Strain identifier

BacDive ID: 6369

Type strain: Yes

Species: Roseburia inulinivorans

Strain Designation: A2-194

Strain history: DSM 16841 <-- S. Duncan A2-194 <-- A. Barcenilla.

NCBI tax ID(s): 622312 (strain), 360807 (species)

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

@ref: 6627

BacDive-ID: 6369

DSM-Number: 16841

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-positive

description: Roseburia inulinivorans A2-194 is an anaerobe, mesophilic, Gram-positive bacterium that was isolated from human faecal sample.

NCBI tax id

NCBI tax idMatching level
622312strain
360807species

strain history

@refhistory
6627<- S. Duncan; A2-194 <- A. Barcenilla
67770DSM 16841 <-- S. Duncan A2-194 <-- A. Barcenilla.

doi: 10.13145/bacdive6369.20230509.8.1

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 inulinivorans
  • full scientific name: Roseburia inulinivorans Duncan et al. 2006

@ref: 6627

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Roseburia

species: Roseburia inulinivorans

full scientific name: Roseburia inulinivorans Duncan et al. 2006

strain designation: A2-194

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6627ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412)yeshttps://mediadive.dsmz.de/medium/412Name: ACETOMICROBIUM FAECALIS MEDIUM (DSMZ Medium 412) Composition: NaHCO3 6.0 g/l Na-acetate 5.0 g/l Glucose 4.0 g/l Yeast extract 2.0 g/l Trypticase peptone 2.0 g/l L-Cysteine HCl x H2O 0.5 g/l KH2PO4 0.255 g/l (NH4)2SO4 0.255 g/l K2HPO4 0.225 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l CoSO4 x 7 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l Resazurin 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l Pyridoxine hydrochloride 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l Nicotinic acid 5e-05 g/l (DL)-alpha-Lipoic acid 5e-05 g/l Thiamine HCl 5e-05 g/l Riboflavin 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Biotin 2e-05 g/l Folic acid 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Distilled water
6627YCFA-MEDIUM (MODIFIED) (DSMZ Medium 1611)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1611.pdf

culture temp

@refgrowthtypetemperaturerange
6627positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
6627anaerobe
69480anaerobe99.589

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 96.362

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
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
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
6627--++--+----------+-------+/----
6627--++--+----------+-------+/-+/---
6627-+/-++--+--------+-----------
6627--++--+----------+/------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6627human faecal sampleScotland, AberdeenUnited KingdomGBREurope
67770Human feces in AberdeenScotlandUnited KingdomGBREurope

isolation source categories

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

Safety information

risk assessment

  • @ref: 6627
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6627Roseburia inulinivorans 16S rRNA gene, type strain A2-194TAJ2704731454ena622312
67770Roseburia inulinivorans gene for 16S ribosomal RNA, partial sequence, strain: JCM 17584AB6614361494ena360807

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseburia inulinivorans DSM 16841 FDAARGOS_1587GCA_020731525contigncbi622312
66792Roseburia inulinivorans DSM 16841622312.4wgspatric622312
66792Roseburia inulinivorans DSM 16841643886006draftimg622312
67770Roseburia inulinivorans DSM 16841GCA_000174195contigncbi622312

GC content

@refGC-contentmethod
662741.4
6777041.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes60no
gram-positiveyes85.984no
anaerobicyes99.681no
halophileno87.136no
spore-formingyes64.587no
glucose-utilyes89.942no
thermophileno99.076no
flagellatedno61.57no
aerobicno99.33yes
motileyes82.01no
glucose-fermentyes81.8no

External links

@ref: 6627

culture collection no.: DSM 16841, CIP 109405, JCM 17584, NCIMB 14030

straininfo link

  • @ref: 75842
  • straininfo: 294497

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism16740940Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium "Roseburia inulinivorans".Scott KP, Martin JC, Campbell G, Mayer CD, Flint HJJ Bacteriol10.1128/JB.00137-062006Bacteria, Anaerobic/*genetics/growth & development/metabolism/physiology, Colon/microbiology, Culture Media, Fucose, *Genes, Bacterial, *Genome, Bacterial, Humans, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Polysaccharides/*metabolism, Propanols/metabolism, Propionates/metabolism, Propylene Glycols, Sugar Alcohol Dehydrogenases/genetics, Up-RegulationGenetics
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
Phylogeny17074899Cell-associated alpha-amylases of butyrate-producing Firmicute bacteria from the human colon.Ramsay AG, Scott KP, Martin JC, Rincon MT, Flint HJMicrobiology (Reading)10.1099/mic.0.29233-02006Bacteria, Anaerobic/classification/*enzymology/metabolism, Butyrates/*metabolism, Cell Wall/*enzymology, Colon/*microbiology, Genes, Bacterial, Humans, Hydrolases/classification/genetics, Molecular Sequence Data, Molecular Weight, Phylogeny, Protein Structure, Tertiary, Starch/metabolism, alpha-Amylases/chemistry/genetics/*metabolismMetabolism
Phylogeny18456856Transfer of conjugative elements from rumen and human Firmicutes bacteria to Roseburia inulinivorans.Scott KP, Martin JC, Mrazek J, Flint HJAppl Environ Microbiol10.1128/AEM.02807-072008Animals, *Conjugation, Genetic, DNA Transposable Elements, DNA, Bacterial/chemistry/*genetics, DNA, Ribosomal/chemistry/genetics, Gastrointestinal Tract/*microbiology, Gram-Positive Bacteria/*genetics/isolation & purification, Humans, Molecular Sequence Data, RNA, Ribosomal, 16S/genetics, Rumen/*microbiology, Sequence Analysis, DNAPathogenicity
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
Metabolism20679207Substrate-driven gene expression in Roseburia inulinivorans: importance of inducible enzymes in the utilization of inulin and starch.Scott KP, Martin JC, Chassard C, Clerget M, Potrykus J, Campbell G, Mayer CD, Young P, Rucklidge G, Ramsay AG, Flint HJProc Natl Acad Sci U S A10.1073/pnas.10000911072010ATP-Binding Cassette Transporters/metabolism, Base Sequence, Culture Media/pharmacology, DNA Primers/genetics, *Gene Expression Regulation, Bacterial, Gram-Positive Endospore-Forming Rods/enzymology/*genetics, Humans, Intestine, Large/*microbiology, Inulin/*metabolism/pharmacology, Molecular Sequence Data, Oligonucleotide Array Sequence Analysis, Phosphofructokinase-1/metabolism, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA, Starch/*metabolism/pharmacology, beta-Fructofuranosidase/metabolismTranscriptome
Pathogenicity26490635Influence of H7N9 virus infection and associated treatment on human gut microbiota.Qin N, Zheng B, Yao J, Guo L, Zuo J, Wu L, Zhou J, Liu L, Guo J, Ni S, Li A, Zhu Y, Liang W, Xiao Y, Ehrlich SD, Li LSci Rep10.1038/srep147712015Adult, Aged, Aged, 80 and over, Clostridium/genetics/pathogenicity, Enterococcus faecium/genetics/pathogenicity, Escherichia coli/genetics/pathogenicity, Female, Gastrointestinal Microbiome/*genetics, High-Throughput Nucleotide Sequencing, Humans, Influenza A Virus, H7N9 Subtype/*genetics/pathogenicity, Influenza, Human/*genetics/microbiology/virology, Male, *Metagenomics, Middle AgedGenetics
Pathogenicity31228669Heterologous gene expression in the human gut bacteria Eubacterium rectale and Roseburia inulinivorans by means of conjugative plasmids.Sheridan PO, Martin JC, Minton NP, Flint HJ, O'Toole PW, Scott KPAnaerobe10.1016/j.anaerobe.2019.06.0082019Clostridiales/*genetics, *Conjugation, Genetic, Escherichia coli/genetics, Eubacterium/*genetics, *Gene Expression, *Gene Transfer Techniques, Genetic Vectors, Genetics, Microbial/*methods, Humans, *Plasmids, Transformation, Bacterial

Reference

@idauthorscataloguedoi/urltitle
6627Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16841)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16841
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
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
75842Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID294497.1StrainInfo: A central database for resolving microbial strain identifiers