Strain identifier

BacDive ID: 14336

Type strain: Yes

Species: Sediminispirochaeta bajacaliforniensis

Strain Designation: BA-2

Strain history: <- L. Margulis, University of Massachusetts, Department of Geosciences, Amherst, USA; BA-2 <- ATCC <- S. P. Fracek and J. F. Stolz, Boston University, Department of Biology, Boston, USA

NCBI tax ID(s): 1123274 (strain), 148 (species)

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General

@ref: 6243

BacDive-ID: 14336

DSM-Number: 16054

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic

description: Sediminispirochaeta bajacaliforniensis BA-2 is an anaerobe, mesophilic bacterium that was isolated from mud sample.

NCBI tax id

NCBI tax idMatching level
148species
1123274strain

strain history

  • @ref: 6243
  • history: <- L. Margulis, University of Massachusetts, Department of Geosciences, Amherst, USA; BA-2 <- ATCC <- S. P. Fracek and J. F. Stolz, Boston University, Department of Biology, Boston, USA

doi: 10.13145/bacdive14336.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/spirochaetota
  • domain: Bacteria
  • phylum: Spirochaetota
  • class: Spirochaetia
  • order: Spirochaetales
  • family: Spirochaetaceae
  • genus: Sediminispirochaeta
  • species: Sediminispirochaeta bajacaliforniensis
  • full scientific name: Sediminispirochaeta bajacaliforniensis (Fracek and Stolz 2004) Shivani et al. 2016

  • synonyms

    • @ref: 20215
    • synonym: Spirochaeta bajacaliforniensis

@ref: 6243

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Spirochaetaceae

genus: Sediminispirochaeta

species: Sediminispirochaeta bajacaliforniensis

full scientific name: Sediminispirochaeta bajacaliforniensis (Fracek and Stolz 2004) Shivani et al. 2016

strain designation: BA-2

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthmotilityconfidencegram stain
2504815-300 µm0.2-0.3 µm
69480yes97.696
6948099.997negative

colony morphology

  • @ref: 6243
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

  • @ref: 6243
  • name: SEDIMINISPIROCHAETA MEDIUM (DSMZ Medium 1008)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1008
  • composition: Name: SEDIMINISPIROCHAETA MEDIUM (DSMZ Medium 1008) Composition: Cellobiose 2.0 g/l Trypticase peptone 2.0 g/l Na-thioglycolate 1.0 g/l Yeast extract 1.0 g/l Sodium resazurin 0.0005 g/l Charcoal-filtered, natural seawater Distilled water

culture temp

@refgrowthtypetemperaturerange
6243positivegrowth30mesophilic
25048positiveoptimum34.0-36.0mesophilic
25048positivegrowth25.0-44.0

culture pH

@refabilitytypepH
25048positiveoptimum7.5
25048positivegrowth5.9-7.7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6243anaerobe
69480anaerobe99.473

spore formation

@refspore formationconfidence
69481no99
69480no99.871

halophily

@refsalttested relationconcentrationgrowth
25048NaCloptimum1.5 %
25048NaClgrowth0.5-5.0 %positive

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2504816150benzoate-assimilation
2504829806fumarate-assimilation
2504817754glycerol-assimilation
2504829985L-glutamate-assimilation
2504862345L-rhamnose-assimilation
2504830031succinate-assimilation
2504816094thiosulfate-reduction
2504817057cellobiose+assimilation
2504862968cellulose+assimilation
2504815824D-fructose+assimilation
2504812936D-galactose+assimilation
2504817634D-glucose+assimilation
2504816899D-mannitol+assimilation
2504816024D-mannose+assimilation
2504817924D-sorbitol+assimilation
2504816236ethanol+assimilation
2504817234glucose+fermentation
2504815978glycerol 3-phosphate+assimilation
2504830849L-arabinose+assimilation
2504829991L-aspartate+assimilation
2504817716lactose+assimilation
2504817306maltose+assimilation
2504815361pyruvate+assimilation
2504828017starch+assimilation
2504817992sucrose+assimilation
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838017632nitrate+reduction

enzymes

@refvalueactivityec
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase-
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6243-------+/-+/------++/--------------

Isolation, sampling and environmental information

isolation

  • @ref: 6243
  • sample type: mud sample
  • geographic location: Baja California Norte, Laguna Figueroa
  • country: Mexico
  • origin.country: MEX
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Microbial community#Microbial mat

taxonmaps

  • @ref: 69479
  • File name: preview.99_6322.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_484;96_2332;97_2835;98_3523;99_6322&stattab=map
  • Last taxonomy: Sediminispirochaeta bajacaliforniensis
  • 16S sequence: AJ698859
  • Sequence Identity:
  • Total samples: 103
  • soil counts: 5
  • aquatic counts: 94
  • animal counts: 4

Safety information

risk assessment

  • @ref: 6243
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6243
  • description: Spirochaeta bajacaliforniensis 16S rRNA gene, type strain DSM 16054T
  • accession: AJ698859
  • length: 1521
  • database: ena
  • NCBI tax ID: 148

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sediminispirochaeta bajacaliforniensis DSM 16054GCA_000378205scaffoldncbi1123274
66792Spirochaeta bajacaliforniensis DSM 160541123274.3wgspatric1123274
66792Sediminispirochaeta bajacaliforniensis DSM 160542518645589draftimg1123274

GC content

  • @ref: 6243
  • GC-content: 49.2
  • method: sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes88.795no
flagellatedno79.227no
gram-positiveno94.939no
anaerobicyes98.214yes
halophileno78.504no
spore-formingno87.993no
glucose-utilyes86.348no
aerobicno98.689no
thermophileno95.712yes
glucose-fermentyes64.323no

External links

@ref: 6243

culture collection no.: DSM 16054, ATCC 35968

straininfo link

  • @ref: 83481
  • straininfo: 45074

literature

  • topic: Phylogeny
  • Pubmed-ID: 27902269
  • title: Description of 'Candidatus Marispirochaeta associata' and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica comb. nov.
  • authors: Shivani Y, Subhash Y, Sasikala C, Ramana CV
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001545
  • year: 2016
  • mesh: Acyl Coenzyme A/genetics, Bacterial Typing Techniques, Coculture Techniques, DNA, Bacterial/genetics, Erythritol/analogs & derivatives/genetics, Fatty Acids/chemistry, India, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spirochaeta/*classification, Sugar Phosphates/genetics
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6243Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16054)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16054
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
25048Y. S. Shivani, Y.,Sasikala, C.,Ramana, C. V.10.1099/ijsem.0.001545Description of 'Candidatus Marispirochaeta associata' and reclassification of Spirochaeta bajacaliforniensis, Spirochaeta smaragdinae and Spirochaeta sinaica to a new genus Sediminispirochaeta gen. nov. as Sediminispirochaeta bajacaliforniensis comb. nov., Sediminispirochaeta smaragdinae comb. nov. and Sediminispirochaeta sinaica comb. novIJSEM 66: 5485-5492 201627902269
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)
68380Automatically annotated from API rID32A
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
83481Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45074.1StrainInfo: A central database for resolving microbial strain identifiers