Strain identifier

BacDive ID: 1404

Type strain: Yes

Species: Pelagirhabdus fermentum

Strain Designation: Z-7984

Strain history: <- T. N. Zhilina; Z-7984

NCBI tax ID(s): 173041 (species)

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General

@ref: 5182

BacDive-ID: 1404

DSM-Number: 13869

keywords: 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, motile, rod-shaped

description: Pelagirhabdus fermentum Z-7984 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from sediment.

NCBI tax id

  • NCBI tax id: 173041
  • Matching level: species

strain history

  • @ref: 5182
  • history: <- T. N. Zhilina; Z-7984

doi: 10.13145/bacdive1404.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Bacilli
  • order: Caryophanales
  • family: Bacillaceae
  • genus: Pelagirhabdus
  • species: Pelagirhabdus fermentum
  • full scientific name: Pelagirhabdus fermentum (Zhilina et al. 2002) Sultanpuram et al. 2016

  • synonyms

    • @ref: 20215
    • synonym: Amphibacillus fermentum

@ref: 5182

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Bacillales

family: Bacillaceae

genus: Pelagirhabdus

species: Pelagirhabdus fermentum

full scientific name: Pelagirhabdus fermentum (Zhilina et al. 2002) Sultanpuram et al. 2016

strain designation: Z-7984

type strain: yes

Morphology

cell morphology

  • @ref: 23028
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 23028
  • colony color: yellow

Culture and growth conditions

culture medium

  • @ref: 5182
  • name: ALCALIPHILIC AMPHIBACILLUS STRAINS MEDIUM (DSMZ Medium 931)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/931
  • composition: Name: ALCALIPHILIC AMPHIBACILLUS STRAINS MEDIUM (DSMZ Medium 931) Composition: Na2CO3 63.6 g/l NaHCO3 50.4 g/l Sucrose 5.0 g/l Na2S x 9 H2O 0.7 g/l NH4Cl 0.5 g/l Yeast extract 0.2 g/l KCl 0.2 g/l KH2PO4 0.2 g/l MgCl2 0.1 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l CoSO4 x 7 H2O 0.0018 g/l CaCl2 x 2 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Resazurin 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l H3BO3 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
5182positivegrowth37mesophilic
23028positivegrowth20.0-55.0
23028positiveoptimum37.0mesophilic

culture pH

@refabilitytypepHPH range
23028positivegrowth8.0-10.5alkaliphile
23028positiveoptimum9.0

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
5182anaerobe
23028facultative anaerobe

spore formation

  • @ref: 23028
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
23028NaClpositivegrowth0.0-20.0 %(w/v)
23028NaCloptimum9.5-10.5 %(w/v)

murein

  • @ref: 23028
  • murein short key: A31
  • type: A1gamma m-Dpm-direct

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2302816947citrate-carbon source
2302827897tryptophan-energy source
23028casein-hydrolysis
2302862968cellulose-hydrolysis
230285291gelatin-hydrolysis
2302853424tween 20-hydrolysis
2302853423tween 40-hydrolysis
2302853426tween 80-hydrolysis
2302816199urea-hydrolysis
2302817632nitrate-reduction
2302817234glucose+carbon source
23028casein hydrolysate+hydrolysis
2302828017starch+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
2302835581indoleno
2302816136hydrogen sulfideyes

metabolite tests

@refChebi-IDmetaboliteindole testcitrate test
2302835581indole-
2302816947citrate-

enzymes

@refvalueactivityec
23028catalase+1.11.1.6
23028cytochrome oxidase-1.9.3.1
23028tryptophan deaminase-4.1.99.1

Isolation, sampling and environmental information

isolation

  • @ref: 5182
  • sample type: sediment
  • geographic location: Lake Magadi
  • country: Kenya
  • origin.country: KEN
  • continent: Africa

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Sediment

Safety information

risk assessment

  • @ref: 5182
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Amphibacillus fermentum isolate Af19 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723600742ena173041
20218Amphibacillus fermentum isolate Af29 16S ribosomal RNA gene, partial sequence; 16S-23S internal transcribed spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEU723601485ena173041
5182Amphibacillus fermentum 16S ribosomal RNA gene, partial sequenceAF4186031454ena173041

GC content

  • @ref: 5182
  • GC-content: 41.5

External links

@ref: 5182

culture collection no.: DSM 13869, UNIQEM 216

straininfo link

  • @ref: 71055
  • straininfo: 286120

literature

topicPubmed-IDtitleauthorsjournalyearmeshtopic2DOI
Phylogeny11785140[Amphibacillus fermentum sp. nov., Amphibacillus tropicus sp. nov.--new alkaliphilic, facultatively anaerobic, saccharolytic Bacilli from Lake Magadi].Zhilina TN, Garnova ES, Turova TP, Kostrikina NA, Zavarzin GAMikrobiologiia2001Bacillus/*classification/genetics/growth & development/ultrastructure, Carbohydrate Metabolism, DNA, Bacterial/analysis, Kenya, PhylogenyMetabolism
Phylogeny26475440Pelagirhabdus alkalitolerans gen. nov., sp. nov., an alkali-tolerant and thermotolerant bacterium isolated from beach sediment, and reclassification of Amphibacillus fermentum as Pelagirhabdus fermentum comb. nov.Sultanpuram VR, Mothe T, Chintalapati S, Chintalapati VRInt J Syst Evol Microbiol2015Alkalies, Bacillaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAGenetics10.1099/ijsem.0.000678

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5182Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13869)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13869
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
23028Vishnuvardhan Reddy Sultanpuram,Thirumala Mothe,Sasikala Chintalapati,Venkata Ramana Chintalapati10.1099/ijsem.0.000678Pelagirhabdus alkalitolerans gen. nov., sp. nov., an alkali-tolerant and thermotolerant bacterium isolated from beach sediment, and reclassification of Amphibacillus fermentum as Pelagirhabdus fermentum comb. nov.IJSEM 66: 84-90 201626475440
71055Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID286120.1StrainInfo: A central database for resolving microbial strain identifiers