Strain identifier
BacDive ID: 6366
Type strain:
Species: Roseburia intestinalis
Strain Designation: L1-82
Strain history: DSM 14610 <-- S. Duncan L1-82.
NCBI tax ID(s): 166486 (species)
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
@ref | history |
---|---|
5410 | <- S. Duncan; L1-82 |
67770 | DSM 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
67770 | positive | growth | 37 | mesophilic |
5410 | positive | growth | 37 | mesophilic |
Physiology and metabolism
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68380 | 16199 | urea | - | hydrolysis |
68380 | 16024 | D-mannose | - | fermentation |
68380 | 16634 | raffinose | - | fermentation |
68380 | 29985 | L-glutamate | - | degradation |
68380 | 17632 | nitrate | - | reduction |
68380 | 27897 | tryptophan | - | 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
@ref | value | activity | ec |
---|---|---|---|
68380 | serine arylamidase | - | |
68380 | glutamyl-glutamate arylamidase | - | |
68380 | alanine arylamidase | - | 3.4.11.2 |
68380 | tyrosine arylamidase | - | |
68380 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68380 | leucine arylamidase | - | 3.4.11.1 |
68380 | phenylalanine arylamidase | - | |
68380 | leucyl glycin arylamidase | - | 3.4.11.1 |
68380 | proline-arylamidase | - | 3.4.11.5 |
68380 | alkaline phosphatase | - | 3.1.3.1 |
68380 | tryptophan deaminase | - | 4.1.99.1 |
68380 | alpha-fucosidase | - | 3.2.1.51 |
68380 | glutamate decarboxylase | - | 4.1.1.15 |
68380 | beta-glucuronidase | - | 3.2.1.31 |
68380 | alpha-arabinosidase | + | 3.2.1.55 |
68380 | beta-glucosidase | + | 3.2.1.21 |
68380 | alpha-glucosidase | + | 3.2.1.20 |
68380 | beta-Galactosidase 6-phosphate | - | |
68380 | beta-galactosidase | + | 3.2.1.23 |
68380 | alpha-galactosidase | + | 3.2.1.22 |
68380 | urease | - | 3.5.1.5 |
API rID32A
@ref | URE | ADH Arg | alpha GAL | beta GAL | beta GP | alpha GLU | beta GLU | alpha ARA | beta GUR | beta NAG | MNE | RAF | GDC | alpha FUC | NIT | IND | PAL | ArgA | ProA | LGA | PheA | LeuA | PyrA | TyrA | AlaA | GlyA | HisA | GGA | SerA |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
5410 | - | - | + | + | - | + | + | + | - | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - |
5410 | - | +/- | + | + | - | + | + | + | - | +/- | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - |
5410 | - | - | + | + | - | + | + | + | - | +/- | - | - | - | - | - | - | - | +/- | - | - | - | - | - | - | - | - | - | - | - |
5410 | - | - | + | + | - | + | + | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - |
5410 | - | - | + | + | - | + | + | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - |
5410 | - | - | + | + | - | + | + | + | - | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | + | + | - | - |
5410 | - | - | + | + | - | + | + | + | - | + | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - |
5410 | - | - | + | + | - | + | + | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5410 | infant faeces | Scotland, Aberdeen | United Kingdom | GBR | Europe |
67770 | Healthy infant fecal samples |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Roseburia intestinalis strain DSM 14610 16S ribosomal RNA gene, partial sequence | HM007565 | 1329 | ena | 166486 |
5410 | Roseburia intestinalis 16S rRNA gene, strain L1-82 | AJ312385 | 1482 | ena | 536231 |
67770 | Roseburia intestinalis gene for 16S ribosomal RNA, partial sequence, strain: JCM 17583 | AB661435 | 1494 | ena | 166486 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Roseburia intestinalis L1-82 | GCA_900537995 | complete | ncbi | 536231 |
66792 | Roseburia intestinalis L1-82 | GCA_000156535 | scaffold | ncbi | 536231 |
66792 | Roseburia intestinalis L1-82 | 536231.5 | wgs | patric | 536231 |
66792 | Roseburia intestinalis L1-82 | 536231.75 | complete | patric | 536231 |
66792 | Roseburia intestinalis L1-82 | 2836830276 | complete | img | 536231 |
66792 | Roseburia intestinalis L1-82 | 2562617159 | draft | img | 536231 |
GC content
- @ref: 67770
- GC-content: 31
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 63.636 | no |
gram-positive | yes | 83.673 | no |
anaerobic | yes | 99.701 | no |
aerobic | no | 99.172 | no |
halophile | no | 91.789 | no |
spore-forming | yes | 74.51 | no |
thermophile | no | 95.495 | yes |
glucose-util | yes | 90.792 | no |
motile | yes | 80.682 | no |
glucose-ferment | yes | 76.235 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12361264 | Roseburia intestinalis sp. nov., a novel saccharolytic, butyrate-producing bacterium from human faeces. | Duncan SH, Hold GL, Barcenilla A, Stewart CS, Flint HJ | Int J Syst Evol Microbiol | 10.1099/00207713-52-5-1615 | 2002 | Base 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 Topic | Metabolism |
Pathogenicity | 12571040 | Effects 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 HJ | Appl Environ Microbiol | 10.1128/AEM.69.2.1136-1142.2003 | 2003 | Anaerobiosis, 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/genetics | Phylogeny |
Phylogeny | 17012576 | Proposal 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 HJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.64098-0 | 2006 | Bacteria, 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, DNA | Metabolism |
Metabolism | 17056678 | Cross-feeding between Bifidobacterium longum BB536 and acetate-converting, butyrate-producing colon bacteria during growth on oligofructose. | Falony G, Vlachou A, Verbrugghe K, De Vuyst L | Appl Environ Microbiol | 10.1128/AEM.01296-06 | 2006 | Acetates/*metabolism, Bacteria, Anaerobic/classification/growth & development/*metabolism, Bifidobacterium/growth & development/*metabolism, Butyrates/*metabolism, Colon/*microbiology, Culture Media, Ecosystem, Fermentation, Fructose, Humans, Oligosaccharides/*metabolism, *Probiotics | Cultivation |
Metabolism | 19633122 | In 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 L | Appl Environ Microbiol | 10.1128/AEM.00876-09 | 2009 | Butyrates/metabolism, Carbon Dioxide/*analysis, Chromatography, Gas/*methods, Colon/*microbiology, Fermentation, Fructans/*metabolism, Gram-Positive Bacteria/growth & development/isolation & purification/*metabolism, Hydrogen/*analysis, Lactic Acid/metabolism | Enzymology |
Metabolism | 30322445 | Integrated 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 J | Elife | 10.7554/eLife.37090 | 2018 | Bacteria/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/*genetics | Phylogeny |
Enzymology | 31827247 | The 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 M | ISME J | 10.1038/s41396-019-0566-x | 2019 | Animals, 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/*physiology | Phylogeny |
Phylogeny | 33892267 | Butyribacter 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 L | Syst Appl Microbiol | 10.1016/j.syapm.2021.126201 | 2021 | Bacterial 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, DNA | Pathogenicity |
Metabolism | 36067589 | Peanuts 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 KS | Clin Nutr | 10.1016/j.clnu.2022.08.004 | 2022 | Adult, *Arachis/genetics/metabolism, Bacteria, Blood Glucose/metabolism, Butyrates, Carbon/metabolism, Cross-Over Studies, Fasting, Glucose/metabolism, Humans, Oxidoreductases/metabolism, RNA, Ribosomal, 16S/genetics, *Snacks | Pathogenicity |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5410 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14610) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14610 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68380 | Automatically annotated from API rID32A | |||||
69479 | João 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 | |||
75839 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID100933.1 | StrainInfo: A central database for resolving microbial strain identifiers |