Strain identifier

BacDive ID: 14352

Type strain: Yes

Species: Sphaerochaeta pleomorpha

Strain Designation: Grapes

Strain history: <- K. M. Ritalahti, Environmental Engineering, Georgia Inst. Technology, Atlanta, USA; Grapes <- F. E. Löffler {2000}

NCBI tax ID(s): 1131707 (species)

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

@ref: 16511

BacDive-ID: 14352

DSM-Number: 22778

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, coccus-shaped

description: Sphaerochaeta pleomorpha Grapes is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from black, anoxic river sediments downstream of an agricultural and residential area.

NCBI tax id

  • NCBI tax id: 1131707
  • Matching level: species

strain history

  • @ref: 16511
  • history: <- K. M. Ritalahti, Environmental Engineering, Georgia Inst. Technology, Atlanta, USA; Grapes <- F. E. Löffler {2000}

doi: 10.13145/bacdive14352.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/spirochaetota
  • domain: Bacteria
  • phylum: Spirochaetota
  • class: Spirochaetia
  • order: Spirochaetales
  • family: Sphaerochaetaceae
  • genus: Sphaerochaeta
  • species: Sphaerochaeta pleomorpha
  • full scientific name: Sphaerochaeta pleomorpha Ritalahti et al. 2012

@ref: 16511

domain: Bacteria

phylum: Spirochaetes

class: Spirochaetia

order: Spirochaetales

family: Sphaerochaetaceae

genus: Sphaerochaeta

species: Sphaerochaeta pleomorpha

full scientific name: Sphaerochaeta pleomorpha Ritalahti et al. 2012

strain designation: Grapes

type strain: yes

Morphology

cell morphology

  • @ref: 29882
  • gram stain: negative
  • cell width: 0.4-2.5 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 16511
  • incubation period: 8-14 days

Culture and growth conditions

culture medium

  • @ref: 16511
  • name: 1/2 TRYPTIC SOY BROTH (ANAEROBE) (DSMZ Medium 1205)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1205
  • composition: Name: 1/2 TRYPTIC SOY BROTH (ANAEROBIC) (DSMZ Medium 1205) Composition: Trypticase soy broth 13.75 g/l D-Glucose 3.6 g/l NaCl 2.5 g/l Yeast extract 1.0 g/l DL-Dithiothreitol 0.15 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16511positivegrowth25mesophilic
29882positivegrowth15-30
29882positiveoptimum25-30mesophilic

culture pH

  • @ref: 29882
  • ability: positive
  • type: optimum
  • pH: 6.5-7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
16511anaerobe
29882anaerobe

observation

  • @ref: 29882
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2988228757fructose+carbon source
2988228260galactose+carbon source
2988217234glucose+carbon source
2988237684mannose+carbon source
2988216634raffinose+carbon source
2988217992sucrose+carbon source
2988218222xylose+carbon source

Isolation, sampling and environmental information

isolation

  • @ref: 16511
  • sample type: black, anoxic river sediments downstream of an agricultural and residential area
  • geographic location: Michigan, Okemos, Red Cedar River
  • country: USA
  • origin.country: USA
  • continent: North America
  • latitude: 42.6971
  • longitude: -84.3788

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#River (Creek)
#Environmental#Terrestrial#Sediment
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5641.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_431;96_2713;97_3334;98_4203;99_5641&stattab=map
  • Last taxonomy: Sphaerochaeta pleomorpha subclade
  • 16S sequence: AF357917
  • Sequence Identity:
  • Total samples: 1537
  • soil counts: 135
  • aquatic counts: 517
  • animal counts: 779
  • plant counts: 106

Safety information

risk assessment

  • @ref: 16511
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16511
  • description: Sphaerochaeta pleomorpha str. Grapes 16S ribosomal RNA gene, partial sequence
  • accession: AF357917
  • length: 1530
  • database: ena
  • NCBI tax ID: 158190

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sphaerochaeta pleomorpha str. GrapesGCA_000236685completencbi158190
66792Sphaerochaeta pleomorpha str. Grapes158190.3completepatric158190
66792Sphaerochaeta pleomorpha Grapes2508501070completeimg158190

GC content

@refGC-contentmethod
1651148.1high performance liquid chromatography (HPLC)
2988247.0-49.2
1651146.2sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno79.361no
flagellatedno96.576yes
gram-positiveno91.852yes
anaerobicyes98.639no
aerobicno97.659yes
halophileno79.837no
spore-formingno93.035no
thermophileno96.261yes
glucose-utilyes90.159yes
glucose-fermentyes64.512no

External links

@ref: 16511

culture collection no.: DSM 22778, ATCC BAA 1885

straininfo link

  • @ref: 83495
  • straininfo: 402447

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21398503Sphaerochaeta globosa gen. nov., sp. nov. and Sphaerochaeta pleomorpha sp. nov., free-living, spherical spirochaetes.Ritalahti KM, Justicia-Leon SD, Cusick KD, Ramos-Hernandez N, Rubin M, Dornbush J, Loffler FEInt J Syst Evol Microbiol10.1099/ijs.0.023986-02011Aerobiosis, Base Composition, Carbon/metabolism, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Geologic Sediments/microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nitrogen/metabolism, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spirochaetales/*classification/cytology/genetics/*isolation & purification, TemperatureMetabolism
Phylogeny25249566Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta.Miyazaki M, Sakai S, Ritalahti KM, Saito Y, Yamanaka Y, Saito Y, Tame A, Uematsu K, Loffler FE, Takai K, Imachi HInt J Syst Evol Microbiol10.1099/ijs.0.068148-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Spirochaetaceae/*classification/genetics/isolation & purificationGenetics
Phylogeny26341497Sphaerochaeta associata sp. nov., a spherical spirochaete isolated from cultures of Methanosarcina mazei JL01.Troshina O, Oshurkova V, Suzina N, Machulin A, Ariskina E, Vinokurova N, Kopitsyn D, Novikov A, Shcherbakova VInt J Syst Evol Microbiol10.1099/ijsem.0.0005752015Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Methanosarcina, Molecular Sequence Data, Nucleic Acid Hybridization, Permafrost/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spirochaetaceae/*classification/genetics/isolation & purificationGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16511Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22778)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22778
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
29882Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2625528776041
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
83495Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402447.1StrainInfo: A central database for resolving microbial strain identifiers