Strain identifier
BacDive ID: 2614
Type strain:
Species: Romboutsia lituseburensis
Strain Designation: A25K
Strain history: ATCC 25759 <-- L. DS. Smith VPI 2751.
NCBI tax ID(s): 1121325 (strain), 1537 (species)
General
@ref: 453
BacDive-ID: 2614
DSM-Number: 797
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive
description: Romboutsia lituseburensis A25K is an anaerobe, spore-forming, mesophilic bacterium that was isolated from mud.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1121325 | strain |
1537 | species |
strain history
@ref | history |
---|---|
453 | <- ATCC <- L. DS. Smith, Virginia Polytechnical Institute and State University, Blacksburg, V., USA; VPI 2751 <- A. R. Prevot, Institut Pasteur, Paris, France; A25K |
67770 | ATCC 25759 <-- L. DS. Smith VPI 2751. |
doi: 10.13145/bacdive2614.20230509.8.1
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 lituseburensis
- full scientific name: Romboutsia lituseburensis (Laplanche and Saissac 1948) Gerritsen et al. 2014
synonyms
@ref synonym 20215 Clostridium lituseburense 20215 Inflabilis lituseburense
@ref: 453
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Clostridiaceae
genus: Romboutsia
species: Romboutsia lituseburensis
full scientific name: Romboutsia lituseburensis (Laplanche and Saissac 1948) Gerritsen et al. 2014
strain designation: A25K
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
- @ref: 46926
- incubation period: 1 day
Culture and growth conditions
culture medium
- @ref: 453
- name: PY + X MEDIUM (DSMZ Medium 104b)
- growth: yes
- link: https://mediadive.dsmz.de/medium/104b
- composition: Name: 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
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
453 | positive | growth | 37 | mesophilic |
46926 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
453 | anaerobe | |
46926 | anaerobe | |
69480 | anaerobe | 98.648 |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | yes | 96 |
69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
@ref | sample type |
---|---|
453 | mud |
46926 | Mud |
67770 | Mud |
isolation source categories
- Cat1: #Environmental
- Cat2: #Terrestrial
- Cat3: #Mud (Sludge)
Safety information
risk assessment
- @ref: 453
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
453 | [Clostridium] lituseburense strain ATCC 25759 16S ribosomal RNA gene, partial sequence | M59107 | 1510 | ena | 1121325 |
67770 | Romboutsia lituseburensis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1404 | LC007106 | 1464 | ena | 1537 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Romboutsia lituseburensis A25K | GCA_900002825 | scaffold | ncbi | 1537 |
66792 | Romboutsia lituseburensis DSM 797 | 1121325.3 | wgs | patric | 1121325 |
66792 | Romboutsia lituseburensis strain A25K | 1537.3 | wgs | patric | 1537 |
66792 | Romboutsia lituseburensis DSM 797 | 2634166902 | draft | img | 1121325 |
67770 | Romboutsia lituseburensis DSM 797 | GCA_900103615 | scaffold | ncbi | 1121325 |
GC content
@ref | GC-content | method |
---|---|---|
453 | 27.0 | |
67770 | 27 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 96 | no |
motile | yes | 81.857 | no |
flagellated | no | 54.745 | no |
gram-positive | yes | 92.981 | no |
anaerobic | yes | 97.954 | yes |
aerobic | no | 96.939 | yes |
halophile | no | 88.535 | no |
spore-forming | yes | 94.46 | no |
thermophile | no | 98.946 | no |
glucose-util | yes | 88.028 | no |
glucose-ferment | yes | 60.813 | no |
External links
@ref: 453
culture collection no.: DSM 797, ATCC 25759, BCRC 14536, CCUG 18920, JCM 1404, NCIMB 10637, VTT E-021853, VPI 2751
straininfo link
- @ref: 72145
- straininfo: 38658
literature
topic | Pubmed-ID | title | authors | journal | year | mesh | topic2 | DOI |
---|---|---|---|---|---|---|---|---|
Phylogeny | 21090252 | [Identification and metabolism characterization of a Clostridium lituseburense strain isolated from high-altitude soil]. | Liu Q, Liu H, Deng Y, Hu G, Zhang H | Wei Sheng Wu Xue Bao | 2010 | *Altitude, Base Composition/genetics, Clostridium/classification/*genetics/*isolation & purification, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil Microbiology | Metabolism | |
Phylogeny | 23163427 | Characterization of a potentially novel 'blown pack' spoilage bacterium isolated from bovine hide. | Moschonas G, Bolton DJ | J Appl Microbiol | 2012 | Abattoirs, Animals, Cattle/microbiology, Clostridium/*classification/growth & development/isolation & purification, Cold Temperature, Fatty Acids/chemistry, *Food Contamination, *Food Microbiology, Food Preservation, Genes, rRNA, Genotype, Ireland, Meat/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Spores, Bacterial/genetics, Vacuum | Biotechnology | 10.1111/jam.12077 |
Phylogeny | 25609678 | Romboutsia sedimentorum sp. nov., isolated from an alkaline-saline lake sediment and emended description of the genus Romboutsia. | Wang Y, Song J, Zhai Y, Zhang C, Gerritsen J, Wang H, Chen X, Li Y, Zhao B, Zhao B, Ruan Z | Int J Syst Evol Microbiol | 2015 | Bacteria, Anaerobic/classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Glycolipids/chemistry, Gram-Positive Endospore-Forming Rods/*classification/genetics/isolation & purification, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Salinity, Sequence Analysis, DNA | Enzymology | 10.1099/ijs.0.000079 |
Metabolism | 26027356 | [Anaerobic bacteria involved in the degradation of aromatic sulfonates to methane]. | Shcherbakova VA, Laurinavichyus KS, Chuvil'skaya NA, Ryzhmanova YV, Akimenko VK | Prikl Biokhim Mikrobiol | 2015 | Bacteria, Anaerobic/metabolism, Benzenesulfonates/*metabolism, Clostridium/genetics/isolation & purification/*metabolism, Desulfovibrio/genetics/isolation & purification/*metabolism, Methane/*metabolism, Microbial Consortia, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S | Phylogeny | 10.7868/s0555109915020191 |
Phylogeny | 30226461 | Romboutsia hominis sp. nov., the first human gut-derived representative of the genus Romboutsia, isolated from ileostoma effluent. | Gerritsen J, Umanets A, Staneva I, Hornung B, Ritari J, Paulin L, Rijkers GT, de Vos WM, Smidt H | Int J Syst Evol Microbiol | 2018 | 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 | Pathogenicity | 10.1099/ijsem.0.003012 |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
453 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 797) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-797 | |||
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 | |||
46926 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 18920) | https://www.ccug.se/strain?id=18920 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
72145 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38658.1 | StrainInfo: A central database for resolving microbial strain identifiers |