Strain identifier
BacDive ID: 14351
Type strain: 
Species: Sphaerochaeta globosa
Strain Designation: Buddy
Strain history: <- K. M. Ritalahti, Environmental Engineering, Georgia Inst. Technology, Atlanta, USA; Buddy <- F. E. Löffler {2000}
NCBI tax ID(s): 1131703 (species)
version 8.1 (current version)
General
@ref: 16510
BacDive-ID: 14351
DSM-Number: 22777
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, coccus-shaped
description: Sphaerochaeta globosa Buddy is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from black, anoxic river sediments downstream of an agricultural and residential area.
NCBI tax id
- NCBI tax id: 1131703
- Matching level: species
strain history
- @ref: 16510
- history: <- K. M. Ritalahti, Environmental Engineering, Georgia Inst. Technology, Atlanta, USA; Buddy <- F. E. Löffler {2000}
doi: 10.13145/bacdive14351.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/spirochaetota
- domain: Bacteria
- phylum: Spirochaetota
- class: Spirochaetia
- order: Spirochaetales
- family: Sphaerochaetaceae
- genus: Sphaerochaeta
- species: Sphaerochaeta globosa
- full scientific name: Sphaerochaeta globosa Ritalahti et al. 2012
@ref: 16510
domain: Bacteria
phylum: Spirochaetes
class: Spirochaetia
order: Spirochaetales
family: Sphaerochaetaceae
genus: Sphaerochaeta
species: Sphaerochaeta globosa
full scientific name: Sphaerochaeta globosa Ritalahti et al. 2012
strain designation: Buddy
type strain: yes
Morphology
cell morphology
- @ref: 29882
- gram stain: negative
- cell width: 0.4-2.5 µm
- cell shape: coccus-shaped
- motility: no
colony morphology
- @ref: 16510
- incubation period: 8-14 days
Culture and growth conditions
culture medium
- @ref: 16510
- name: 1/2 TRYPTIC SOY BROTH (ANAEROBE) (DSMZ Medium 1205)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1205
- composition: Name: 1/2 TRYPTIC SOY BROTH (ANAEROBIC) (DSMZ Medium 1205) Composition: Trypticase soy broth 13.75 g/l D-Glucose 3.6 g/l NaCl 2.5 g/l Yeast extract 1.0 g/l DL-Dithiothreitol 0.15 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 16510 | positive | growth | 25 | mesophilic |
| 29882 | positive | growth | 15-37 | |
| 29882 | positive | optimum | 25-30 | mesophilic |
culture pH
- @ref: 29882
- ability: positive
- type: optimum
- pH: 6.5-7.5
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 16510 | anaerobe |
| 29882 | anaerobe |
observation
- @ref: 29882
- observation: aggregates in clumps
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29882 | 28757 | fructose | + | carbon source |
| 29882 | 28260 | galactose | + | carbon source |
| 29882 | 17234 | glucose | + | carbon source |
| 29882 | 17716 | lactose | + | carbon source |
| 29882 | 17306 | maltose | + | carbon source |
| 29882 | 16634 | raffinose | + | carbon source |
| 29882 | 17992 | sucrose | + | carbon source |
| 29882 | 18222 | xylose | + | carbon source |
Isolation, sampling and environmental information
isolation
- @ref: 16510
- sample type: black, anoxic river sediments downstream of an agricultural and residential area
- geographic location: Michigan, Okemos, Red Cedar River
- country: USA
- origin.country: USA
- continent: North America
- latitude: 42.6971
- longitude: -84.3788
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #River (Creek) |
| #Environmental | #Terrestrial | #Sediment |
| #Condition | #Anoxic (anaerobic) |
taxonmaps
- @ref: 69479
- File name: preview.99_3888.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_431;96_1992;97_2394;98_2957;99_3888&stattab=map
- Last taxonomy: Sphaerochaeta globosa
- 16S sequence: AF357916
- Sequence Identity:
- Total samples: 1091
- soil counts: 90
- aquatic counts: 424
- animal counts: 492
- plant counts: 85
Safety information
risk assessment
- @ref: 16510
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16510
- description: Sphaerochaeta globus str. Buddy 16S ribosomal RNA gene, partial sequence
- accession: AF357916
- length: 1534
- database: ena
- NCBI tax ID: 158189
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Sphaerochaeta globosa str. Buddy | GCA_000190435 | complete | ncbi | 158189 |
| 66792 | Sphaerochaeta globosa str. Buddy | 158189.3 | complete | patric | 158189 |
| 66792 | Sphaerochaeta globosa Buddy | 650377973 | complete | img | 158189 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 16510 | 46.5 | high performance liquid chromatography (HPLC) |
| 29882 | 45.5-46.4 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | no | 83.656 | no |
| flagellated | no | 97.196 | no |
| gram-positive | no | 91.49 | no |
| anaerobic | yes | 98.9 | yes |
| aerobic | no | 97.466 | yes |
| halophile | no | 84.886 | no |
| spore-forming | no | 93.338 | no |
| glucose-util | yes | 92.404 | no |
| thermophile | no | 97.045 | yes |
| glucose-ferment | yes | 57.164 | no |
External links
@ref: 16510
culture collection no.: DSM 22777, ATCC BAA 1886
straininfo link
- @ref: 83494
- straininfo: 405818
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 21398503 | Sphaerochaeta globosa gen. nov., sp. nov. and Sphaerochaeta pleomorpha sp. nov., free-living, spherical spirochaetes. | Ritalahti KM, Justicia-Leon SD, Cusick KD, Ramos-Hernandez N, Rubin M, Dornbush J, Loffler FE | Int J Syst Evol Microbiol | 10.1099/ijs.0.023986-0 | 2011 | Aerobiosis, Base Composition, Carbon/metabolism, Cluster Analysis, Culture Media/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Fresh Water/*microbiology, Geologic Sediments/microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Nitrogen/metabolism, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spirochaetales/*classification/cytology/genetics/*isolation & purification, Temperature | Metabolism |
| Phylogeny | 25249566 | Sphaerochaeta multiformis sp. nov., an anaerobic, psychrophilic bacterium isolated from subseafloor sediment, and emended description of the genus Sphaerochaeta. | Miyazaki M, Sakai S, Ritalahti KM, Saito Y, Yamanaka Y, Saito Y, Tame A, Uematsu K, Loffler FE, Takai K, Imachi H | Int J Syst Evol Microbiol | 10.1099/ijs.0.068148-0 | 2014 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Pacific Ocean, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Spirochaetaceae/*classification/genetics/isolation & purification | Genetics |
| Phylogeny | 26341497 | Sphaerochaeta associata sp. nov., a spherical spirochaete isolated from cultures of Methanosarcina mazei JL01. | Troshina O, Oshurkova V, Suzina N, Machulin A, Ariskina E, Vinokurova N, Kopitsyn D, Novikov A, Shcherbakova V | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000575 | 2015 | Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Methanosarcina, Molecular Sequence Data, Nucleic Acid Hybridization, Permafrost/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spirochaetaceae/*classification/genetics/isolation & purification | Genetics |
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 16510 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22777) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22777 | |||
| 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 | |||
| 29882 | 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 | 26255 | 28776041 | |
| 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) | |||
| 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 | |||
| 83494 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405818.1 | StrainInfo: A central database for resolving microbial strain identifiers |