
- incubation medium: R2A agar
- agar/liquid: agar
- incubation temperature: 30
- incubation time: 2
- software version: Sherlock 6.0
- library/peak naming table: TSBA6
- system: MIS MIDI
- instrument: Hewlett Packard 6890 N gas chromatograph
- method/protocol: Sasser, 1990
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 |
---|---|---|---|---|---|---|---|---|---|---|---|
43926 | surface-sterilized leaves of Sinopodophyllum hexandrum collected from the Qinling Mountains in Shaanxi Province, northwest China | Qinling Mountains in Shaanxi Province | China | CHN | Asia | 33.95 | 107.75 | R2A agar | supplemented with 50 µg/mL cycloheximide | 2 weeks | 25 |
67771 | From the root of Sinopodophyllum hexandrum (Royle) Ying | Taibai Mountain | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Plants | #Herbaceous plants (Grass,Crops) |
#Host Body-Site | #Plant | #Leaf (Phyllosphere) |
#Host Body-Site | #Plant | #Sterilized plant part |
taxonmaps
- @ref: 69479
- File name: preview.99_37125.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_282;96_5377;97_21761;98_27318;99_37125&stattab=map
- Last taxonomy: Brevilactibacter sinopodophylli subclade
- 16S sequence: KX009027
- Sequence Identity:
- Total samples: 2340
- soil counts: 52
- aquatic counts: 1769
- animal counts: 502
- plant counts: 17
Sequence information
16S sequences
- @ref: 43926
- description: 16S rRNA gene sequence
- accession: KX009027
- database: nuccore
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Propioniciclava sinopodophylli KCTC 33808 | GCA_004324755 | contig | ncbi | 1837344 |
66792 | Propioniciclava sinopodophylli strain KCTC 33808 | 1837344.3 | wgs | patric | 1837344 |
66792 | Propioniciclava sinopodophylli KCTC 33808 | 2867481428 | draft | img | 1837344 |
GC content
- @ref: 43926
- GC-content: 71.2
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 95.299 | no |
gram-positive | yes | 88.331 | yes |
anaerobic | no | 97.278 | yes |
aerobic | yes | 67.651 | no |
halophile | no | 96.922 | yes |
spore-forming | no | 93.196 | no |
glucose-util | yes | 90.492 | no |
flagellated | no | 97.695 | no |
glucose-ferment | no | 66.073 | no |
thermophile | no | 96.746 | yes |
External links
@ref: 43926
culture collection no.: CCTCC AB 2015257, KCTC 33808
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 28901898 | Propioniciclava sinopodophylli sp. nov., isolated from leaves of Sinopodophyllum hexandrum (Royle) Ying. | Zhang L, Li Q, Chen C, Li X, Li M, Hu J, Shen X | Int J Syst Evol Microbiol | 10.1099/ijsem.0.002265 | 2017 | Bacterial Typing Techniques, Base Composition, Berberidaceae/*microbiology, Cell Wall/chemistry, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Leaves/*microbiology, Propionibacteriaceae/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistry | Transcriptome |
Phylogeny | 34020025 | Genomic description and characterization of Nigeribacterium massiliense gen. nov., sp. nov., isolated from the human gut. | Khare M, Sinha D, Zgheib R, Traore SI, Lagier JC, Raoult D, Fournier PE | Microbes Infect | 10.1016/j.micinf.2021.104842 | 2021 | Base Composition, Child, Preschool, DNA, Bacterial/genetics, *Genomics, Humans, Male, Phylogeny, RNA, Ribosomal, 16S/genetics | Genetics |
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 | ||
43926 | Lei Zhang, Qiqi Li, Chaoqiong Chen, Xin Li, Muhang Li, Jingjiang Hu, Xihui Shen | Propioniciclava sinopodophylli sp. nov., isolated from leaves of Sinopodophyllum hexandrum (Royle) Ying | 10.1099/ijsem.0.002265 | IJSEM 67: 4111-4115 2017 | 28901898 |
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 |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||
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 |