Strain identifier
BacDive ID: 2602
Type strain: 
Species: Lacrimispora indolis
Strain Designation: 7
Strain history: <- DSM <- NCIB <- RH Vaughn, 7
NCBI tax ID(s): 69825 (species)
version 8.1 (current version)
General
@ref: 427
BacDive-ID: 2602
DSM-Number: 755
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, Gram-positive
description: Lacrimispora indolis 7 is an anaerobe, spore-forming, mesophilic bacterium of the family Lachnospiraceae.
NCBI tax id
- NCBI tax id: 69825
- Matching level: species
strain history
| @ref | history |
|---|---|
| 427 | <- NCIB <- R.H. Vaughn, 7 |
| 67770 | ATCC 25771 <-- L. DS. Smith VPI 4520 (NCIB 9731). |
| 67771 | <- DSM <- NCIB <- RH Vaughn, 7 |
doi: 10.13145/bacdive2602.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Lachnospiraceae
- genus: Lacrimispora
- species: Lacrimispora indolis
- full scientific name: Lacrimispora indolis (McClung and McCoy 1957) Haas and Blanchard 2020
synonyms
- @ref: 20215
- synonym: Clostridium indolis
@ref: 427
domain: Bacteria
phylum: Firmicutes
class: Clostridia
order: Clostridiales
family: Lachnospiraceae
genus: Lacrimispora
species: Lacrimispora indolis
full scientific name: Lacrimispora indolis (McClung and McCoy 1957) Haas and Blanchard 2020
strain designation: 7
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | positive | |
| 69480 | positive | 100 |
colony morphology
- @ref: 60650
- incubation period: 1 day
Culture and growth conditions
culture medium
- @ref: 427
- name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)
- growth: yes
- link: https://mediadive.dsmz.de/medium/110
- composition: Name: CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l K2HPO4 5.0 g/l Yeast extract 5.0 g/l D-Glucose 4.0 g/l Starch 1.0 g/l Maltose 1.0 g/l Cellobiose 1.0 g/l L-Cysteine HCl 0.5 g/l Ethanol 0.19 g/l Vitamin K3 0.05 g/l Hemin 0.005 g/l Sodium resazurin 0.0005 g/l Vitamin K1 NaOH Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 427 | positive | growth | 37 | mesophilic |
| 60650 | positive | growth | 37 | mesophilic |
| 67770 | positive | growth | 37 | mesophilic |
| 67771 | positive | growth | 37 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 427 | anaerobe | |
| 60650 | anaerobe | |
| 67771 | anaerobe | |
| 69480 | anaerobe | 99.113 |
spore formation
| @ref | type of spore | spore formation | confidence |
|---|---|---|---|
| 67771 | spore | yes | |
| 69481 | yes | 99 | |
| 69480 | yes | 99.448 |
Isolation, sampling and environmental information
taxonmaps
- @ref: 69479
- File name: preview.99_2175.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16;96_286;97_316;98_1698;99_2175&stattab=map
- Last taxonomy: Lacrimispora
- 16S sequence: Y18184
- Sequence Identity:
- Total samples: 3608
- soil counts: 195
- aquatic counts: 207
- animal counts: 3154
- plant counts: 52
Safety information
risk assessment
- @ref: 427
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Clostridium indolis strain DSM 755 16S ribosomal RNA gene, partial sequence | HM245946 | 839 | ena | 69825 |
| 427 | Clostridium indolis 16S rRNA gene, partial, strain DSM 755 | Y18184 | 1488 | ena | 69825 |
| 67770 | [Clostridium] indolis gene for 16S ribosomal RNA, partial sequence, strain: JCM 1380 | AB971794 | 1494 | ena | 69825 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Clostridium indolis DSM 755 | 1304881.3 | wgs | patric | 1304881 |
| 66792 | [Clostridium] indolis strain NCTC11811 | 69825.3 | wgs | patric | 69825 |
| 66792 | Clostridium indolis DSM 755 | 2524614838 | draft | img | 1304881 |
| 67771 | [Clostridium] indolis DSM 755 | GCA_000526995 | contig | ncbi | 1304881 |
| 67771 | Lacrimispora indolis NCTC11811 | GCA_900618075 | contig | ncbi | 69825 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 427 | 44.0 | |
| 67770 | 44 | thermal denaturation, midpoint method (Tm) |
| 67771 | 44.93 | genome sequence analysis |
| 67771 | 44.0 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 99 | no |
| motile | yes | 84.448 | no |
| gram-positive | yes | 61.037 | no |
| anaerobic | yes | 98.181 | no |
| halophile | no | 93.396 | no |
| spore-forming | yes | 88.472 | yes |
| thermophile | no | 99.641 | yes |
| glucose-util | yes | 87.276 | no |
| aerobic | no | 97.89 | yes |
| flagellated | yes | 55.765 | no |
| glucose-ferment | yes | 75.163 | no |
External links
@ref: 427
culture collection no.: CCUG 55582, JCM 1380, NCTC 11811, KCTC 5151, BCRC 11667, DSM 755, ATCC 25771, NCIB 9731, NCIMB 9731, VPI 4520, VTT E-042445
straininfo link
- @ref: 72133
- straininfo: 125932
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 24522483 | Clostridium geopurificans strain MJ1 sp. nov., a strictly anaerobic bacterium that grows via fermentation and reduces the cyclic nitramine explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). | Kwon MJ, Wei N, Millerick K, Popovic J, Finneran K | Curr Microbiol | 10.1007/s00284-014-0531-x | 2014 | Anaerobiosis, Bacterial Typing Techniques, Base Composition, Clostridium/*classification/genetics/isolation & purification/*physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Environmental Microbiology, Explosive Agents/*metabolism, Fatty Acids/analysis, Fermentation, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Triazines/*metabolism, United States | Metabolism |
| Genetics | 25197485 | The complete genome sequence of Clostridium indolis DSM 755(T.). | Biddle AS, Leschine S, Huntemann M, Han J, Chen A, Kyrpides N, Markowitz V, Palaniappan K, Ivanova N, Mikhailova N, Ovchinnikova G, Schaumberg A, Pati A, Stamatis D, Reddy T, Lobos E, Goodwin L, Nordberg HP, Cantor MN, Hua SX, Woyke T, Blanchard JL | Stand Genomic Sci | 10.4056/sigs.5281010 | 2014 | ||
| Phylogeny | 30676311 | Clostridium indicum sp. nov., a novel anaerobic bacterium isolated from the sludge of an industrial effluent. | Gundawar K, Kumari S, Sharma S, Grover V, Patil PB, Korpole S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003199 | 2019 | Bacterial Typing Techniques, Base Composition, Clostridium/*classification/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, India, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 427 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 755) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-755 | |||
| 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 | |
| 60650 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 55582) | https://www.ccug.se/strain?id=55582 | |||
| 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/ | ||||
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
| 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 | |||
| 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 | |||
| 72133 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID125932.1 | StrainInfo: A central database for resolving microbial strain identifiers |