Strain identifier
BacDive ID: 132007
Type strain:
Species: Thermobifida alba
Strain Designation: A-0077, 1900
Strain history: CIP <- 1998, JCM <- KCC: strain A-0077 <- K. Locci, IPV: strain 1900
NCBI tax ID(s): 53522 (species)
General
@ref: 11250
BacDive-ID: 132007
DSM-Number: 43795
keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-positive, rod-shaped
description: Thermobifida alba A-0077 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from garden soil.
NCBI tax id
- NCBI tax id: 53522
- Matching level: species
strain history
@ref | history |
---|---|
11250 | <- NBRC; NBRC 16095 <- IFO; 16095 <- JCM; 3077 <- KACC; KCC A-0077 <- Inst. di Pathol. Veg., Italy; IPV 1900 |
67770 | KCC A-0077 <-- IPV 1900. |
116180 | CIP <- 1998, JCM <- KCC: strain A-0077 <- K. Locci, IPV: strain 1900 |
doi: 10.13145/bacdive132007.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Streptosporangiales
- family: Nocardiopsidaceae
- genus: Thermobifida
- species: Thermobifida alba
- full scientific name: Thermobifida alba (Locci et al. 1967) Zhang et al. 1998
synonyms
@ref synonym 20215 Actinobifida alba 20215 Thermomonospora mesouviformis 20215 Thermomonospora alba
@ref: 11250
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Nocardiopsaceae
genus: Thermobifida
species: Thermobifida alba
full scientific name: Thermobifida alba (Locci et al. 1967) Zhang et al. 1998
strain designation: A-0077, 1900
type strain: yes
Morphology
cell morphology
- @ref: 116180
- gram stain: positive
- cell shape: rod-shaped
- motility: no
multimedia
- @ref: 11250
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43795.jpg
- caption: Medium 65 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
11250 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
39322 | MEDIUM 287 - for Thermobifida alba | yes | Distilled water make up to (1000.000 ml);Iron (II) sulphate heptahydrate (0.500 g);Sodium nitrate (3.000 g);Magnesium sulphate heptahydrate (0.500 g);Agar (13.000 g);Yeast extract (2.000 g);Sucrose (30.000 g);Casamino acids (6.100 g);L-Tryptophan (0.020 g | |
11250 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium65.pdf | |
116180 | CIP Medium 287 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=287 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
11250 | positive | growth | 37 | mesophilic |
39322 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
116180 | positive | growth | 22-41 | |
116180 | no | growth | 5 | psychrophilic |
116180 | no | growth | 15 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 116180
- oxygen tolerance: obligate aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
116180 | NaCl | positive | growth | 2 % |
116180 | NaCl | no | growth | 0 % |
116180 | NaCl | no | growth | 4 % |
116180 | NaCl | no | growth | 6 % |
116180 | NaCl | no | growth | 8 % |
116180 | NaCl | no | growth | 10 % |
observation
- @ref: 67770
- observation: quinones: MK-10(H6), MK-10(H8), MK-10(H10), MK-11(H8)
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | + | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | gluconate | - | builds acid from | 24265 |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | turanose | - | builds acid from | 32528 |
68371 | gentiobiose | - | builds acid from | 28066 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | glycogen | + | builds acid from | 28087 |
68371 | starch | - | builds acid from | 28017 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | trehalose | - | builds acid from | 27082 |
68371 | sucrose | - | builds acid from | 17992 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | maltose | - | builds acid from | 17306 |
68371 | salicin | - | builds acid from | 17814 |
68371 | esculin | + | builds acid from | 4853 |
68371 | arbutin | - | builds acid from | 18305 |
68371 | amygdalin | - | builds acid from | 27613 |
68371 | N-acetylglucosamine | - | builds acid from | 59640 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
116180 | esculin | + | hydrolysis | 4853 |
116180 | nitrate | - | reduction | 17632 |
116180 | nitrite | - | reduction | 16301 |
116180 | glucose | - | degradation | 17234 |
116180 | nitrate | - | respiration | 17632 |
metabolite production
- @ref: 116180
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
116180 | 15688 | acetoin | - | |
116180 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
116180 | oxidase | - | |
116180 | alcohol dehydrogenase | - | 1.1.1.1 |
116180 | gelatinase | + | |
116180 | amylase | + | |
116180 | DNase | + | |
116180 | caseinase | + | 3.4.21.50 |
116180 | catalase | + | 1.11.1.6 |
116180 | tween esterase | + | |
116180 | gamma-glutamyltransferase | - | 2.3.2.2 |
116180 | lecithinase | + | |
116180 | lipase | + | |
116180 | lysine decarboxylase | - | 4.1.1.18 |
116180 | ornithine decarboxylase | - | 4.1.1.17 |
116180 | protease | + | |
116180 | tryptophan deaminase | - | |
116180 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | - | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116180 | - | + | + | + | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
116180 | - | - | - | - | +/- | +/- | - | - | - | - | +/- | +/- | +/- | +/- | - | - | - | - | - | - | - | - | - | - | + | - | +/- | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | +/- | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
11250 | garden soil | Milano | Italy | ITA | Europe |
67770 | Garden soil | Milan | Italy | ITA | Europe |
116180 | Environment, Garden soil |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Terrestrial | #Soil |
#Engineered | #Agriculture | #Garden |
taxonmaps
- @ref: 69479
- File name: preview.99_80713.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_595;97_696;98_35937;99_80713&stattab=map
- Last taxonomy: Thermobifida
- 16S sequence: AF002260
- Sequence Identity:
- Total samples: 39
- soil counts: 29
- aquatic counts: 1
- animal counts: 6
- plant counts: 3
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
11250 | 1 | Risk group (German classification) |
116180 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 11250
- description: Thermomonospora alba 16S ribosomal RNA gene, partial sequence
- accession: AF002260
- length: 1468
- database: ena
- NCBI tax ID: 53522
Genome sequences
- @ref: 66792
- description: Thermobifida alba DSM 43795
- accession: GCA_023208015
- assembly level: complete
- database: ncbi
- NCBI tax ID: 53522
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 97.872 | no |
gram-positive | yes | 90.08 | no |
anaerobic | no | 98.628 | no |
aerobic | yes | 83.886 | no |
halophile | no | 63.276 | no |
spore-forming | yes | 89.767 | no |
motile | no | 93.631 | no |
glucose-ferment | no | 92.675 | no |
thermophile | no | 92.52 | yes |
glucose-util | yes | 84.326 | no |
External links
@ref: 11250
culture collection no.: DSM 43795, CECT 3324, CIP 105591, CUB 1002, CUB 432, DSM 43310, IFM 1271, IFO (now NBRC) 15853, IFO (now NBRC) 16095, IMET 9528, IMSNU 22187, JCM 3077, KCC A-0077, KCTC 9618, NBRC 15853, NBRC 16095, NCIB 10169, IPV 1900, IFO 15853, IFO 16095, NCIMB 10169
straininfo link
- @ref: 90393
- straininfo: 50429
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12148627 | Thermobifida cellulolytica sp. nov., a novel lignocellulose-decomposing actinomycete. | Kukolya J, Nagy I, Laday M, Toth E, Oravecz O, Marialigeti K, Hornok L | Int J Syst Evol Microbiol | 10.1099/00207713-52-4-1193 | 2002 | Actinomycetales/chemistry/*classification/genetics/physiology, Bacterial Typing Techniques, Base Composition, Cellulose/*metabolism, DNA, Ribosomal, Genes, rRNA, Lignin/*metabolism, Manure/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S, *Refuse Disposal, Sequence Analysis, DNA, Spores, Bacterial/physiology/ultrastructure | Metabolism |
Metabolism | 32841608 | Biotransformation of cladribine by a nanostabilized extremophilic biocatalyst. | Rivero CW, De Benedetti EC, Sambeth J, Trelles JA | J Biotechnol | 10.1016/j.jbiotec.2020.08.012 | 2020 | Acrylic Resins, Antineoplastic Agents/therapeutic use, Biosynthetic Pathways, *Biotransformation, Cladribine/*metabolism/therapeutic use, Deoxyadenosines, Extremophiles/*physiology, Geobacillus, Leukemia, Hairy Cell/drug therapy, Nanocomposites, Temperature, Thermobifida/growth & development/metabolism |
Reference
@id | authors | catalogue | doi/url | title |
---|---|---|---|---|
11250 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43795) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-43795 | |
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 | |
39322 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/17627 | ||
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/ | ||
68371 | Automatically annotated from API 50CH acid | |||
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 | |
90393 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID50429.1 | StrainInfo: A central database for resolving microbial strain identifiers | |
116180 | Curators of the CIP | Collection of Institut Pasteur (CIP 105591) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105591 |