Strain identifier
BacDive ID: 132400
Type strain: 
Species: Kroppenstedtia pulmonis
Strain Designation: 165-08, W9323
Strain history: <- M. Bell, CDC; W9323 <- New York State Health Department
NCBI tax ID(s): 1380685 (species)
version 8.1 (current version)
General
@ref: 24189
BacDive-ID: 132400
DSM-Number: 45752
keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, thermophilic, Gram-positive, human pathogen
description: Kroppenstedtia pulmonis 165-08 is an aerobe, spore-forming, thermophilic human pathogen that was isolated from lung biopsy of a 78-year-old male patient.
NCBI tax id
- NCBI tax id: 1380685
- Matching level: species
strain history
- @ref: 24189
- history: <- M. Bell, CDC; W9323 <- New York State Health Department
doi: 10.13145/bacdive132400.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Caryophanales
- family: Thermoactinomycetaceae
- genus: Kroppenstedtia
- species: Kroppenstedtia pulmonis
- full scientific name: Kroppenstedtia pulmonis Bell et al. 2016
@ref: 24189
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Bacillales
family: Thermoactinomycetaceae
genus: Kroppenstedtia
species: Kroppenstedtia pulmonis
full scientific name: Kroppenstedtia pulmonis Bell et al. 2016
strain designation: 165-08, W9323
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: positive
- confidence: 100
colony morphology
- @ref: 63456
- incubation period: 6-7 days
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 24189 | BHI MEDIUM (DSMZ Medium 215) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium215.pdf | |
| 24189 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium535.pdf | |
| 24189 | TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) | yes | https://mediadive.dsmz.de/medium/535a | Name: TRYPTICASE SOY BROTH AGAR+BLOOD (DSMZ Medium 535a) Composition: None 50.0 g/l Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 63456 | positive | growth | 42 | thermophilic |
| 24189 | positive | growth | 45 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 63456
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | yes | 100 |
| 69480 | yes | 100 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 24189 | lung biopsy of a 78-year-old male patient | New York | USA | USA | North America | |
| 63456 | Human lung sample | New York | USA | USA | North America | 2008 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Infection | #Patient | #Biopsy |
| #Infection | #Patient | |
| #Host Body-Site | #Oral cavity and airways | #Lung |
| #Host | #Human | #Male |
taxonmaps
- @ref: 69479
- File name: preview.99_117377.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_358;96_46474;97_59657;98_79251;99_117377&stattab=map
- Last taxonomy: Kroppenstedtia pulmonis subclade
- 16S sequence: KC875234
- Sequence Identity:
- Total samples: 1760
- soil counts: 989
- aquatic counts: 142
- animal counts: 432
- plant counts: 197
Safety information
risk assessment
- @ref: 24189
- pathogenicity human: yes, in single cases
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 24189
- description: Kroppenstedtia pulmonis strain W9323 16S ribosomal RNA gene, partial sequence
- accession: KC875234
- length: 1473
- database: ena
- NCBI tax ID: 1380685
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Kroppenstedtia pulmonis W9323 | GCA_013265585 | complete | ncbi | 1380685 |
| 66792 | Kroppenstedtia pulmonis W9323 | 2910262097 | complete | img | 1380685 |
GC content
- @ref: 24189
- GC-content: 45.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | yes | 100 | no |
| motile | no | 80.768 | no |
| flagellated | no | 91.437 | no |
| gram-positive | yes | 88.416 | no |
| anaerobic | no | 98.239 | yes |
| aerobic | yes | 93.027 | no |
| halophile | no | 67.133 | no |
| spore-forming | yes | 94.31 | no |
| glucose-util | yes | 89.57 | no |
| thermophile | yes | 96.848 | yes |
| glucose-ferment | no | 93.213 | no |
External links
@ref: 24189
culture collection no.: DSM 45752, CCUG 68107
straininfo link
- @ref: 90742
- straininfo: 400135
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 26910402 | Kroppenstedtia pulmonis sp. nov. and Kroppenstedtia sanguinis sp. nov., isolated from human patients. | Bell ME, Lasker BA, Klenk HP, Hoyles L, Sproer C, Schumann P, Brown JM | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0663-z | 2016 | Adolescent, Aged, Bacterial Typing Techniques, DNA, Bacterial/genetics, Female, Gram-Positive Bacterial Infections/blood/cerebrospinal fluid/*microbiology, Humans, Lung/microbiology, Male, Middle Aged, Phylogeny, RNA, Ribosomal, 16S/genetics, Spores, Bacterial/cytology, Thermoactinomyces/classification/cytology/genetics/*isolation & purification | Pathogenicity |
| 33122418 | Complete and Circularized Genome Assemblies of the Kroppenstedtia eburnea Genus Type Strain and the Kroppenstedtia pulmonis Species Type Strain with MiSeq and MinION Sequence Data. | Gulvik CA, Batra D, Rowe LA, Sheth M, Humrighouse BW, Howard DT, Lee J, McQuiston JR, Lasker BA | Microbiol Resour Announc | 10.1128/MRA.00650-20 | 2020 |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |
| 24189 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45752 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45752) | |
| 63456 | Curators of the CCUG | https://www.ccug.se/strain?id=68107 | Culture Collection University of Gothenburg (CCUG) (CCUG 68107) | |
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |
| 90742 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID400135.1 |