Strain identifier
BacDive ID: 2601
Type strain:
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)
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
@ref | history |
---|---|
984 | <- NCIB <- NCTC, strain Weinberg <- M. Robertson <- M. Weinberg |
67770 | ATCC 19401 <-- NCTC 503 <-- M. Robertson <-- M. Weinberg. |
119925 | CIP <- 1993, R. Mercier, bioMérieux, La Balme les Grottes, France: strain LRA 050 07 85 <- 1985, Analytab, Plainview, USA |
doi: 10.13145/bacdive2601.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Clostridia
- order: Eubacteriales
- family: Clostridiaceae
- genus: Hathewaya
- species: Hathewaya histolytica
- full scientific name: Hathewaya histolytica (Weinberg and Séguin 1916) Lawson and Rainey 2016
synonyms
@ref synonym 20215 Bacillus histolyticus 20215 Clostridium histolyticum
@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
@ref | gram stain | cell length | cell width | cell shape | motility | flagellum arrangement | confidence |
---|---|---|---|---|---|---|---|
43779 | positive | 1.3-9.2 µm | 0.5-0.9 µm | rod-shaped | yes | peritrichous | |
69480 | positive | 100 | |||||
119925 | positive | rod-shaped | yes |
colony morphology
@ref | type of hemolysis | hemolysis ability | colony size | colony color | colony shape | medium used |
---|---|---|---|---|---|---|
43779 | beta | 1 | 0.5-2 mm | Grey-white | circular | Blood agar plates |
119925 |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
984 | CHOPPED MEAT MEDIUM (DSMZ Medium 78) | yes | https://mediadive.dsmz.de/medium/78 | Name: 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 |
38136 | MEDIUM 20 - for Anaerobic bacteria | yes | Agar (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) | |
43779 | Blood agar plates | yes | ||
119925 | CIP Medium 20 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=20 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
984 | positive | growth | 37 | mesophilic |
38136 | positive | growth | 37 | mesophilic |
43779 | positive | optimum | 37 | mesophilic |
44794 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
culture pH
- @ref: 43779
- ability: positive
- type: optimum
- pH: 8.5
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance | confidence |
---|---|---|
984 | anaerobe | |
44794 | anaerobe | |
69480 | anaerobe | 98.648 |
119925 | anaerobe |
spore formation
@ref | spore description | type of spore | spore formation | confidence |
---|---|---|---|---|
43779 | Oval, central to subterminal, and may slightly sewll the cell | spore | yes | |
69481 | yes | 90 | ||
69480 | yes | 99.447 | ||
119925 | yes |
observation
@ref | observation |
---|---|
43779 | Supernatant culture fluids are toxic to mice |
43779 | Strains are highly pathogenic to laboratory animals |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
43779 | 26986 | threonine | + | assimilation |
43779 | casein | + | degradation | |
43779 | 3815 | collagen | + | degradation |
43779 | 4767 | elastin | + | degradation |
43779 | 5054 | fibrin | + | degradation |
43779 | 5291 | gelatin | + | degradation |
43779 | meat extract | + | degradation | |
43779 | milk | + | degradation | |
43779 | 29016 | arginine | + | energy source |
43779 | 35391 | aspartate | + | energy source |
43779 | 29987 | glutamate | + | energy source |
43779 | 15428 | glycine | + | energy source |
43779 | 17822 | serine | + | energy source |
119925 | 4853 | esculin | - | hydrolysis |
119925 | 17632 | nitrate | - | reduction |
119925 | 16301 | nitrite | - | reduction |
119925 | 17632 | nitrate | + | respiration |
antibiotic resistance
@ref | ChEBI | metabolite | is antibiotic | is sensitive |
---|---|---|---|---|
43779 | 17698 | chloramphenicol | yes | yes |
43779 | 3745 | clindamycin | yes | yes |
43779 | 48923 | erythromycin | yes | yes |
43779 | 18208 | penicillin g | yes | yes |
43779 | 27902 | tetracycline | yes | yes |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
43779 | 16449 | alanine | yes |
43779 | 16134 | ammonia | yes |
43779 | 18276 | dihydrogen | yes |
43779 | 16136 | hydrogen sulfide | yes |
43779 | 24898 | isoleucine | yes |
43779 | 25017 | leucine | yes |
43779 | 25094 | lysine | yes |
43779 | 26271 | proline | yes |
43779 | 27266 | valine | yes |
119925 | 35581 | indole | no |
enzymes
@ref | value | activity | ec |
---|---|---|---|
43779 | DNase | + | |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | - | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
119925 | oxidase | - | |
119925 | beta-galactosidase | + | 3.2.1.23 |
119925 | gelatinase | +/- | |
119925 | amylase | - | |
119925 | DNase | + | |
119925 | caseinase | + | 3.4.21.50 |
119925 | catalase | - | 1.11.1.6 |
119925 | tween esterase | - | |
119925 | lecithinase | - | |
119925 | lipase | - | |
119925 | protease | + | |
119925 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119925 | - | - | - | - | - | + | - | - | + | - | - | + | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119925 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | sampling date |
---|---|---|
984 | gas gangrene | |
43779 | Soil, war wounds, gas gangrene in humans and horses, human intestinal contents; gingival plaque of institutionalized and primitive populations | |
44794 | Gas gangrene | 1916 |
67770 | Gas gangrene | |
119925 | Human, Gangrene |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | biosafety level | biosafety level comment |
---|---|---|
984 | 2 | Risk group (German classification) |
119925 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Clostridium histolyticum 16S ribosomal RNA | M59094 | 1465 | ena | 1498 |
20218 | Clostridium histolyticum partial 16S rRNA gene, strain ATCC 19401 | HF558362 | 1460 | ena | 1498 |
20218 | Clostridium histolyticum strain DSM 2158 16S ribosomal RNA gene, partial sequence | HM245945 | 745 | ena | 1498 |
984 | Clostridium histolyticum gene for 16S ribosomal RNA, partial sequence | AB566416 | 1476 | ena | 1498 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Hathewaya histolytica NCTC503 | GCA_901482605 | complete | ncbi | 1498 |
66792 | Hathewaya histolytica strain NCTC503 | 1498.4 | complete | patric | 1498 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | yes | 90 | no |
flagellated | yes | 62.173 | yes |
gram-positive | yes | 91.588 | yes |
anaerobic | yes | 98.587 | yes |
aerobic | no | 97.347 | yes |
halophile | no | 86.179 | no |
spore-forming | yes | 97.231 | yes |
thermophile | no | 98.416 | yes |
glucose-util | yes | 83.078 | no |
motile | yes | 86.566 | yes |
glucose-ferment | yes | 66.112 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Enzymology | 7961400 | Cloning and nucleotide sequence analysis of the colH gene from Clostridium histolyticum encoding a collagenase and a gelatinase. | Yoshihara K, Matsushita O, Minami J, Okabe A | J Bacteriol | 10.1128/jb.176.21.6489-6496.1994 | 1994 | Amino 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 Relationship | Transcriptome |
Phylogeny | 23811141 | Oceanirhabdus 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 XF | Int J Syst Evol Microbiol | 10.1099/ijs.0.051243-0 | 2013 | 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, Molecular Sequence Data, *Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Enzymology |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
984 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2158) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-2158 | |||
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 | |
38136 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/15541 | ||||
43779 | Paul A. Lawson, Fred A. Rainey | 10.1099/ijsem.0.000824 | Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species | IJSEM 66: 1009-1016 2016 | 26643615 | |
44794 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 4854) | https://www.ccug.se/strain?id=4854 | |||
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/ | ||||
68382 | Automatically annotated from API zym | |||||
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 | |||
72132 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID36971.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119925 | Curators of the CIP | Collection of Institut Pasteur (CIP 103713) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103713 |