Strain identifier

BacDive ID: 6366

Type strain: Yes

Species: Roseburia intestinalis

Strain Designation: L1-82

Strain history: DSM 14610 <-- S. Duncan L1-82.

NCBI tax ID(s): 166486 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5410

BacDive-ID: 6366

DSM-Number: 14610

keywords: genome sequence, 16S sequence, Bacteria, mesophilic

description: Roseburia intestinalis L1-82 is a mesophilic bacterium that was isolated from infant faeces.

NCBI tax id

  • NCBI tax id: 166486
  • Matching level: species

strain history

@refhistory
5410<- S. Duncan; L1-82
67770DSM 14610 <-- S. Duncan L1-82.

doi: 10.13145/bacdive6366.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Lachnospiraceae
  • genus: Roseburia
  • species: Roseburia intestinalis
  • full scientific name: Roseburia intestinalis Duncan et al. 2002

@ref: 5410

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Roseburia

species: Roseburia intestinalis

full scientific name: Roseburia intestinalis Duncan et al. 2002 emend. Duncan et al. 2006

strain designation: L1-82

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 5410
  • name: YCFA-MEDIUM (MODIFIED) (DSMZ Medium 1611)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1611
  • composition: Name: YCFA MEDIUM (modified) (DSMZ Medium 1611) Composition: Casitone 10.0 g/l Glucose 5.0 g/l NaHCO3 4.0 g/l Yeast extract 2.5 g/l Acetic acid 1.78695 g/l L-Cysteine HCl 1.0 g/l NaCl 0.9 g/l Propionic acid 0.62559 g/l KH2PO4 0.45 g/l K2HPO4 0.45 g/l CaCl2 x 2 H2O 0.09 g/l n-Valeric acid 0.08451 g/l iso-Valeric acid 0.0837899 g/l iso-Butyric acid 0.07695 g/l MgSO4 x 7 H2O 0.045 g/l Hemin 0.01 g/l Resazurin 0.001 g/l Pyridoxine hydrochloride 0.0001 g/l Nicotinic acid 5e-05 g/l Thiamine-HCl x 2 H2O 5e-05 g/l Riboflavin 5e-05 g/l D-Calcium pantothenate 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Lipoic acid 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Vitamin B12 1e-06 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
67770positivegrowth37mesophilic
5410positivegrowth37mesophilic

Physiology and metabolism

metabolite utilization

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

metabolite production

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

metabolite tests

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

enzymes

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

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
5410--++-+++-+-------+-----------
5410-+/-++-+++-+/--------+-----------
5410--++-+++-+/--------+/------------
5410--++-+++---------+-----------
5410--++-+++---------+-----------
5410--++-+++-+-------+-------++--
5410--++-+++-+-------+-----------
5410--++-+++---------+-----------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
5410infant faecesScotland, AberdeenUnited KingdomGBREurope
67770Healthy infant fecal samples

isolation source categories

Cat1Cat2Cat3
#Infection#Patient
#Host Body Product#Gastrointestinal tract#Feces (Stool)
#Host#Human#Child

taxonmaps

  • @ref: 69479
  • File name: preview.99_3891.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_1872;97_2249;98_2959;99_3891&stattab=map
  • Last taxonomy: Roseburia intestinalis subclade
  • 16S sequence: HM007565
  • Sequence Identity:
  • Total samples: 38220
  • soil counts: 217
  • aquatic counts: 311
  • animal counts: 37648
  • plant counts: 44

Safety information

risk assessment

  • @ref: 5410
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Roseburia intestinalis strain DSM 14610 16S ribosomal RNA gene, partial sequenceHM0075651329ena166486
5410Roseburia intestinalis 16S rRNA gene, strain L1-82AJ3123851482ena536231
67770Roseburia intestinalis gene for 16S ribosomal RNA, partial sequence, strain: JCM 17583AB6614351494ena166486

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseburia intestinalis L1-82GCA_900537995completencbi536231
66792Roseburia intestinalis L1-82GCA_000156535scaffoldncbi536231
66792Roseburia intestinalis L1-82536231.5wgspatric536231
66792Roseburia intestinalis L1-82536231.75completepatric536231
66792Roseburia intestinalis L1-822836830276completeimg536231
66792Roseburia intestinalis L1-822562617159draftimg536231

GC content

  • @ref: 67770
  • GC-content: 31
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno63.636no
gram-positiveyes83.673no
anaerobicyes99.701no
aerobicno99.172no
halophileno91.789no
spore-formingyes74.51no
thermophileno95.495yes
glucose-utilyes90.792no
motileyes80.682no
glucose-fermentyes76.235no

External links

@ref: 5410

culture collection no.: DSM 14610, CIP 107878, JCM 17583, NCIMB 13810, VTT E-052785

straininfo link

  • @ref: 75839
  • straininfo: 100933

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12361264Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces.Duncan SH, Hold GL, Barcenilla A, Stewart CS, Flint HJInt J Syst Evol Microbiol10.1099/00207713-52-5-16152002Base Composition, Butyrates/metabolism, Clostridium/classification, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Eubacterium/classification, Feces/microbiology, Fermentation, Gram-Positive Rods/*classification/*isolation & purification/metabolism/ultrastructure, Humans, Microscopy, Electron, Scanning, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicMetabolism
Pathogenicity12571040Effects of alternative dietary substrates on competition between human colonic bacteria in an anaerobic fermentor system.Duncan SH, Scott KP, Ramsay AG, Harmsen HJ, Welling GW, Stewart CS, Flint HJAppl Environ Microbiol10.1128/AEM.69.2.1136-1142.20032003Anaerobiosis, Bacteria, Anaerobic/classification/drug effects/genetics/*growth & development, Butyrates/metabolism, Colon/*microbiology, Colony Count, Microbial, Culture Media, Dietary Carbohydrates/metabolism/*pharmacology, *Ecosystem, Fermentation, Humans, In Situ Hybridization, Fluorescence, Oligonucleotide Probes, *Probiotics, RNA, Ribosomal, 16S/geneticsPhylogeny
Phylogeny17012576Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces.Duncan SH, Aminov RI, Scott KP, Louis P, Stanton TB, Flint HJInt J Syst Evol Microbiol10.1099/ijs.0.64098-02006Bacteria, Anaerobic/*classification/genetics/growth & development/isolation & purification, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/analysis, Fatty Acids/metabolism, Feces/*microbiology, Humans, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAMetabolism
Metabolism17056678Cross-feeding between Bifidobacterium longum BB536 and acetate-converting, butyrate-producing colon bacteria during growth on oligofructose.Falony G, Vlachou A, Verbrugghe K, De Vuyst LAppl Environ Microbiol10.1128/AEM.01296-062006Acetates/*metabolism, Bacteria, Anaerobic/classification/growth & development/*metabolism, Bifidobacterium/growth & development/*metabolism, Butyrates/*metabolism, Colon/*microbiology, Culture Media, Ecosystem, Fermentation, Fructose, Humans, Oligosaccharides/*metabolism, *ProbioticsCultivation
Metabolism19633122In vitro kinetics of prebiotic inulin-type fructan fermentation by butyrate-producing colon bacteria: implementation of online gas chromatography for quantitative analysis of carbon dioxide and hydrogen gas production.Falony G, Verschaeren A, De Bruycker F, De Preter V, Verbeke K, Leroy F, De Vuyst LAppl Environ Microbiol10.1128/AEM.00876-092009Butyrates/metabolism, Carbon Dioxide/*analysis, Chromatography, Gas/*methods, Colon/*microbiology, Fermentation, Fructans/*metabolism, Gram-Positive Bacteria/growth & development/isolation & purification/*metabolism, Hydrogen/*analysis, Lactic Acid/metabolismEnzymology
Metabolism30322445Integrated culturing, modeling and transcriptomics uncovers complex interactions and emergent behavior in a three-species synthetic gut community.D'hoe K, Vet S, Faust K, Moens F, Falony G, Gonze D, Llorens-Rico V, Gelens L, Danckaert J, De Vuyst L, Raes JElife10.7554/eLife.370902018Bacteria/metabolism, Cells, Cultured, Computer Simulation, Fermentation, Formates/metabolism, Fructose/metabolism, Gastrointestinal Microbiome/*genetics, Gene Expression Regulation, Bacterial, Humans, Kinetics, Metabolome/genetics, Models, Biological, Prokaryotic Cells/metabolism, RNA, Ribosomal, 16S/genetics, Species Specificity, Transcriptome/*geneticsPhylogeny
Enzymology31827247The enemy from within: a prophage of Roseburia intestinalis systematically turns lytic in the mouse gut, driving bacterial adaptation by CRISPR spacer acquisition.Cornuault JK, Moncaut E, Loux V, Mathieu A, Sokol H, Petit MA, De Paepe MISME J10.1038/s41396-019-0566-x2019Animals, Bacteriophages/genetics/isolation & purification/physiology, Clostridiales/*genetics/*virology, Clustered Regularly Interspaced Short Palindromic Repeats, Feces/microbiology, Female, *Gastrointestinal Microbiome, Humans, Lysogeny, Mice/*microbiology/*virology, Mice, Inbred C3H, Prophages/genetics/isolation & purification/*physiologyPhylogeny
Phylogeny33892267Butyribacter intestini gen. nov., sp. nov., a butyric acid-producing bacterium of the family Lachnospiraceae isolated from human faeces, and reclassification of Acetivibrio ethanolgignens as Acetanaerobacter ethanolgignens gen. nov., comb. nov.Zou Y, Xue W, Lin X, Lv M, Luo G, Dai Y, Sun H, Liu SW, Sun CH, Hu T, Xiao LSyst Appl Microbiol10.1016/j.syapm.2021.1262012021Bacterial Typing Techniques, Base Composition, Butyric Acid/*metabolism, Clostridiales/*classification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Feces/microbiology, Firmicutes/*classification/isolation & purification, Humans, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity
Metabolism36067589Peanuts as a nighttime snack enrich butyrate-producing bacteria compared to an isocaloric lower-fat higher-carbohydrate snack in adults with elevated fasting glucose: A randomized crossover trial.Sapp PA, Kris-Etherton PM, Arnesen EA, Chen See JR, Lamendella R, Petersen KSClin Nutr10.1016/j.clnu.2022.08.0042022Adult, *Arachis/genetics/metabolism, Bacteria, Blood Glucose/metabolism, Butyrates, Carbon/metabolism, Cross-Over Studies, Fasting, Glucose/metabolism, Humans, Oxidoreductases/metabolism, RNA, Ribosomal, 16S/genetics, *SnacksPathogenicity

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5410Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14610)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14610
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
75839Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100933.1StrainInfo: A central database for resolving microbial strain identifiers