Strain identifier

BacDive ID: 11586

Type strain: Yes

Species: Paenibacillus xylanilyticus

Strain Designation: XIL14

Strain history: CIP <- 2005, CECT

NCBI tax ID(s): 248903 (species)

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

@ref: 6856

BacDive-ID: 11586

DSM-Number: 17255

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, spore-forming, mesophilic, Gram-positive, motile, rod-shaped

description: Paenibacillus xylanilyticus XIL14 is a facultative anaerobe, spore-forming, mesophilic bacterium that was isolated from air.

NCBI tax id

  • NCBI tax id: 248903
  • Matching level: species

strain history

@refhistory
6856<- E. Velázquez Pérez <- R. Rivas
405022005, CECT
123995CIP <- 2005, CECT

doi: 10.13145/bacdive11586.20230509.8.1

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 xylanilyticus
  • full scientific name: Paenibacillus xylanilyticus Rivas et al. 2005

@ref: 6856

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus xylanilyticus

full scientific name: Paenibacillus xylanilyticus Rivas et al. 2005

strain designation: XIL14

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31270positive3.95 µm1.525 µmrod-shapedyes
123995positiverod-shapedyes

colony morphology

  • @ref: 123995

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6856CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220; with strain-specific modifications) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l MnSO4 Distilled water
40502MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123995CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6856positivegrowth30mesophilic
31270positiveoptimum37mesophilic
40502positivegrowth30mesophilic

culture pH

  • @ref: 31270
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31270facultative anaerobe
123995facultative anaerobe

spore formation

  • @ref: 31270
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3127022599arabinose+carbon source
3127017234glucose+carbon source
3127017306maltose+carbon source
3127029864mannitol+carbon source
3127037684mannose+carbon source
3127028053melibiose+carbon source
31270506227N-acetylglucosamine+carbon source
3127026546rhamnose+carbon source
3127017992sucrose+carbon source
3127018222xylose+carbon source
3127017632nitrate+reduction
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate+builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose+builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose+builds acid from
6837128066gentiobiose+builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837128017starch+builds acid from
6837116634raffinose+builds acid from
683716731melezitose+builds acid from
6837115443inulin+builds acid from
6837127082trehalose+builds acid from
6837117992sucrose+builds acid from
6837128053melibiose+builds acid from
6837117716lactose+builds acid from
6837117306maltose+builds acid from
6837117057cellobiose+builds acid from
6837117814salicin+builds acid from
683714853esculin+builds acid from
6837118305arbutin+builds acid from
6837127613amygdalin+builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside+builds acid from
6837143943methyl alpha-D-mannoside+builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol+builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose+builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose+builds acid from
6837174863methyl beta-D-xylopyranoside+builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose+builds acid from
6837116988D-ribose+builds acid from
6837130849L-arabinose+builds acid from
6837117113erythritol-builds acid from
6837117754glycerol+builds acid from
12399517632nitrate+reduction
12399516301nitrite-reduction

metabolite production

  • @ref: 123995
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31270catalase+1.11.1.6
31270gelatinase+
123995oxidase-
123995alcohol dehydrogenase-1.1.1.1
123995catalase+1.11.1.6
123995lysine decarboxylase-4.1.1.18
123995ornithine decarboxylase-4.1.1.17
123995urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase-3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase+3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123995-+++-----++-+++++---

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123995+-+/-+++--+++++-+-+++/-++++++++++++++++++-++---+--+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
6856airSpainESPEurope
123995Air in a research laboratory form Salamanca UniversitySpainESPEuropeSalamanca

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Air

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68561Risk group (German classification)
1239951Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31270
  • description: Paenibacillus xylanilyticus strain XIL14 16S ribosomal RNA gene, complete sequence
  • accession: AY427832
  • length: 1546
  • database: nuccore
  • NCBI tax ID: 248903

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus xylanilyticus LMG 21957GCA_013359935contigncbi248903
66792Paenibacillus xylanilyticus strain LMG 21957248903.5wgspatric248903

GC content

  • @ref: 31270
  • GC-content: 50.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes87.244no
gram-positiveyes81.135no
anaerobicno97.923yes
aerobicyes88.015no
halophileno79.735no
spore-formingyes95.826yes
glucose-utilyes92.225no
flagellatedyes79.861no
thermophileno99.733yes
glucose-fermentno82.79no

External links

@ref: 6856

culture collection no.: DSM 17255, CECT 5839, LMG 21957, CIP 109086

straininfo link

  • @ref: 80814
  • straininfo: 99862

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15653909Paenibacillus xylanilyticus sp. nov., an airborne xylanolytic bacterium.Rivas R, Mateos PF, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.63173-02005*Air Microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Gram-Positive Endospore-Forming Rods/chemistry/*classification/genetics/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Xylans/*metabolismGenetics
Phylogeny18319478Paenibacillus provencensis sp. nov., isolated from human cerebrospinal fluid, and Paenibacillus urinalis sp. nov., isolated from human urine.Roux V, Fenner L, Raoult DInt J Syst Evol Microbiol10.1099/ijs.0.65228-02008Adult, Bacterial Typing Techniques, Cerebrospinal Fluid/*microbiology, DNA, Bacterial/analysis, Fatty Acids/analysis, Female, Genes, rRNA, Genotype, Gram-Negative Bacteria/*classification/genetics/*isolation & purification, Gram-Negative Bacterial Infections/*microbiology, Humans, Male, Middle Aged, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Urine/*microbiologyGenetics
Phylogeny26063444Paenibacillus enshidis sp. nov., Isolated from the Nodules of Robinia pseudoacacia L.Yin J, He D, Li X, Zeng X, Tian M, Cheng GCurr Microbiol10.1007/s00284-015-0854-22015Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Locomotion, Microscopy, Electron, Scanning, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Robinia/*microbiology, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Spores, Bacterial/cytology, Vitamin K 2/analysisTranscriptome
Phylogeny28177800Diversity of Bacillus-like bacterial community in the sediments of the Bamenwan mangrove wetland in Hainan, China.Liu M, Cui Y, Chen Y, Lin X, Huang H, Bao SCan J Microbiol10.1139/cjm-2016-04492016Animals, Bacillaceae/classification/*isolation & purification/physiology, *Biodiversity, China, DNA, Bacterial, DNA, Ribosomal/genetics, Geologic Sediments/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Staphylococcus aureus, *Water Microbiology, *WetlandsTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6856Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17255)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17255
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
31270Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2759028776041
40502Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6788
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
80814Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99862.1StrainInfo: A central database for resolving microbial strain identifiers
123995Curators of the CIPCollection of Institut Pasteur (CIP 109086)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109086