Strain identifier

BacDive ID: 158358

Type strain: Yes

Species: Romboutsia hominis

Strain Designation: FRIFI

Strain history: <- Jacoline Gerritsen, Wageningen Univ., FRIFI

NCBI tax ID(s): 1507512 (species)

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General

@ref: 65034

BacDive-ID: 158358

DSM-Number: 28814

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive, motile, rod-shaped, colony-forming

description: Romboutsia hominis FRIFI is an anaerobe, mesophilic, Gram-positive bacterium that forms circular colonies and was isolated from human ileostoma effluent.

NCBI tax id

  • NCBI tax id: 1507512
  • Matching level: species

strain history

@refhistory
65034<- J. Gerritsen, Wageningen University, Laboratory of Microbiology, Netherlands; FRIFI <- I. Staneva {2011}
67771<- Jacoline Gerritsen, Wageningen Univ., FRIFI

doi: 10.13145/bacdive158358.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Romboutsia
  • species: Romboutsia hominis
  • full scientific name: Romboutsia hominis Gerritsen et al. 2018

@ref: 65034

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Romboutsia

species: Romboutsia hominis

full scientific name: Romboutsia hominis Gerritsen et al. 2018

strain designation: FRIFI

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
66726positive2.7-16.3 µm1.1-2.1 µmrod-shapedyes
67771rod-shapedyes
67771positive

colony morphology

@refcolony sizecolony colorcolony shapeincubation periodmedium used
667261-2 mmwhite or light greycircular1 dayDSMZ 104b medium
667262-4 mmcircular3 daysDSMZ 104b medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
65034PY + X MEDIUM (DSMZ Medium 104b)yeshttps://mediadive.dsmz.de/medium/104bName: PY + X MEDIUM (DSMZ Medium 104b) Composition: Yeast extract 10.0 g/l D-Glucose 5.0 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
66726bacterial peptoneyes
66726CRIByes
66726DSMZ 104b mediumyes
66726PYGyes
66726Yeast extractyes

culture temp

@refgrowthtypetemperaturerange
65034positivegrowth37mesophilic
67771positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: anaerobe

spore formation

@refspore formation
66726no
67771no

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
667266731melezitose-builds acid from
6672612936D-galactose-builds acid from
6672615443inulin-builds acid from
6672615963ribitol-builds acid from
6672616024D-mannose-builds acid from
6672616443D-tagatose-builds acid from
6672616634raffinose-builds acid from
6672616813galactitol-builds acid from
6672616899D-mannitol-builds acid from
6672616988D-ribose-builds acid from
6672617057cellobiose-builds acid from
6672617108D-arabinose-builds acid from
6672617113erythritol-builds acid from
6672617151xylitol-builds acid from
6672617266L-sorbose-builds acid from
6672617268myo-inositol-builds acid from
6672617306maltose-builds acid from
6672617716lactose-builds acid from
6672617814salicin-builds acid from
6672617924D-sorbitol-builds acid from
6672617992sucrose-builds acid from
6672618305arbutin-builds acid from
6672618333D-arabitol-builds acid from
6672618403L-arabitol-builds acid from
6672627082trehalose-builds acid from
6672627613amygdalin-builds acid from
6672628017starch-builds acid from
6672628053melibiose-builds acid from
6672628066gentiobiose-builds acid from
6672628087glycogen-builds acid from
6672628847D-fucose-builds acid from
6672630849L-arabinose-builds acid from
6672632032potassium gluconate-builds acid from
6672632528turanose-builds acid from
6672643943methyl alpha-D-mannoside-builds acid from
6672659640N-acetylglucosamine-builds acid from
6672662318D-lyxose-builds acid from
6672662345L-rhamnose-builds acid from
6672665327D-xylose-builds acid from
6672665328L-xylose-builds acid from
6672674863methyl beta-D-xylopyranoside-builds acid from
66726320061methyl alpha-D-glucopyranoside-builds acid from
66726potassium 2-dehydro-D-gluconate-builds acid from
66726potassium 5-dehydro-D-gluconate-builds acid from
6672615824D-fructose+builds acid from
6672617634D-glucose+builds acid from
6672617754glycerol+builds acid from
6672618287L-fucose+builds acid from
66726esculin ferric citrate+builds acid from
667265291gelatin-hydrolysis
6672628017starch-hydrolysis

metabolite production

  • @ref: 66726
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
66726urease-3.5.1.5
66726catalase-1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentlatitudelongitudegeographic locationenrichment cultureisolation procedure
65034human ileostoma effluentNetherlandsNLDEurope51.8255.8556
66726material directly from the ileostomy bag of female human volunteer who was otherwise healthyNetherlandsNLDEuropeUniversity Medical Centre St. Radboud, Nijmegenliquid anoxic bicarbonate-buffered CRIB medium (pH 7.0)Enrichment was achieved by repeated serial dilutions
67771From ileostoma effluent of an otherwise healthy human volunteerNetherlandsNLDEuropeWageningen University

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Gastrointestinal tract#Small intestine
#Host Body Product#Gastrointestinal tract
#Host#Human
#Infection#Medical device

Sequence information

16S sequences

  • @ref: 65034
  • description: Romboutsia sp. Frifi 16S ribosomal RNA gene, partial sequence
  • accession: KT372679
  • length: 1491
  • database: ena
  • NCBI tax ID: 1507512

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Romboutsia hominis FRIFIGCA_900002575chromosomencbi1507512
66792Romboutsia hominis FRIFI2832941562completeimg1507512

GC content

@refGC-contentmethod
6503428.3sequence analysis
6672644.7genome sequence analysis
6777127.8

External links

@ref: 65034

culture collection no.: DSM 28814, KCTC 15553

straininfo link

  • @ref: 111163
  • straininfo: 401985

literature

  • topic: Phylogeny
  • Pubmed-ID: 30226461
  • title: Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent.
  • authors: Gerritsen J, Umanets A, Staneva I, Hornung B, Ritari J, Paulin L, Rijkers GT, de Vos WM, Smidt H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.003012
  • year: 2018
  • mesh: Bacterial Typing Techniques, Base Composition, Clostridiales/*classification/genetics/isolation & purification, Cyclopropanes/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Humans, Ileostomy, Ileum/*microbiology, Netherlands, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Pathogenicity

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
65034Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28814Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28814)
66726Jacoline Gerritsen, Alexander Umanets, Ivelina Staneva, Bastian Hornung, Jarmo Ritari, Lars Paulin, Ger T. Rijkers, Willem M. de Vos, Hauke SmidtRomboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia , isolated from ileostoma effluent10.1099/ijsem.0.003012IJSEM 68: 3479-3486 201830226461
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
111163Reimer, 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-ID401985.1