Strain identifier

BacDive ID: 159608

Type strain: Yes

Species: Alistipes communis

Strain Designation: 5CBH24

Strain history: M. Sakamoto; RIKEN BRC-JCM, Japan; 5CBH24.

NCBI tax ID(s): 2585118 (species)

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General

@ref: 66434

BacDive-ID: 159608

DSM-Number: 108979

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, colony-forming

description: Alistipes communis 5CBH24 is an anaerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from Feces of woman.

NCBI tax id

  • NCBI tax id: 2585118
  • Matching level: species

strain history

@refhistory
66434<- M. Sakamoto, JCM, RIKEN Bioresource Research Center, Tsukuba, Japan; JCM 32850
67770M. Sakamoto; RIKEN BRC-JCM, Japan; 5CBH24.

doi: 10.13145/bacdive159608.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Bacteroidia
  • order: Bacteroidales
  • family: Rikenellaceae
  • genus: Alistipes
  • species: Alistipes communis
  • full scientific name: Alistipes communis Sakamoto et al. 2020

  • synonyms

    • @ref: 20215
    • synonym: Alistipes obesi

@ref: 66434

domain: Bacteria

phylum: Bacteroidetes

class: Bacteroidia

order: Bacteroidales

family: Rikenellaceae

genus: Alistipes

species: Alistipes communis

full scientific name: Alistipes communis Sakamoto et al. 2020

strain designation: 5CBH24

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell lengthcell widthcell shapemotility
69480negative99.949
695441.7 µm0.8 µmrod-shapedno
69544coccus-shaped

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
695440.1-0.2 mmgreycircular4 daysEG agar
695440.1-1 mmgraycircular4 daysEG agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
66434CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
69544EG agaryes

culture temp

@refgrowthtypetemperaturerange
66434positivegrowth37mesophilic
67770positivegrowth37mesophilic
69544positivegrowth25-37mesophilic
69544positiveoptimum37mesophilic

culture pH

@refabilitytypepH
69544positivegrowth6.3-7.8
69544positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
69480anaerobe99.999
69544anaerobe

spore formation

@refspore formationconfidence
69480no99.998
69481no100
69544no

observation

@refobservation
69544Growth occurs on medium containing 20 % (w/v) bile. Aesculin is hydrolysed. Gelatin is not digested. Indole is not produced, pigmented variable.
69544The major end-products in peptone-yeast extract-glucose broth (1 %, w/v, of each) are succinate, acetate and propionate.

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
695445291gelatin-assimilation
6954435581indole-assimilation
6954465327D-xylose-builds acid from
6954430849L-arabinose-builds acid from
6954417814salicin-builds acid from
695444853esculin-hydrolysis
695445291gelatin+assimilation
6954435581indole+assimilation
6954417057cellobiose+builds acid from
6954416899D-mannitol+builds acid from
6954416024D-mannose+builds acid from
6954417924D-sorbitol+builds acid from
6954417234glucose+builds acid from
6954417754glycerol+builds acid from
6954462345L-rhamnose+builds acid from
6954417716lactose+builds acid from
6954417306maltose+builds acid from
695446731melezitose+builds acid from
6954416634raffinose+builds acid from
6954417992sucrose+builds acid from
6954427082trehalose+builds acid from
695444853esculin+hydrolysis
6954465327D-xylose+/-builds acid from
6954430849L-arabinose+/-builds acid from
6954417814salicin+/-builds acid from

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
695442676amoxicillinyesyes
6954417698chloramphenicolyesyes
69544100241ciprofloxacinyesyes
6954448923erythromycinyesyes
6954427701oxytetracyclineyesyes
6954417334penicillinyesyes

enzymes

@refvalueactivityec
69544catalase-1.11.1.6
69544catalase+/-1.11.1.6
69544urease-3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
66434Feces of womanTsukubaJapanJPNAsia
67770Feces of a woman in the fortiesJapanJPNAsia
69544the faecal samples of healthy Japanese humans.TsukubaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human#Female

taxonmaps

  • @ref: 69479
  • File name: preview.99_776.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_110;96_471;97_538;98_619;99_776&stattab=map
  • Last taxonomy: Alistipes communis subclade
  • 16S sequence: LC468799
  • Sequence Identity:
  • Total samples: 78772
  • soil counts: 518
  • aquatic counts: 1636
  • animal counts: 76517
  • plant counts: 101

Sequence information

16S sequences

  • @ref: 66434
  • description: Alistipes communis 5CBH24 gene for 16S ribosomal RNA, partial sequence
  • accession: LC468799
  • length: 1484
  • database: ena
  • NCBI tax ID: 2585118

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Alistipes communis 5CBH24GCA_006542665completencbi2585118
66792Alistipes sp. 5CBH242585118.3completepatric2585118

GC content

@refGC-contentmethod
6777058.5genome sequence analysis
6954461.3genome sequence analysis
6954458genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno90.687no
flagellatedno97.165no
gram-positiveno98.362no
anaerobicyes98.917no
aerobicno97.423no
halophileno84.564no
spore-formingno97.539no
glucose-utilyes85.514no
thermophileno97.647yes
glucose-fermentyes56.684no

External links

@ref: 66434

culture collection no.: DSM 108979, JCM 32850

straininfo link

  • @ref: 112084
  • straininfo: 404981

literature

  • topic: Phylogeny
  • Pubmed-ID: 31633480
  • title: Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov.
  • authors: Sakamoto M, Ikeyama N, Ogata Y, Suda W, Iino T, Hattori M, Ohkuma M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003778
  • year: 2020
  • mesh: Bacterial Typing Techniques, Bacteroidetes/*classification/isolation & purification, Base Composition, DNA, Bacterial/genetics, Feces/*microbiology, Humans, Japan, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
66434Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-108979Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 108979)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
69544Mitsuo Sakamoto, Nao Ikeyama, Yusuke Ogata, Wataru Suda, Takao Iino, Masahira Hattori, Moriya Ohkuma.Alistipes communis sp. nov., Alistipes dispar sp. nov. and Alistipes onderdonkii subsp. vulgaris subsp. nov., isolated from human faeces, and creation of Alistipes onderdonkii subsp. onderdonkii subsp. nov.10.1099/ijsem.0.003778
112084Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID404981.1