Strain identifier

BacDive ID: 131525

Type strain: Yes

Species: Longicatena caecimuris

Strain Designation: PG-426-CC-2

Strain history: <- Barbel Fosel, DSM

NCBI tax ID(s): 1796635 (species)

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General

@ref: 22752

BacDive-ID: 131525

DSM-Number: 29481

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, rod-shaped

description: Longicatena caecimuris PG-426-CC-2 is an anaerobe, mesophilic, rod-shaped bacterium that was isolated from caecal content; TNFdeltaARE/+ C57BL/6 mouse.

NCBI tax id

  • NCBI tax id: 1796635
  • Matching level: species

strain history

@refhistory
22752<- T. Clavel, TU Munich, Freising-Weihenstephan, Germany; PG-426-CC-2
67770DSM 29481 <-- T. Clavel; Tech. Univ. of Munich, Germany; PG-426-CC-2.
67771<- Barbel Fosel, DSM

doi: 10.13145/bacdive131525.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Erysipelotrichia
  • order: Erysipelotrichales
  • family: Erysipelotrichaceae
  • genus: Longicatena
  • species: Longicatena caecimuris
  • full scientific name: Longicatena caecimuris Lagkouvardos et al. 2016

@ref: 22752

domain: Bacteria

phylum: Firmicutes

class: Erysipelotrichia

order: Erysipelotrichales

family: Erysipelotrichaceae

genus: Longicatena

species: Longicatena caecimuris

full scientific name: Longicatena caecimuris Lagkouvardos et al. 2016

strain designation: PG-426-CC-2

type strain: yes

Morphology

cell morphology

@refcell shape
67771rod-shaped
67771filament-shaped

colony morphology

  • @ref: 22752
  • incubation period: 2-3 days

Culture and growth conditions

culture medium

  • @ref: 22752
  • name: PYG MEDIUM (MODIFIED) (DSMZ Medium 104)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/104
  • composition: Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

culture temp

@refgrowthtypetemperature
22752positivegrowth37
67770positivegrowth37
67771positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
22752anaerobe
67771anaerobe
125439anaerobe97.2

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838027897tryptophan-energy source
6838017632nitrate-reduction
6838016634raffinose-fermentation
6838029985L-glutamate-degradation
6838029016arginine-hydrolysis
6838016024D-mannose-fermentation
6838016199urea-hydrolysis

metabolite production

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase-3.2.1.22
68380urease-3.5.1.5
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380tyrosine arylamidase-
68380phenylalanine arylamidase-
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380N-acetyl-beta-glucosaminidase-3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase-3.2.1.21
68380alpha-glucosidase-3.2.1.20
68380arginine dihydrolase-3.5.3.6

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
22752-----------------------------
22752-----------------------------
22752-----------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
22752caecal content; TNFdeltaARE/+ C57BL/6 mouseFreisingGermanyDEUEurope
67770Cecum of a mouseFreisingGermanyDEUEurope
67771From mouse instine, caecal content; TNFdeltaARE/+ C57BL/6 mouseFreisingGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Gastrointestinal tract#Large intestine
#Host Body Product#Gastrointestinal tract#Caecal content

taxonmaps

  • @ref: 69479
  • File name: preview.99_2354.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_135;96_1271;97_1507;98_1835;99_2354&stattab=map
  • Last taxonomy: Longicatena caecimuris subclade
  • 16S sequence: KR364771
  • Sequence Identity:
  • Total samples: 16250
  • soil counts: 30
  • aquatic counts: 168
  • animal counts: 16023
  • plant counts: 29

Safety information

risk assessment

  • @ref: 22752
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22752
  • description: Longicatena caecimuris strain PG-426-CC-2 16S ribosomal RNA gene, partial sequence
  • accession: KR364771
  • length: 1433
  • database: nuccore
  • NCBI tax ID: 1796635

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Longicatena caecimuris strain DSM 294811796635.10wgspatric1796635
66792Longicatena caecimuris DSM 294812791354872draftimg1796635
67771Longicatena caecimuris DSM 29481GCA_004341945contigncbi1796635
66792Longicatena caecimuris DSM 29481GCA_024622185contigncbi1796635

GC content

  • @ref: 67770
  • GC-content: 37.8
  • method: genome sequence analysis

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes77.403no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes81.542no
125438spore-formingspore-formingAbility to form endo- or exosporesno60.861no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.286yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno90.6no
125438motile2+flagellatedAbility to perform flagellated movementno66.528no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno65
125439BacteriaNetmotilityAbility to perform movementno60.9
125439BacteriaNetgram_stainReaction to gram-stainingpositive71.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe97.2

External links

@ref: 22752

culture collection no.: DSM 29481, KCTC 15535, JCM 32781

straininfo link

  • @ref: 89939
  • straininfo: 396751

literature

  • topic: Phylogeny
  • Pubmed-ID: 33083133
  • title: Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces.
  • authors: Ghimire S, Wongkuna S, Scaria J
  • journal: PeerJ
  • DOI: 10.7717/peerj.10071
  • year: 2020

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
22752Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29481Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29481)
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
89939Reimer, 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-ID396751.1
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG