Strain identifier

BacDive ID: 2850

Type strain: Yes

Species: Clostridium amylolyticum

Strain Designation: SW408

Strain history: <- DSM <- JCM/RIKEN <- X Dong, Graduate School, CAS, Beijing, China, SW408

NCBI tax ID(s): 1121299 (strain), 1121298 (species)

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General

@ref: 16000

BacDive-ID: 2850

DSM-Number: 21864

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

description: Clostridium amylolyticum SW408 is an anaerobe, spore-forming, mesophilic bacterium that was isolated from H2-producing upflow anaerobic sludge blanket reactor.

NCBI tax id

NCBI tax idMatching level
1121299strain
1121298species

strain history

@refhistory
16000<- JCM/RIKEN <- X. Dong, Graduate School, CAS, Beijing, China; SW408
67770X. Dong SW408.
67771<- DSM <- JCM/RIKEN <- X Dong, Graduate School, CAS, Beijing, China, SW408

doi: 10.13145/bacdive2850.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Clostridium
  • species: Clostridium amylolyticum
  • full scientific name: Clostridium amylolyticum Song and Dong 2008

@ref: 16000

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Clostridium

species: Clostridium amylolyticum

full scientific name: Clostridium amylolyticum Song and Dong 2008

strain designation: SW408

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
32527positive2-7.5 µm0.5-0.7 µmrod-shapedyes
67771rod-shapedyesperitrichous
67771positive
69480positive100

pigmentation

  • @ref: 32527
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16000
  • 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

@refgrowthtypetemperaturerange
16000positivegrowth37mesophilic
32527positivegrowth25-45
32527positiveoptimum37mesophilic
67770positivegrowth37mesophilic
67771positivegrowth37mesophilic

culture pH

@refabilitytypepHPH range
32527positivegrowth04-09alkaliphile
32527positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
16000anaerobe
32527anaerobe
67771anaerobe
69480anaerobe98.649

spore formation

@refspore formationconfidence
32527yes
69481yes100
69480yes99.695

observation

  • @ref: 32527
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3252717057cellobiose+carbon source
3252728757fructose+carbon source
3252728260galactose+carbon source
3252717234glucose+carbon source
3252717716lactose+carbon source
3252717306maltose+carbon source
3252729864mannitol+carbon source
3252737684mannose+carbon source
3252733942ribose+carbon source
3252717992sucrose+carbon source
3252727082trehalose+carbon source
325274853esculin+hydrolysis

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
16000H2-producing upflow anaerobic sludge blanket reactorChinaCHNAsia
67770Laboratory-scale H2-producing upflow anaerobic sludge blanket reactor
67771From laboratory-scale H_2_-producing upflow anaerobic sludge blanket reactorChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Environmental#Terrestrial#Mud (Sludge)
#Condition#Anoxic (anaerobic)

taxonmaps

  • @ref: 69479
  • File name: preview.99_8283.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_1231;97_1458;98_6028;99_8283&stattab=map
  • Last taxonomy: Clostridium amylolyticum subclade
  • 16S sequence: NR_044386
  • Sequence Identity:
  • Total samples: 648
  • soil counts: 141
  • aquatic counts: 119
  • animal counts: 367
  • plant counts: 21

Safety information

risk assessment

  • @ref: 16000
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
16000Clostridium amylolyticum strain SW408 16S ribosomal RNA gene, partial sequenceEU0379031505ena1121298
67771Clostridium amylolyticum strain SW408 16S ribosomal RNA, partial sequenceNR_0443861505nuccore1121298

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Clostridium amylolyticum strain DSM 218641121298.3wgspatric1121298
66792Clostridium amylolyticum DSM 218642703719061draftimg1121298
67771Clostridium amylolyticum DSM 21864GCA_900142075scaffoldncbi1121298

GC content

@refGC-contentmethod
1600033.1thermal denaturation, midpoint method (Tm)
3252733.1

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileyes84.761no
flagellatedyes71.517yes
gram-positiveyes85.555yes
anaerobicyes97.095yes
aerobicno96.574yes
halophileno94.831no
spore-formingyes93.753yes
thermophileno94.788yes
glucose-utilyes88.939no
glucose-fermentyes67.945no

External links

@ref: 16000

culture collection no.: DSM 21864, AS 1.5069, CGMCC 1.5069, JCM 14823, KCTC 15216

straininfo link

  • @ref: 72374
  • straininfo: 402220

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18768618Clostridium amylolyticum sp. nov., isolated from H2-producing UASB granules.Song L, Dong XInt J Syst Evol Microbiol10.1099/ijs.0.65635-02008Acetates/metabolism, Amylopectin/metabolism, Anaerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carbon Dioxide/metabolism, Clostridium/*classification/genetics/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Ethanol/metabolism, Genes, rRNA, Hydrogen/metabolism, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sewage/*microbiology, TemperatureMetabolism
Phylogeny25103947Clostridium swellfunianum sp. nov., a novel anaerobic bacterium isolated from the pit mud of Chinese Luzhou-flavor liquor production.Liu C, Huang D, Liu L, Zhang J, Deng Y, Chen L, Zhang W, Wu Z, Fan A, Lai D, Dai LAntonie Van Leeuwenhoek10.1007/s10482-014-0251-z2014Anaerobiosis, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Carbohydrates/analysis, Cell Wall/chemistry, China, Clostridium/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Ethanol/metabolism, Fatty Acids/analysis, *Food Microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Peptidoglycan/analysis, Peptones/metabolism, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16000Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21864)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21864
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
32527Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2874528776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
72374Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402220.1StrainInfo: A central database for resolving microbial strain identifiers