Strain identifier

BacDive ID: 2601

Type strain: Yes

Species: Hathewaya histolytica

Strain Designation: Weinberg, LRA 050 07 85

Strain history: CIP <- 1993, R. Mercier, bioMérieux, La Balme les Grottes, France: strain LRA 050 07 85 <- 1985, Analytab, Plainview, USA

NCBI tax ID(s): 1498 (species)

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General

@ref: 984

BacDive-ID: 2601

DSM-Number: 2158

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

description: Hathewaya histolytica Weinberg is an anaerobe, spore-forming, mesophilic bacterium that forms circular colonies and was isolated from gas gangrene.

NCBI tax id

  • NCBI tax id: 1498
  • Matching level: species

strain history

@refhistory
984<- NCIB <- NCTC, strain Weinberg <- M. Robertson <- M. Weinberg
67770ATCC 19401 <-- NCTC 503 <-- M. Robertson <-- M. Weinberg.
119925CIP <- 1993, R. Mercier, bioMérieux, La Balme les Grottes, France: strain LRA 050 07 85 <- 1985, Analytab, Plainview, USA

doi: 10.13145/bacdive2601.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacillota
  • domain: Bacteria
  • phylum: Bacillota
  • class: Clostridia
  • order: Eubacteriales
  • family: Clostridiaceae
  • genus: Hathewaya
  • species: Hathewaya histolytica
  • full scientific name: Hathewaya histolytica (Weinberg and Séguin 1916) Lawson and Rainey 2016

  • synonyms

    @refsynonym
    20215Clostridium histolyticum
    20215Bacillus histolyticus

@ref: 984

domain: Bacteria

phylum: Firmicutes

class: Clostridia

order: Clostridiales

family: Clostridiaceae

genus: Hathewaya

species: Hathewaya histolytica

full scientific name: Hathewaya histolytica (Weinberg and Séguin 1916) Lawson and Rainey 2016

strain designation: Weinberg, LRA 050 07 85

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangement
43779positive1.3-9.2 µm0.5-0.9 µmrod-shapedyesperitrichous
119925positiverod-shapedyes

colony morphology

@reftype of hemolysishemolysis abilitycolony sizecolony colorcolony shapemedium used
43779beta10.5-2 mmGrey-whitecircularBlood agar plates
119925

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
984CHOPPED MEAT MEDIUM (DSMZ Medium 78)yeshttps://mediadive.dsmz.de/medium/78Name: CHOPPED MEAT MEDIUM (DSMZ Medium 78) Composition: Ground beef 500.0 g/l Casitone 30.0 g/l Agar 15.0 g/l Ethanol 9.5 g/l (optional) K2HPO4 5.0 g/l Yeast extract 5.0 g/l L-Cysteine HCl 0.5 g/l Haemin 0.005 g/l (optional) Resazurin 0.001 g/l Vitamin K3 0.0005 g/l (optional) Vitamin K1 (optional) NaOH (optional) Distilled water
38136MEDIUM 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)
43779Blood agar platesyes
119925CIP Medium 20yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20

culture temp

@refgrowthtypetemperature
984positivegrowth37
38136positivegrowth37
43779positiveoptimum37
44794positivegrowth37
67770positivegrowth37

culture pH

  • @ref: 43779
  • ability: positive
  • type: optimum
  • pH: 8.5
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
984anaerobe
44794anaerobe
119925anaerobe
125438anaerobe90.913
125439anaerobe99.8

spore formation

@refspore descriptiontype of sporespore formation
43779Oval, central to subterminal, and may slightly sewll the cellsporeyes
119925yes

observation

@refobservation
43779Supernatant culture fluids are toxic to mice
43779Strains are highly pathogenic to laboratory animals

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4377926986threonine+assimilation
43779casein+degradation
437793815collagen+degradation
437794767elastin+degradation
437795054fibrin+degradation
437795291gelatin+degradation
43779meat extract+degradation
43779milk+degradation
4377929016arginine+energy source
4377935391aspartate+energy source
4377929987glutamate+energy source
4377915428glycine+energy source
4377917822serine+energy source
1199254853esculin-hydrolysis
11992517632nitrate-reduction
11992516301nitrite-reduction
11992517632nitrate+respiration

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitive
4377917698chloramphenicolyesyes
437793745clindamycinyesyes
4377948923erythromycinyesyes
4377918208penicillin gyesyes
4377927902tetracyclineyesyes

metabolite production

@refChebi-IDmetaboliteproduction
4377916449alanineyes
4377916134ammoniayes
4377918276dihydrogenyes
4377916136hydrogen sulfideyes
4377924898isoleucineyes
4377925017leucineyes
4377925094lysineyes
4377926271prolineyes
4377927266valineyes
11992535581indoleno

enzymes

@refvalueactivityec
43779DNase+
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
119925oxidase-
119925beta-galactosidase+3.2.1.23
119925gelatinase+/-
119925amylase-
119925DNase+
119925caseinase+3.4.21.50
119925catalase-1.11.1.6
119925tween esterase-
119925lecithinase-
119925lipase-
119925protease+
119925urease-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
119925-----+--+--+--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119925---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typesampling date
984gas gangrene
43779Soil, war wounds, gas gangrene in humans and horses, human intestinal contents; gingival plaque of institutionalized and primitive populations
44794Gas gangrene1916
67770Gas gangrene
119925Human, Gangrene

isolation source categories

Cat1Cat2Cat3
#Infection#Disease
#Environmental#Terrestrial#Soil
#Host#Human
#Host Body-Site#Gastrointestinal tract
#Host Body-Site#Oral cavity and airways#Gingiva
#Host Body-Site#Oral cavity and airways#Plaque

taxonmaps

  • @ref: 69479
  • File name: preview.99_21415.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_34;96_10839;97_13127;98_16153;99_21415&stattab=map
  • Last taxonomy: Hathewaya histolytica subclade
  • 16S sequence: HF558362
  • Sequence Identity:
  • Total samples: 1657
  • soil counts: 97
  • aquatic counts: 299
  • animal counts: 1240
  • plant counts: 21

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
9842Risk group (German classification)
1199252Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Clostridium histolyticum 16S ribosomal RNAM590941465nuccore1498
20218Clostridium histolyticum partial 16S rRNA gene, strain ATCC 19401HF5583621460nuccore1498
20218Clostridium histolyticum strain DSM 2158 16S ribosomal RNA gene, partial sequenceHM245945745nuccore1498
984Clostridium histolyticum gene for 16S ribosomal RNA, partial sequenceAB5664161476nuccore1498

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Hathewaya histolytica NCTC503GCA_901482605completencbi1498
66792Hathewaya histolytica strain NCTC5031498.4completepatric1498

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes79.119yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)yes90.913no
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no97.483yes
125438spore-formingspore-formingAbility to form endo- or exosporesyes81.461yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno88.44yes
125438motile2+flagellatedAbility to perform flagellated movementyes80.834yes
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes69.6
125439BacteriaNetmotilityAbility to perform movementyes72.3
125439BacteriaNetgram_stainReaction to gram-stainingpositive81.1
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthanaerobe99.8

External links

@ref: 984

culture collection no.: DSM 2158, ATCC 19401, BCRC 10644, CCUG 4854, CIP 103713, CN 1693, JCM 1403, NCIMB 503, NCTC 503, CECT 4109, KCTC 5010

straininfo link

  • @ref: 72132
  • straininfo: 36971

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Enzymology7961400Cloning and nucleotide sequence analysis of the colH gene from Clostridium histolyticum encoding a collagenase and a gelatinase.Yoshihara K, Matsushita O, Minami J, Okabe AJ Bacteriol10.1128/jb.176.21.6489-6496.19941994Amino Acid Sequence, Base Sequence, Blotting, Southern, Chromosomes, Bacterial, Cloning, Molecular, Clostridium/enzymology/*genetics, Collagenases/*genetics/isolation & purification/metabolism, Gelatinases/*genetics/metabolism, Genes, Bacterial/*genetics, Molecular Sequence Data, Peptide Fragments/chemistry, Peptide Mapping, Restriction Mapping, Sequence Analysis, Sequence Homology, Amino Acid, Structure-Activity RelationshipTranscriptome
Phylogeny23811141Oceanirhabdus sediminicola gen. nov., sp. nov., an anaerobic bacterium isolated from sea sediment.Pi RX, Zhang WW, Fang MX, Zhang YZ, Li TT, Wu M, Zhu XFInt J Syst Evol Microbiol10.1099/ijs.0.051243-02013Bacteria, 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, Molecular Sequence Data, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNAEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
984Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2158)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2158
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
38136Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15541
43779Paul A. Lawson, Fred A. Rainey10.1099/ijsem.0.000824Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related speciesIJSEM 66: 1009-1016 201626643615
44794Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 4854)https://www.ccug.se/strain?id=4854
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
72132Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID36971.1StrainInfo: A central database for resolving microbial strain identifiers
119925Curators of the CIPCollection of Institut Pasteur (CIP 103713)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103713
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