Strain identifier

BacDive ID: 132355

Type strain: Yes

Species: Filobacterium rodentium

Strain Designation: SMR-C

Strain history: F. Ike and T. Kokubo SMR-C <-- T. Kokubo and S. Matsushita SMR.

NCBI tax ID(s): 28192 (species)

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General

@ref: 24144

BacDive-ID: 132355

DSM-Number: 100392

keywords: 16S sequence, Bacteria, microaerophile, mesophilic, Gram-negative, motile, filament-shaped, animal pathogen

description: Filobacterium rodentium SMR-C is a microaerophile, mesophilic, Gram-negative animal pathogen that builds net-like structure and was isolated from lung of a rat with chronic respiratory disease.

NCBI tax id

  • NCBI tax id: 28192
  • Matching level: species

strain history

@refhistory
24144<- M. Sakamoto, JCM; SMR-C <- F. Ike <- S. Matsushita, Fundamental Techn. Center, Nat. Inst. of Radiological Scs., Chiba, Japan
67770F. Ike and T. Kokubo SMR-C <-- T. Kokubo and S. Matsushita SMR.

doi: 10.13145/bacdive132355.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Sphingobacteriia
  • order: Sphingobacteriales
  • family: Filobacteriaceae
  • genus: Filobacterium
  • species: Filobacterium rodentium
  • full scientific name: Filobacterium rodentium Ike et al. 2016

@ref: 24144

domain: Bacteria

phylum: Bacteroidetes

class: Sphingobacteriia

order: Sphingobacteriales

family: Filobacteriaceae

genus: Filobacterium

species: Filobacterium rodentium

full scientific name: Filobacterium rodentium Ike et al. 2016

strain designation: SMR-C

type strain: yes

Morphology

cell morphology

  • @ref: 44047
  • gram stain: negative
  • cell length: 8.0-10.0 µm
  • cell width: 0.8-1.0 µm
  • cell shape: filament-shaped
  • motility: yes
  • flagellum arrangement: gliding

multicellular morphology

  • @ref: 44047
  • forms multicellular complex: yes
  • complex name: net-like structure

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
44047Vero E6 cellsyeswith rodent-physiological salt concentration. CO2/air (5:95 v/v) in a humidified chamber
24144SP4-Z MEDIUM (DSMZ Medium 1076b)yesName: SP4-Z MEDIUM (DSMZ Medium 1076b) Composition: Agar 10.0 g/l Tryptone 10.0 g/l Bacto peptone 5.0 g/l PPLO broth 3.5 g/l Urea 2.0 g/l Glucose 1.0 g/l None 1.0 g/l Yeast extract 0.4 g/l DNA 0.2 g/l CMRL 1066 Fetal bovine serum Swine serum Distilled waterhttps://mediadive.dsmz.de/medium/1076b

culture temp

@refgrowthtypetemperaturerange
44047positivegrowth37mesophilic
24144positivegrowth37mesophilic
67770positivegrowth37mesophilic

culture pH

  • @ref: 44047
  • ability: positive
  • type: growth
  • pH: 6-8

Physiology and metabolism

oxygen tolerance

  • @ref: 44047
  • oxygen tolerance: microaerophile

spore formation

  • @ref: 44047
  • type of spore: spore
  • spore formation: no

observation

@refobservation
44047growth on classical agar
44047argentophilic
44047attaching to cultureware surface

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4404737684mannose-fermentation
4404716634raffinose-fermentation
4404717632nitrate-reduction

metabolite production

  • @ref: 44047
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
44047urease+3.5.1.5
44047beta-N-acetylgalactosaminidase+
44047alkaline phosphatase+3.1.3.1
44047arginine arylamidase+
44047leucyl glycin arylamidase+3.4.11.1
44047phenylalanine arylamidase+
44047leucine arylamidase+3.4.11.1
44047tyrosine arylamidase+
44047alanine arylamidase+3.4.11.2
44047glycin arylamidase+
44047histidine arylamidase+
44047glutamyl-glutamate arylamidase+
44047serine arylamidase+
44047arginine dihydrolase-3.5.3.6
44047alpha-galactosidase-3.2.1.22
44047beta-galactosidase-3.2.1.23
440476-phospho-beta-galactosidase-3.2.1.85
44047alpha-glucosidase-3.2.1.20
44047beta-glucosidase-3.2.1.21
44047alpha-arabinosidase-3.2.1.55
44047beta-glucuronidase-3.2.1.31
44047glutamate decarboxylase-4.1.1.15
44047alpha-fucosidase-3.2.1.51
44047proline-arylamidase-3.4.11.5
44047pyroglutamic acid arylamidase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    44047C15:0 anteiso25.8
    44047C17:0 anteiso1.7
    44047C14:010.3
    44047C16:017
    44047C15:0 iso41
    44047C16:0 iso4.4
  • type of FA analysis: whole cell analysis
  • incubation medium: Vero E6
  • incubation temperature: 37
  • incubation time: 7
  • library/peak naming table: ANAER6
  • system: MIS MIDI

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentenrichment culture
24144lung of a rat with chronic respiratory diseaseJapanJPNAsia
44047lung of a rat with chronic respiratory diseasemamallian cell culture / co-culture
67770Lung of a rat with chronic respiratory disease

isolation source categories

Cat1Cat2Cat3
#Infection#Inflammation
#Host#Mammals#Muridae (Mouse/Rat)
#Host Body-Site#Oral cavity and airways#Lung
#Infection#Disease

taxonmaps

  • @ref: 69479
  • File name: preview.99_100374.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9399;96_40756;97_52018;98_68616;99_100374&stattab=map
  • Last taxonomy: Filobacterium rodentium subclade
  • 16S sequence: LC055729
  • Sequence Identity:
  • Total samples: 471
  • soil counts: 21
  • aquatic counts: 26
  • animal counts: 423
  • plant counts: 1

Safety information

risk assessment

  • @ref: 44047
  • pathogenicity animal: yes

Sequence information

16S sequences

  • @ref: 24144
  • description: Filobacterium rodentium gene for 16S ribosomal RNA, partial sequence, strain: SMR-C
  • accession: LC055729
  • length: 1521
  • database: ena
  • NCBI tax ID: 28192

GC content

@refGC-contentmethod
2414447.7sequence analysis
6777047.7genome sequence analysis

External links

@ref: 24144

culture collection no.: DSM 100392, JCM 19453

straininfo link

  • @ref: 90701
  • straininfo: 403665

literature

  • topic: Phylogeny
  • Pubmed-ID: 26476525
  • title: Filobacterium rodentium gen. nov., sp. nov., a member of Filobacteriaceae fam. nov. within the phylum Bacteroidetes; includes a microaerobic filamentous bacterium isolated from specimens from diseased rodent respiratory tracts.
  • authors: Ike F, Sakamoto M, Ohkuma M, Kajita A, Matsushita S, Kokubo T
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.000685
  • year: 2015
  • mesh: Animals, Bacterial Typing Techniques, Bacteroidetes/*classification/genetics/isolation & purification, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rats, Rats, Wistar, Respiratory System/*microbiology, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24144Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100392Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100392)
44047Fumio Ike, Mitsuo Sakamoto, Moriya Ohkuma, Ayako Kajita, Satoru Matsushita and Toshiaki KokuboFilobacterium rodentium gen. nov., sp. nov., a member of Filobacteriaceae fam. nov. within the phylum Bacteroidetes; includes a microaerobic filamentous bacterium isolated from specimens from diseased rodent respiratory tracts10.1099/ijsem.0.000685IJSEM 66: 150-157 201626476525
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/
90701Reimer, 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-ID403665.1