Strain identifier

BacDive ID: 158510

Type strain: Yes

Species: Phascolarctobacterium wakonense

Strain Designation: MB11

Strain history: Y. Shigeno; RIKEN Cluster for Sci. Technol. & Innovation Hub, Japan; MB11.

NCBI tax ID(s): 2654621 (species)

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General

@ref: 65187

BacDive-ID: 158510

DSM-Number: 107697

keywords: 16S sequence, Bacteria, mesophilic, Gram-negative, pleomorphic-shaped, colony-forming

description: Phascolarctobacterium wakonense MB11 is a mesophilic, Gram-negative, pleomorphic-shaped bacterium that forms circular colonies and was isolated from common marmoset faeces.

NCBI tax id

  • NCBI tax id: 2654621
  • Matching level: species

strain history

@refhistory
65187<- Y. Shigeno, RIKEN, Wako, Saitama, Japan; MB11 <- Y. Benno
67770Y. Shigeno; RIKEN Cluster for Sci. Technol. & Innovation Hub, Japan; MB11.

doi: 10.13145/bacdive158510.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Negativicutes
  • order: Acidaminococcales
  • family: Acidaminococcaceae
  • genus: Phascolarctobacterium
  • species: Phascolarctobacterium wakonense
  • full scientific name: Phascolarctobacterium wakonense Shigeno et al. 2019

@ref: 65187

domain: Bacteria

phylum: Firmicutes

class: Negativicutes

order: Selenomonadales

family: Acidaminococcaceae

genus: Phascolarctobacterium

species: Phascolarctobacterium wakonense

full scientific name: Phascolarctobacterium wakonense Shigeno et al. 2019

strain designation: MB11

type strain: yes

Morphology

cell morphology

  • @ref: 67947
  • gram stain: negative
  • cell length: 0.8-35.8 µm
  • cell shape: pleomorphic-shaped
  • motility: no

colony morphology

  • @ref: 67947
  • type of hemolysis: gamma
  • colony size: 1 mm
  • colony shape: circular
  • incubation period: 2 days
  • medium used: blood agar with 5?% (v/v) defibrinated horse blood

Culture and growth conditions

culture medium

  • @ref: 65187
  • name: PY + X MEDIUM (DSMZ Medium 104b)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104b
  • composition: Name: PY + X MEDIUM (DSMZ Medium 104b; with strain-specific modifications) Composition: Yeast extract 10.0 g/l Disodium succinate 8.0 g/l Trypticase peptone 5.0 g/l Meat peptone 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l KH2PO4 0.04 g/l K2HPO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Sodium resazurin 0.0005 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
65187positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

  • @ref: 67947
  • spore formation: no

observation

@refobservation
67947Propionic acid is the main end-product from succinate
67947propionic acid and acetic acid are produced from pyruvate

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6794730849L-arabinose-builds acid from
6794717057cellobiose-builds acid from
6794717234glucose-builds acid from
6794717754glycerol-builds acid from
6794717716lactose-builds acid from
6794717306maltose-builds acid from
6794716899D-mannitol-builds acid from
6794716024D-mannose-builds acid from
679476731melezitose-builds acid from
6794716634raffinose-builds acid from
6794762345L-rhamnose-builds acid from
6794717814salicin-builds acid from
6794717992sucrose-builds acid from
6794730911sorbitol-builds acid from
6794727082trehalose-builds acid from
6794765327D-xylose-builds acid from
6794717632nitrate-reduction
679474853esculin-hydrolysis
6794730031succinate+growth
6794715361pyruvate+growth
6794716449alanine-assimilation
6794729016arginine-assimilation
6794715356cysteine-assimilation
679475390glutamyl-glutamic acid-assimilation
6794715428glycine-assimilation
6794715971L-histidine-assimilation
6794728044phenylalanine-assimilation
6794726271proline-assimilation
6794718183L-pyroglutamic acid-assimilation
6794717822serine-assimilation
6794718186tyrosine-assimilation

enzymes

@refvalueactivityec
67947naphthol-AS-BI-phosphohydrolase+
67947acid phosphatase+3.1.3.2
67947esterase+
67947urease-3.5.1.5
67947protease-
67947valine arylamidase-
67947leucyl glycin arylamidase-3.4.11.1
67947tyrosine arylamidase-
67947alkaline phosphatase-3.1.3.1
67947N-acetyl-beta-glucosaminidase-3.2.1.52
67947alpha-arabinosidase-
67947alpha-fucosidase-3.2.1.51
67947alpha-galactosidase-3.2.1.22
67947beta-galactosidase-3.2.1.23
679476-phospho-beta-galactosidase-3.2.1.85
67947alpha-glucosidase-3.2.1.20
67947beta-glucosidase-3.2.1.21
67947beta-glucuronidase-3.2.1.31
67947alpha-mannosidase-3.2.1.24
67947alpha-chymotrypsin-3.4.21.1
67947esterase Lipase (C 8)-
67947arginine dihydrolase-3.5.3.6
67947lipase (C 14)-
67947trypsin-3.4.21.4

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    67947C11:011.1
    67947C12:02.8
    67947C13:05.8
    67947C15:05.5
    67947C16:01.9
    67947C18:01.4
    67947C16:1 w9c7.4
    67947C16:1 w7c2.2
    67947C18:1 w9c3.1
    67947C18:2 w6,9c1.2
    67947C15:0 3OH2.5
    67947C14:0 DMA23
    67947unknown 14.76219.8
    67947C15:0 DMA/C14:0 3OH2.2
    67947C17:1 w8c / C17:23.8
    67947unknown 13.4932.1
  • type of FA analysis: whole cell analysis
  • incubation medium: PYS
  • agar/liquid: liquid
  • incubation temperature: 37
  • incubation time: 1
  • software version: Sherlock 6.0
  • library/peak naming table: Moore library version 6.00
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
65187common marmoset (Callithrix jacchus) faecesRIKEN, 2-1 Hirosawa, wako-city, SaitamaJapanJPNAsia
67770Common marmoset (Callithrixjacchus) fecesSaitamaJapanJPNAsiaCallithrixjacchus
67947common marmoset (Callithrix jacchus) faecesRIKEN Brain Science Institute, SaitamaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Mammals#Primates

Sequence information

16S sequences

  • @ref: 65187
  • description: Phascolarctobacterium wakonense MB11 gene for 16S ribosomal RNA, partial sequence
  • accession: LC389065
  • length: 1482
  • database: ena
  • NCBI tax ID: 2654621

GC content

@refGC-contentmethod
6518747
6794747.3-47.4high performance liquid chromatography (HPLC)

External links

@ref: 65187

culture collection no.: DSM 107697, JCM 32899

straininfo link

  • @ref: 111305
  • straininfo: 407603

literature

  • topic: Phylogeny
  • Pubmed-ID: 31038451
  • title: Phascolarctobacterium wakonense sp. nov., isolated from common marmoset (Callithrix jacchus) faeces.
  • authors: Shigeno Y, Kitahara M, Shime M, Benno Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003407
  • year: 2019
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, Callithrix/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/*microbiology, Japan, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Veillonellaceae/*classification/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournal
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
65187Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107697Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107697)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67947Yuko Shigeno, Maki Kitahara, Mari Shime, Yoshimi BennoPhascolarctobacterium wakonense sp. nov., isolated from common marmoset (Callithrix jacchus) faeces10.1099/ijsem.0.003407IJSEM 69: 1941-1946 2019
111305Reimer, 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-ID407603.1