Strain identifier

BacDive ID: 132619

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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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

@refnamegrowthlinkcomposition
43141TSB agaryes
24408CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: 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

@refgrowthtypetemperaturerange
43141positiveoptimum30-37mesophilic
43141positivegrowth5-40
24408positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
43141positivegrowth6.0-10.5alkaliphile
43141positiveoptimum8.5-9.0

Physiology and metabolism

oxygen tolerance

  • @ref: 43141
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 43141
  • type of spore: spore
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
43141NaClpositivegrowth0-4 %(w/v)
43141NaClpositiveoptimum0 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4314117234glucose-fermentation
4314117632nitrate-reduction
431415291gelatin-hydrolysis
4314128017starch-hydrolysis
4314116947citrate-assimilation
4314115792malonate-assimilation
4314162968cellulose-degradation
4314136219alpha-lactose+carbon source
4314115824D-fructose+carbon source
4314116024D-mannose+carbon source
4314165327D-xylose+carbon source
4314128017starch+carbon source
4314117306maltose+carbon source
4314130849L-arabinose+carbon source
4314127082trehalose+carbon source
4314116634raffinose+carbon source
4314117234glucose-carbon source
4314115603L-leucine-carbon source
4314117203L-proline-carbon source
4314135962sorbic acid-carbon source
4314117115L-serine-carbon source
4314117057cellobiose-carbon source
4314112936D-galactose-carbon source
4314116988D-ribose-carbon source
4314116467L-arginine-carbon source
4314117268myo-inositol-carbon source
4314115729L-ornithine-carbon source
4314115428glycine-carbon source
4314130911sorbitol-carbon source
4314117234glucose+builds acid from
4314117992sucrose+builds acid from
4314116634raffinose+builds acid from
4314117057cellobiose+builds acid from
4314115824D-fructose+builds acid from
4314130849L-arabinose+builds acid from
4314165327D-xylose+builds acid from
4314127082trehalose+builds acid from
4314116988D-ribose+builds acid from
4314136219alpha-lactose+builds acid from
4314130911sorbitol+builds acid from
4314129864mannitol+builds acid from
4314117306maltose+builds acid from
4314128017starch+builds acid from
4314116024D-mannose-builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.
4314127902tetracyclineyesyes30 µg (disc)
4314128971ampicillinyesyes10 µg (disc)
4314117698chloramphenicolyesyes30 µg (disc)
4314148923erythromycinyesyes5 µg (disc)
4314117833gentamicinyesyes10 µg (disc)
431416104kanamycinyesyes30 µg (disc)
43141100147nalidixic acidyesyes30 µg (disc)
431417507neomycinyesyes30 µg (disc)
4314128368novobiocinyesyes30 µg (disc)
4314128077rifampicinyesyes5 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
4314115688acetoinno
4314135581indoleno
4314116136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4314117234glucose-
4314115688acetoin-

enzymes

@refvalueactivityec
43141catalase+1.11.1.6
43141cytochrome oxidase+1.9.3.1
43141esterase+
43141urease-3.5.1.5
43141phenylalaninase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43141C12:01.8
    43141C14:03
    43141C16:013.5
    43141C14:0 iso7.1
    43141C15:0 iso5.9
    43141C16:0 iso19.6
    43141C17:0 iso1.6
    43141C15:0 anteiso43.9
    43141C17:0 anteiso2.3
  • 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

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
24408soil, tropical rainforestHainan, Jianfengling Nature Reserve (18° 30'–18° 40' N 108° 59'–109° 01' E )ChinaCHNAsia18.5833109
43141tropical rainforest soil sampleJianfengling Nature Reserve, Hainan, ChinaChinaCHNAsia18108

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus segetis CGMCC 1.12769GCA_014639155scaffoldncbi1325360
66792Paenibacillus segetis strain CGMCC 1.127691325360.3wgspatric1325360

GC content

  • @ref: 24408
  • GC-content: 53.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes84.079no
gram-positiveyes87.386yes
anaerobicno96.3yes
aerobicyes60.644no
halophileno94.509yes
spore-formingyes95.383no
glucose-utilyes81.356yes
thermophileno99.795yes
motileyes90.223no
glucose-fermentno84.602yes

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

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24408Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28014Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28014)
43141Huiqin Huang, Fengzhao Feng, Min Liu, Fute Zhang, Qianguang Sun, Songyu Qin and Shixiang BaoPaenibacillus segetis sp. nov., isolated from soil of a tropical rainforest10.1099/ijsem.0.001258IJSEM 66: 3703-3707 201627373881
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João 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 betahttps://microbeatlas.org/
90933Reimer, 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 identifiers10.60712/SI-ID396672.1