Strain identifier
BacDive ID: 132619
Type strain:
Species: Paenibacillus segetis
Strain Designation: DB13260
Strain history: <- H. Huang, Inst. Tropical Bioscience and Biotechnol., Haikou, China <- Ying Cui; DB13260
NCBI tax ID(s): 1325360 (species)
General
@ref: 24408
BacDive-ID: 132619
DSM-Number: 28014
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped, colony-forming
description: Paenibacillus segetis DB13260 is a facultative anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from soil, tropical rainforest.
NCBI tax id
- NCBI tax id: 1325360
- Matching level: species
strain history
- @ref: 24408
- history: <- H. Huang, Inst. Tropical Bioscience and Biotechnol., Haikou, China <- Ying Cui; DB13260
doi: 10.13145/bacdive132619.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Paenibacillaceae
- genus: Paenibacillus
- species: Paenibacillus segetis
- full scientific name: Paenibacillus segetis Huang et al. 2016
@ref: 24408
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Paenibacillaceae
genus: Paenibacillus
species: Paenibacillus segetis
full scientific name: Paenibacillus segetis Huang et al. 2016
strain designation: DB13260
type strain: yes
Morphology
cell morphology
- @ref: 43141
- gram stain: positive
- cell length: 1.2-3.5 µm
- cell width: 0.5-1.0 µm
- cell shape: rod-shaped
- motility: yes
colony morphology
- @ref: 43141
- colony size: 0.3-1.0 mm
- colony color: creamy white
- colony shape: circular
- incubation period: 1 day
- medium used: TSB agar
pigmentation
- @ref: 43141
- production: no
- name: Melanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
43141 | TSB agar | yes | ||
24408 | 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 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
43141 | positive | optimum | 30-37 | mesophilic |
43141 | positive | growth | 5-40 | |
24408 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
43141 | positive | growth | 6.0-10.5 | alkaliphile |
43141 | positive | optimum | 8.5-9.0 |
Physiology and metabolism
oxygen tolerance
- @ref: 43141
- oxygen tolerance: facultative anaerobe
spore formation
- @ref: 43141
- type of spore: spore
- spore formation: yes
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
43141 | NaCl | positive | growth | 0-4 %(w/v) |
43141 | NaCl | positive | optimum | 0 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43141 | 17234 | glucose | - | fermentation |
43141 | 17632 | nitrate | - | reduction |
43141 | 5291 | gelatin | - | hydrolysis |
43141 | 28017 | starch | - | hydrolysis |
43141 | 16947 | citrate | - | assimilation |
43141 | 15792 | malonate | - | assimilation |
43141 | 62968 | cellulose | - | degradation |
43141 | 36219 | alpha-lactose | + | carbon source |
43141 | 15824 | D-fructose | + | carbon source |
43141 | 16024 | D-mannose | + | carbon source |
43141 | 65327 | D-xylose | + | carbon source |
43141 | 28017 | starch | + | carbon source |
43141 | 17306 | maltose | + | carbon source |
43141 | 30849 | L-arabinose | + | carbon source |
43141 | 27082 | trehalose | + | carbon source |
43141 | 16634 | raffinose | + | carbon source |
43141 | 17234 | glucose | - | carbon source |
43141 | 15603 | L-leucine | - | carbon source |
43141 | 17203 | L-proline | - | carbon source |
43141 | 35962 | sorbic acid | - | carbon source |
43141 | 17115 | L-serine | - | carbon source |
43141 | 17057 | cellobiose | - | carbon source |
43141 | 12936 | D-galactose | - | carbon source |
43141 | 16988 | D-ribose | - | carbon source |
43141 | 16467 | L-arginine | - | carbon source |
43141 | 17268 | myo-inositol | - | carbon source |
43141 | 15729 | L-ornithine | - | carbon source |
43141 | 15428 | glycine | - | carbon source |
43141 | 30911 | sorbitol | - | carbon source |
43141 | 17234 | glucose | + | builds acid from |
43141 | 17992 | sucrose | + | builds acid from |
43141 | 16634 | raffinose | + | builds acid from |
43141 | 17057 | cellobiose | + | builds acid from |
43141 | 15824 | D-fructose | + | builds acid from |
43141 | 30849 | L-arabinose | + | builds acid from |
43141 | 65327 | D-xylose | + | builds acid from |
43141 | 27082 | trehalose | + | builds acid from |
43141 | 16988 | D-ribose | + | builds acid from |
43141 | 36219 | alpha-lactose | + | builds acid from |
43141 | 30911 | sorbitol | + | builds acid from |
43141 | 29864 | mannitol | + | builds acid from |
43141 | 17306 | maltose | + | builds acid from |
43141 | 28017 | starch | + | builds acid from |
43141 | 16024 | D-mannose | - | builds acid from |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive | sensitivity conc. |
---|---|---|---|---|---|
43141 | 27902 | tetracycline | yes | yes | 30 µg (disc) |
43141 | 28971 | ampicillin | yes | yes | 10 µg (disc) |
43141 | 17698 | chloramphenicol | yes | yes | 30 µg (disc) |
43141 | 48923 | erythromycin | yes | yes | 5 µg (disc) |
43141 | 17833 | gentamicin | yes | yes | 10 µg (disc) |
43141 | 6104 | kanamycin | yes | yes | 30 µg (disc) |
43141 | 100147 | nalidixic acid | yes | yes | 30 µg (disc) |
43141 | 7507 | neomycin | yes | yes | 30 µg (disc) |
43141 | 28368 | novobiocin | yes | yes | 30 µg (disc) |
43141 | 28077 | rifampicin | yes | yes | 5 µg (disc) |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43141 | 15688 | acetoin | no |
43141 | 35581 | indole | no |
43141 | 16136 | hydrogen sulfide | no |
metabolite tests
@ref | Chebi-ID | metabolite | methylred-test | voges-proskauer-test |
---|---|---|---|---|
43141 | 17234 | glucose | - | |
43141 | 15688 | acetoin | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43141 | catalase | + | 1.11.1.6 |
43141 | cytochrome oxidase | + | 1.9.3.1 |
43141 | esterase | + | |
43141 | urease | - | 3.5.1.5 |
43141 | phenylalaninase | - |
fatty acid profile
fatty acids
@ref fatty acid percentage 43141 C12:0 1.8 43141 C14:0 3 43141 C16:0 13.5 43141 C14:0 iso 7.1 43141 C15:0 iso 5.9 43141 C16:0 iso 19.6 43141 C17:0 iso 1.6 43141 C15:0 anteiso 43.9 43141 C17:0 anteiso 2.3 - type of FA analysis: whole cell analysis
- incubation medium: TSB
- incubation temperature: 28
- incubation time: 3
- system: MIS MIDI
- method/protocol: Kuykendall et al. 1988
- cutoff value:
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
24408 | soil, tropical rainforest | Hainan, Jianfengling Nature Reserve (18° 30'–18° 40' N 108° 59'–109° 01' E ) | China | CHN | Asia | 18.5833 | 109 |
43141 | tropical rainforest soil sample | Jianfengling Nature Reserve, Hainan, China | China | CHN | Asia | 18 | 108 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Forest |
#Environmental | #Terrestrial | #Soil |
#Climate | #Hot | #Tropical |
taxonmaps
- @ref: 69479
- File name: preview.99_40261.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_18589;97_22986;98_28980;99_40261&stattab=map
- Last taxonomy: Paenibacillus
- 16S sequence: KC835079
- Sequence Identity:
- Total samples: 16
- soil counts: 9
- animal counts: 1
- plant counts: 6
Safety information
risk assessment
- @ref: 24408
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24408
- description: Paenibacillus segetis strain DB13260 16S ribosomal RNA gene, partial sequence
- accession: KC835079
- length: 1419
- database: ena
- NCBI tax ID: 1325360
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Paenibacillus segetis CGMCC 1.12769 | GCA_014639155 | scaffold | ncbi | 1325360 |
66792 | Paenibacillus segetis strain CGMCC 1.12769 | 1325360.3 | wgs | patric | 1325360 |
GC content
- @ref: 24408
- GC-content: 53.7
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | yes | 84.079 | no |
gram-positive | yes | 87.386 | yes |
anaerobic | no | 96.3 | yes |
aerobic | yes | 60.644 | no |
halophile | no | 94.509 | yes |
spore-forming | yes | 95.383 | no |
glucose-util | yes | 81.356 | yes |
thermophile | no | 99.795 | yes |
motile | yes | 90.223 | no |
glucose-ferment | no | 84.602 | yes |
External links
@ref: 24408
culture collection no.: DSM 28014, CGMCC 1.12769
straininfo link
- @ref: 90933
- straininfo: 396672
literature
- topic: Phylogeny
- Pubmed-ID: 27373881
- title: Paenibacillus segetis sp. nov., isolated from soil of a tropical rainforest.
- authors: Huang H, Feng F, Liu M, Zhang F, Sun Q, Qin S, Bao S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijsem.0.001258
- year: 2016
- mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rainforest, Sequence Analysis, DNA, *Soil Microbiology, Tropical Climate, 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 | |||
24408 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28014 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28014) | |||
43141 | Huiqin Huang, Fengzhao Feng, Min Liu, Fute Zhang, Qianguang Sun, Songyu Qin and Shixiang Bao | Paenibacillus segetis sp. nov., isolated from soil of a tropical rainforest | 10.1099/ijsem.0.001258 | IJSEM 66: 3703-3707 2016 | 27373881 | |
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/ | |||
90933 | 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-ID396672.1 |