Strain identifier

BacDive ID: 2704

Type strain: Yes

Species: Lacrimispora sphenoides

Strain Designation: Thorlby, Tholby, 10086

Strain history: CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10086 <- NCTC <- M. Robertson, Lister Inst., UK: strain Tholby

NCBI tax ID(s): 1297793 (strain), 29370 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 9.3 (current version)

General

@ref: 334

BacDive-ID: 2704

DSM-Number: 632

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, spore-forming, mesophilic, motile, rod-shaped

description: Lacrimispora sphenoides Thorlby is an anaerobe, spore-forming, mesophilic bacterium that was isolated from human gas gangrene.

NCBI tax id

NCBI tax idMatching level
1297793strain
29370species

strain history

@refhistory
334<- G. Gottschalk <- NCIB <- NCTC <- M. Robertson, strain Thorlby
67770ATCC 19403 <-- NCTC 507 <-- M. Robertson strain Thorlby.
123259CIP <- 1994, J.P. Carlier, Inst. Pasteur, Paris, France: strain 10086 <- NCTC <- M. Robertson, Lister Inst., UK: strain Tholby

doi: 10.13145/bacdive2704.20250331.9.3

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 sphenoides
  • full scientific name: Lacrimispora sphenoides (Douglas et al. 1919) Haas and Blanchard 2020

  • synonyms

    @refsynonym
    20215Desulfotomaculum guttoideum
    20215Bacillus sphenoides
    20215Clostridium sphenoides

@ref: 334

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Lachnospiraceae

genus: Lacrimispora

species: Lacrimispora sphenoides

full scientific name: Lacrimispora sphenoides (Douglas et al. 1919) Haas and Blanchard 2020

strain designation: Thorlby, Tholby, 10086

type strain: yes

Morphology

cell morphology

  • @ref: 123259
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 123259

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
334CHOPPED MEAT MEDIUM WITH CARBOHYDRATES (DSMZ Medium 110)yeshttps://mediadive.dsmz.de/medium/110Name: 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
41095MEDIUM 20 - for Anaerobic bacteriayesAgar (15.000 g);Glucose (5.000 g);Yeast extract (20.000 g);Tryptone (30.000 g);Cysteine hydrochloride (0.500 g);distilled water (1000.000 ml);Hemin solution -M00149 (25.000 ml)
123259CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
334positivegrowth37
41095positivegrowth37
67770positivegrowth37
123259positivegrowth37

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
334anaerobe
125439anaerobe96.8

spore formation

  • @ref: 125439
  • spore formation: yes
  • confidence: 90.8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1232594853esculin+hydrolysis
123259132112sodium thiosulfate-builds gas from

antibiotic resistance

  • @ref: 123259
  • ChEBI: 6909
  • metabolite: metronidazole
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 123259
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase+3.2.1.22
68382acid phosphatase+3.1.3.2
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase (C 4)-
68382esterase lipase (C 8)-
68382alkaline phosphatase+3.1.3.1
123259oxidase-
123259alcohol dehydrogenase-1.1.1.1
123259gelatinase-
123259amylase-
123259DNase+
123259caseinase-3.4.21.50
123259catalase-1.11.1.6
123259lysine decarboxylase-4.1.1.18
123259ornithine decarboxylase-4.1.1.17
123259urease-3.5.1.5
68382alpha-glucosidase+3.2.1.20

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123259-+--------+-++-++---

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
334human gas gangrene
67770Human gas gangrene
123259Human, Gas gangreneUnited KingdomGBREurope1920

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Host#Human
#Host#Microbial#Bacteria

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
3342Risk group (German classification)
1232592Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium sphenoides strain DSM 632 16S ribosomal RNA gene, partial sequenceHM245951846nuccore1297793
20218Clostridium sphenoides 16S rRNA gene, strain DSM 632X734491522nuccore1297793
334Clostridium sphenoides gene for 16S rRNA, partial sequence, strain: ATCC 19403AB0757721504nuccore1297793
67770[Clostridium] sphenoides gene for 16S ribosomal RNA, partial sequence, strain: JCM 1415LC0538401493nuccore1297793
124043Lacrimispora sphenoides DSM 632 gene for 16S rRNA, partial sequence.LC752451162nuccore1297793

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Clostridium] sphenoides JCM 1415 ATCC 19403GCA_900105615chromosomencbi1297793
66792[Clostridium] sphenoides JCM 14151297793.5wgspatric1297793
66792[Clostridium] sphenoides JCM 14151297793.6completepatric1297793
66792[Clostridium] sphenoides strain NCTC50729370.3wgspatric29370
66792Lachnoclostridium sphenoides ATCC 194032675902961draftimg1297793
66792Lachnoclostridium sphenoides JCM 14152728369722draftimg1297793
66792Lachnoclostridium sphenoides NCTC 5072808606748draftimg29370
67770[Clostridium] sphenoides JCM 1415GCA_001312385contigncbi1297793
67770Lacrimispora sphenoides NCTC507GCA_900461315contigncbi29370

GC content

@refGC-contentmethod
33441.0
6777041thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes58.653no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes89.412yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes71.93no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no93.74yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.209yes
125438motile2+flagellatedAbility to perform flagellated movementyes75.72no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes90.8
125439BacteriaNetmotilityAbility to perform movementyes87.4
125439BacteriaNetgram_stainReaction to gram-stainingvariable80.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe96.8

External links

@ref: 334

culture collection no.: DSM 632, ATCC 19403, NCIB 10627, NCTC 507, JCM 1415, BCRC 14515, CECT 796, CIP 104283, LMG 10390, NCIMB 10627

straininfo link

  • @ref: 72232
  • straininfo: 13622

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism10556712Identification of the syntrophic partners in a coculture coupling anaerobic methanol oxidation to Fe(III) reduction.Daniel R, Warnecke F, Potekhina JS, Gottschalk GFEMS Microbiol Lett10.1111/j.1574-6968.1999.tb08796.x1999Anaerobiosis, Clostridium/classification/genetics/growth & development/*metabolism, Culture Media, Ferric Compounds/*metabolism, Geologic Sediments, Methane/metabolism, Methanol/*metabolism, Oxidation-Reduction, RNA, Ribosomal, 16S/genetics, Shewanella/genetics/isolation & purification, Shewanella putrefaciens/classification/genetics/growth & development/*metabolism, *Water MicrobiologyPhylogeny
Phylogeny24522483Clostridium 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 KCurr Microbiol10.1007/s00284-014-0531-x2014Anaerobiosis, 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 StatesMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
334Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 632)https://www.dsmz.de/collection/catalogue/details/culture/DSM-632
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
41095Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16174
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/
68382Automatically annotated from API zym
72232Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13622.1StrainInfo: A central database for resolving microbial strain identifiers
123259Curators of the CIPCollection of Institut Pasteur (CIP 104283)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104283
124043Isabel Schober, Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1