Strain identifier
BacDive ID: 8583
Type strain:
Species: Mycobacterium mantenii
Strain Designation: 04-1474, NLA000401474
Strain history: CIP <- 2008, J. Van Inge, RIVM, Bilthoven, The Netherlands: strain NLA000401474 <- E. J. Kuijper, Leiden Univ., Leiden, The Netherlands
NCBI tax ID(s): 560555 (species)
General
@ref: 15933
BacDive-ID: 8583
DSM-Number: 45255
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, rod-shaped
description: Mycobacterium mantenii 04-1474 is a mesophilic, rod-shaped bacterium that was isolated from lymph node biopsy of a child.
NCBI tax id
- NCBI tax id: 560555
- Matching level: species
strain history
@ref | history |
---|---|
15933 | <- J. van Ingen; NLA000401474 <- E. J. Kuijper |
67770 | CIP 109863 <-- J. van Ingen NLA000401474 (=04-1474) <-- E. J. Kuijper. |
120782 | CIP <- 2008, J. Van Inge, RIVM, Bilthoven, The Netherlands: strain NLA000401474 <- E. J. Kuijper, Leiden Univ., Leiden, The Netherlands |
doi: 10.13145/bacdive8583.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/actinomycetota
- domain: Bacteria
- phylum: Actinomycetota
- class: Actinomycetes
- order: Mycobacteriales
- family: Mycobacteriaceae
- genus: Mycobacterium
- species: Mycobacterium mantenii
- full scientific name: Mycobacterium mantenii van Ingen et al. 2009
@ref: 15933
domain: Bacteria
phylum: Actinobacteria
class: Actinobacteria
order: Actinomycetales
family: Mycobacteriaceae
genus: Mycobacterium
species: Mycobacterium mantenii
full scientific name: Mycobacterium mantenii van Ingen et al. 2009 emend. Nouioui et al. 2018
strain designation: 04-1474, NLA000401474
type strain: yes
Morphology
cell morphology
@ref | cell shape | gram stain | confidence | motility |
---|---|---|---|---|
29294 | rod-shaped | |||
69480 | positive | 100 | ||
120782 | no |
pigmentation
- @ref: 29294
- production: yes
multimedia
- @ref: 15933
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45255.jpg
- caption: Medium 645 37°C
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
15933 | MIDDLEBROOK MEDIUM (DSMZ Medium 645) | yes | https://mediadive.dsmz.de/medium/645 | Name: MIDDLEBROOK MEDIUM (DSMZ Medium 645) Composition: Bacto Middlebrook 7H10 agar 20.9945 g/l Glycerol Distilled water |
37864 | MEDIUM 55 - for Mycobacterium | yes | ||
120782 | CIP Medium 750 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=750 | |
120782 | CIP Medium 55 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=55 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
15933 | positive | growth | 37 | mesophilic |
29294 | positive | growth | 25-45 | |
29294 | positive | optimum | 36 | mesophilic |
37864 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 37 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
29294 | no | |
69481 | no | 96 |
69480 | no | 99.957 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
120782 | 17632 | nitrate | - | reduction |
120782 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 120782
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
29294 | catalase | + | 1.11.1.6 |
29294 | urease | + | 3.5.1.5 |
120782 | oxidase | - | |
120782 | catalase | + | 1.11.1.6 |
120782 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120782 | - | + | - | + | - | + | - | - | - | - | + | + | - | - | - | + | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
15933 | lymph node biopsy of a child | Leiden | Netherlands | NLD | Europe | |
67770 | Human, lymph node biopsy specimen | Leiden | Netherlands | NLD | Europe | |
120782 | Human, Lymph node biopsy | Leiden | Netherlands | NLD | Europe | 2004 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Infection | #Patient | #Biopsy |
#Infection | #Patient | |
#Host Body-Site | #Organ | #Lymph node |
#Host | #Human | #Child |
taxonmaps
- @ref: 69479
- File name: preview.99_475.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_37;97_39;98_43;99_475&stattab=map
- Last taxonomy: Mycobacterium
- 16S sequence: FJ042897
- Sequence Identity:
- Total samples: 2232
- soil counts: 1602
- aquatic counts: 300
- animal counts: 128
- plant counts: 202
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
15933 | 2 | Risk group (German classification) |
120782 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
15933 | Mycobacterium mantenii strain NLA000401474 16S ribosomal RNA gene, partial sequence | FJ042897 | 1471 | ena | 560555 |
67770 | Mycobacterium mantenii strain NLA000401474 16S-23S ribosomal RNA intergenic spacer, partial sequence | FJ232522 | 281 | ena | 560555 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Mycobacterium mantenii JCM 18113 | GCA_010731775 | complete | ncbi | 560555 |
66792 | Mycobacterium mantenii strain DSM 45255 | 560555.3 | wgs | patric | 560555 |
66792 | Mycobacterium mantenii strain JCM 18113 | 560555.10 | complete | patric | 560555 |
67770 | Mycobacterium mantenii DSM 45255 | GCA_002086335 | contig | ncbi | 560555 |
66792 | Mycobacterium mantenii DSM 45255 | GCA_025822645 | scaffold | ncbi | 560555 |
GC content
- @ref: 67770
- GC-content: 66.9
- method: genome sequence analysis
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 96 | no |
motile | no | 94.164 | no |
flagellated | no | 99.013 | no |
gram-positive | yes | 88.569 | no |
anaerobic | no | 99.012 | no |
aerobic | yes | 89.982 | no |
halophile | no | 92.588 | no |
spore-forming | no | 87.621 | no |
glucose-util | yes | 67.462 | no |
thermophile | no | 97.637 | no |
glucose-ferment | no | 90.778 | no |
External links
@ref: 15933
culture collection no.: DSM 45255, CIP 109863, JCM 18113
straininfo link
- @ref: 77967
- straininfo: 364721
literature
- topic: Phylogeny
- Pubmed-ID: 19625425
- title: Mycobacterium mantenii sp. nov., a pathogenic, slowly growing, scotochromogenic species.
- authors: van Ingen J, Lindeboom JA, Hartwig NG, de Zwaan R, Tortoli E, Dekhuijzen PN, Boeree MJ, van Soolingen D
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.010405-0
- year: 2009
- mesh: Aged, Aged, 80 and over, Bacterial Proteins/genetics, Child, Preschool, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Female, Humans, Infant, Lymph Nodes/microbiology, Male, Molecular Sequence Data, Mycobacterium/classification/*isolation & purification/metabolism/pathogenicity, Mycobacterium Infections/*microbiology, Phylogeny, Pigments, Biological/*metabolism, RNA, Ribosomal, 16S/genetics
- topic2: Pathogenicity
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
15933 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45255) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45255 | |||
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 | |||
29294 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 25710 | 28776041 | |
37864 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7655 | ||||
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/ | ||||
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 | |||
77967 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID364721.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120782 | Curators of the CIP | Collection of Institut Pasteur (CIP 109863) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109863 |