Strain identifier

BacDive ID: 11616

Type strain: Yes

Species: Paenibacillus humicus

Strain Designation: PC-147

Strain history: CIP <- 2013, DSM <- C. Manaia, Univ. Portugal, Porto, Portugal <- I. Vaz-Moreia strain: PC-147

NCBI tax ID(s): 1349778 (strain), 412861 (species)

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General

@ref: 7695

BacDive-ID: 11616

DSM-Number: 18784

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-negative, motile, rod-shaped

description: Paenibacillus humicus PC-147 is an aerobe, spore-forming, thermophilic bacterium that was isolated from poultry litter compost.

NCBI tax id

NCBI tax idMatching level
1349778strain
412861species

strain history

@refhistory
7695<- C. Manaia <- I. Vaz-Moreia, PC-147
119986CIP <- 2013, DSM <- C. Manaia, Univ. Portugal, Porto, Portugal <- I. Vaz-Moreia strain: PC-147

doi: 10.13145/bacdive11616.20230509.8.1

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 humicus
  • full scientific name: Paenibacillus humicus Vaz-Moreira et al. 2007

@ref: 7695

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Paenibacillaceae

genus: Paenibacillus

species: Paenibacillus humicus

full scientific name: Paenibacillus humicus Vaz-Moreira et al. 2007

strain designation: PC-147

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32205negative2 µm0.5 µmrod-shapedyes
69480yes96.566
69480positive100
119986positiverod-shapedyes

pigmentation

  • @ref: 32205
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7695CASO 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
119986CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
7695positivegrowth40thermophilic
32205positivegrowth15-40
32205positiveoptimum27.5mesophilic

culture pH

@refabilitytypepHPH range
32205positivegrowth5.5-10alkaliphile
32205positiveoptimum7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 32205
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32205yes
69481yes100
69480yes100
119986yes

halophily

@refsaltgrowthtested relationconcentration
32205NaClpositivegrowth02-04 %
32205NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3220517057cellobiose+carbon source
3220528757fructose+carbon source
3220528260galactose+carbon source
3220517234glucose+carbon source
3220528087glycogen+carbon source
3220517716lactose+carbon source
3220517306maltose+carbon source
3220529864mannitol+carbon source
3220528053melibiose+carbon source
3220516634raffinose+carbon source
3220517814salicin+carbon source
3220517992sucrose+carbon source
3220527082trehalose+carbon source
3220518222xylose+carbon source
322054853esculin+hydrolysis

enzymes

@refvalueactivityec
32205catalase+1.11.1.6
32205gelatinase+
32205cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7695poultry litter compostPortoPortugalPRTEurope
119986Environment, 2007, Poultry litter compostPortoPortugalPRTEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Biodegradation#Composting
#Engineered#Waste
#Host#Birds
#Host#Other#Decomposing animal

taxonmaps

  • @ref: 69479
  • File name: preview.99_1569.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15358;96_893;97_1042;98_1237;99_1569&stattab=map
  • Last taxonomy: Paenibacillus humicus subclade
  • 16S sequence: AM411528
  • Sequence Identity:
  • Total samples: 5269
  • soil counts: 2649
  • aquatic counts: 710
  • animal counts: 1422
  • plant counts: 488

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
76951Risk group (German classification)
1199861Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Paenibacillus humicus gene for 16S rRNA, partial sequence, strain: NBRC 102415AB6817711471ena412861
7695Paenibacillus humicus partial 16S rRNA gene, type strain PC-147TAM4115281503ena412861

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenibacillus humicus NBRC 102415GCA_004000905contigncbi1349778
66792Paenibacillus humicus NBRC 1024151349778.3wgspatric1349778

GC content

  • @ref: 7695
  • GC-content: 58

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes85.462no
gram-positiveyes75.814yes
anaerobicno99.088yes
halophileno89.86no
spore-formingyes94.253yes
glucose-utilyes89.039yes
flagellatedyes82.247no
thermophileno99.645no
aerobicyes94.006yes
glucose-fermentno91.484no

External links

@ref: 7695

culture collection no.: DSM 18784, CIP 110609, LMG 23886, NBRC 102415, NRBC 102415

straininfo link

  • @ref: 80842
  • straininfo: 293010

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17911294Paenibacillus humicus sp. nov., isolated from poultry litter compost.Vaz-Moreira I, Faria C, Nobre MF, Schumann P, Nunes OC, Manaia CMInt J Syst Evol Microbiol10.1099/ijs.0.65124-02007Animals, Bacterial Typing Techniques, Base Composition, Catalase/biosynthesis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Feces/microbiology, Gelatin/metabolism, Genes, rRNA, Gram-Positive Endospore-Forming Bacteria/chemistry/*classification/genetics/*isolation & purification, Hydrogen-Ion Concentration, Molecular Sequence Data, Oxidoreductases/biosynthesis, Peptidoglycan/chemistry, Phylogeny, Poultry/*microbiology, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, Starch/metabolism, TemperatureMetabolism
Phylogeny21216920Paenibacillus wooponensis sp. nov., isolated from wetland freshwater.Baik KS, Choe HN, Park SC, Kim EM, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.028308-02011Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Fresh Water/*microbiology, Molecular Sequence Data, Paenibacillus/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, WetlandsMetabolism
Phylogeny26155771Paenibacillus herberti sp. nov., an endophyte isolated from Herbertus sendtneri.Guo GN, Zhou X, Zhao R, Chen XY, Chen ZL, Li XD, Li YHAntonie Van Leeuwenhoek10.1007/s10482-015-0514-32015Aerobiosis, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, DNA-Directed RNA Polymerases, Diaminopimelic Acid/analysis, Endophytes/*classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Hepatophyta/*microbiology, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Paenibacillus/*classification/genetics/*isolation & purification/physiology, Peptidoglycan/analysis, Phospholipids/analysis, Phylogeny, Polymorphism, Restriction Fragment Length, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spores, Bacterial/cytologyEnzymology
Phylogeny34997867Paenibacillus albicereus sp. nov. and Niallia alba sp. nov., isolated from digestive syrup.Thorat V, Kirdat K, Tiwarekar B, Dhanavade P, Karodi P, Shouche Y, Sathe S, Lodha T, Yadav AArch Microbiol10.1007/s00203-021-02749-x2022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, *Paenibacillus/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
7695Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18784)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18784
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
32205Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128447
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
80842Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID293010.1StrainInfo: A central database for resolving microbial strain identifiers
119986Curators of the CIPCollection of Institut Pasteur (CIP 110609)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110609