Strain identifier

BacDive ID: 6367

Type strain: Yes

Species: Roseburia hominis

Strain Designation: A2-183

Strain history: DSM 16839 <-- S. Duncan A2-183 <-- A. Barcenilla.

NCBI tax ID(s): 301301 (species)

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General

@ref: 6625

BacDive-ID: 6367

DSM-Number: 16839

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

description: Roseburia hominis A2-183 is an anaerobe, mesophilic bacterium that was isolated from human faecal sample.

NCBI tax id

  • NCBI tax id: 301301
  • Matching level: species

strain history

@refhistory
6625<- S. Duncan; A2-183 <- A. Barcenilla
67770DSM 16839 <-- S. Duncan A2-183 <-- A. Barcenilla.

doi: 10.13145/bacdive6367.20230509.8.1

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

@ref: 6625

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Roseburia

species: Roseburia hominis

full scientific name: Roseburia hominis Duncan et al. 2006

strain designation: A2-183

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 6625
  • name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/58
  • composition: Name: BIFIDOBACTERIUM MEDIUM (DSMZ Medium 58) Composition: Glucose 10.0 g/l Casein peptone 10.0 g/l Bacto Soytone 5.0 g/l Meat extract 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l MnSO4 x H2O 0.05 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 Tween 80 Resazurin Distilled water

culture temp

@refgrowthtypetemperaturerange
6625positivegrowth37mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 6625
  • oxygen tolerance: anaerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose-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-
68380histidine arylamidase-
68380glycin 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
68380L-arginine arylamidase-
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-Galactosidase 6-phosphate-
68380beta-galactosidase+3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
6625--++--+/-----+-----------------
6625--++-+/-++/-+/---------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6625human faecal sampleScotland, AberdeenUnited KingdomGBREurope
67770Human feces in AberdeenScotlandUnited KingdomGBREurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_3606.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_1872;97_2249;98_2760;99_3606&stattab=map
  • Last taxonomy: Roseburia hominis subclade
  • 16S sequence: AB661434
  • Sequence Identity:
  • Total samples: 57468
  • soil counts: 184
  • aquatic counts: 676
  • animal counts: 56516
  • plant counts: 92

Safety information

risk assessment

  • @ref: 6625
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
6625Roseburia hominis A2-183 16S rRNA gene, type strain A2-183TAJ2704821485ena585394
67770Roseburia hominis gene for 16S ribosomal RNA, partial sequence, strain: JCM 17582AB6614341493ena301301

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Roseburia hominis A2-183GCA_000225345completencbi585394
66792Roseburia hominis A2-183585394.18completepatric585394
66792Roseburia hominis A2-183, DSM 168392511231128completeimg585394

GC content

@refGC-contentmethod
662547.4
6777047.4high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes78.484no
flagellatedno56.387no
gram-positiveyes82.953no
anaerobicyes99.999yes
aerobicno99.279yes
halophileno90.03no
spore-formingyes67.561no
thermophileno89.441no
glucose-utilyes88.51no
glucose-fermentyes77.866no

External links

@ref: 6625

culture collection no.: DSM 16839, CIP 109406, JCM 17582, NCIMB 14029, BCRC 81266

straininfo link

  • @ref: 75840
  • straininfo: 237167

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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
Metabolism18537837Distribution of beta-glucosidase and beta-glucuronidase activity and of beta-glucuronidase gene gus in human colonic bacteria.Dabek M, McCrae SI, Stevens VJ, Duncan SH, Louis PFEMS Microbiol Ecol10.1111/j.1574-6941.2008.00520.x2008Bacteria/*enzymology/*genetics/growth & development/isolation & purification, Carbon/metabolism, Colon/*microbiology, Feces/microbiology, Genes, Bacterial/*genetics, Glucuronidase/*metabolism, Glycoside Hydrolases/metabolism, Humans, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, beta-Glucosidase/*metabolismPhylogeny
Metabolism19118369Mechanism of conjugated linoleic acid and vaccenic acid formation in human faecal suspensions and pure cultures of intestinal bacteria.McIntosh FM, Shingfield KJ, Devillard E, Russell WR, Wallace RJMicrobiology (Reading)10.1099/mic.0.022921-02009Adult, Butyrivibrio/*growth & development/isolation & purification/metabolism, Culture Media/metabolism, Feces/chemistry/*microbiology, Gram-Positive Bacteria/*growth & development/isolation & purification/metabolism, Humans, Intestines/*microbiology, Isomerism, Linoleic Acids, Conjugated/chemistry/*metabolism, Middle Aged, Oleic Acids/chemistry/*metabolismEnzymology
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
Genetics26543119Complete Genome Sequence of the Human Gut Symbiont Roseburia hominis.Travis AJ, Kelly D, Flint HJ, Aminov RIGenome Announc10.1128/genomeA.01286-152015
29018440Human Gut Symbiont Roseburia hominis Promotes and Regulates Innate Immunity.Patterson AM, Mulder IE, Travis AJ, Lan A, Cerf-Bensussan N, Gaboriau-Routhiau V, Garden K, Logan E, Delday MI, Coutts AGP, Monnais E, Ferraria VC, Inoue R, Grant G, Aminov RIFront Immunol10.3389/fimmu.2017.011662017
Phylogeny35559790Pararoseburia lenta gen. nov., sp. nov. isolated from human faeces.Abdugheni R, Wang YJ, Li DH, Du MX, Liu C, Zhou N, Liu SJInt J Syst Evol Microbiol10.1099/ijsem.0.0053712022*Bacteria, Anaerobic, Bacterial Typing Techniques, Base Composition, Butyrates, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Feces/microbiology, Humans, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAPathogenicity

Reference

@idauthorscataloguedoi/urltitle
6625Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16839)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16839
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
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
75840Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID237167.1StrainInfo: A central database for resolving microbial strain identifiers