Strain identifier
BacDive ID: 131413
Type strain: 
Species: Allochromatium humboldtianum
Strain Designation: AX1YC10, AX1YPE
Strain history: <- Wilbert Serrano, Universitat Bremen
NCBI tax ID(s): 504901 (species)
version 8.1 (current version)
General
@ref: 22640
BacDive-ID: 131413
DSM-Number: 21881
keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, motile, rod-shaped
description: Allochromatium humboldtianum AX1YC10 is an anaerobe, mesophilic, motile bacterium that was isolated from shallow water, soft marine sediments.
NCBI tax id
- NCBI tax id: 504901
- Matching level: species
strain history
| @ref | history |
|---|---|
| 22640 | <- W. Serrano, Univ. Bremen, Germany; AX1YC10 |
| 67771 | <- Wilbert Serrano, Universitat Bremen |
doi: 10.13145/bacdive131413.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Chromatiales
- family: Chromatiaceae
- genus: Allochromatium
- species: Allochromatium humboldtianum
- full scientific name: Allochromatium humboldtianum Serrano et al. 2015
@ref: 22640
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Chromatiales
family: Chromatiaceae
genus: Allochromatium
species: Allochromatium humboldtianum
full scientific name: Allochromatium humboldtianum Serrano et al. 2015
strain designation: AX1YC10, AX1YPE
type strain: yes
Morphology
cell morphology
| @ref | cell shape | motility | flagellum arrangement | gram stain | confidence |
|---|---|---|---|---|---|
| 67771 | rod-shaped | yes | monotrichous, polar | ||
| 67771 | negative | ||||
| 69480 | yes | 96.413 | |||
| 69480 | negative | 100 |
Culture and growth conditions
culture medium
- @ref: 22640
- name: PFENNIG'S MEDIUM I (modified 1988, for purple sulfur bacteria) (DSMZ Medium 28)
- growth: yes
- link: https://mediadive.dsmz.de/medium/28
- composition: Name: PFENNIG'S MEDIUM I (DSMZ Medium 28; with strain-specific modifications) Composition: NaCl 30.0 g/l NaHCO3 1.5 g/l Na2S x 9 H2O 0.592592 g/l MgSO4 x 7 H2O 0.500001 g/l Ammonium chloride 0.349999 g/l KCl 0.349999 g/l KH2PO4 0.349999 g/l CaCl2 x 2 H2O 0.25 g/l Yeast extract 0.25 g/l Ammonium acetate 0.25 g/l Pyruvic acid sodium salt 0.25 g/l Dextrose 0.25 g/l Na2-EDTA 0.003 g/l Resazurin 0.00225 g/l FeSO4 x 7 H2O 0.0011 g/l Vitamin B12 0.001 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 2 H2O 5e-05 g/l ZnCl2 4.2e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Na2MoO4 x 2 H2O 1.8e-05 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 22640 | positive | growth | 30 | mesophilic |
| 67771 | positive | growth | 25 | mesophilic |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance | confidence |
|---|---|---|
| 67771 | anaerobe | |
| 69480 | anaerobe | 98.898 |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.981 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
|---|---|---|---|---|---|---|---|
| 22640 | shallow water, soft marine sediments | central coast, Callao Bay (12° 02' S 72° 13' W) at a depth of 47 m | Peru | PER | Middle and South America | -12.051 | -77.129 |
| 67771 | From marine coastal sediments at 47 m depth in Callao Bay | central coast | Peru | PER | Middle and South America |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Aquatic | #Sediment |
Safety information
risk assessment
- @ref: 22640
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22640
- description: Allochromatium humboldtianum strain AX1YPE 16S ribosomal RNA gene, partial sequence
- accession: EU442182
- length: 1451
- database: ena
- NCBI tax ID: 504901
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Allochromatium humboldtianum DSM 21881 | GCA_013385175 | contig | ncbi | 504901 |
| 66792 | Allochromatium humboldtianum strain DSM 21881 | 504901.4 | wgs | patric | 504901 |
| 66792 | Allochromatium humboldtianum DSM 21881 | 2914811602 | draft | img | 504901 |
GC content
- @ref: 22640
- GC-content: 63.9
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 99.09 | yes |
| anaerobic | yes | 97.826 | yes |
| halophile | no | 92.473 | no |
| spore-forming | no | 90.727 | no |
| glucose-util | yes | 61.19 | no |
| aerobic | no | 94.485 | no |
| thermophile | no | 94.439 | yes |
| motile | yes | 90.506 | yes |
| flagellated | yes | 52.435 | no |
| glucose-ferment | no | 83.783 | no |
External links
@ref: 22640
culture collection no.: DSM 21881, KCTC 15448
straininfo link
- @ref: 89842
- straininfo: 407631
literature
- topic: Phylogeny
- Pubmed-ID: 26025943
- title: Allochromatium humboldtianum sp. nov., isolated from soft coastal sediments.
- authors: Serrano W, Schrubbers J, Amann R, Fischer U
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000364
- year: 2015
- mesh: Bacterial Typing Techniques, Bacteriochlorophyll A/metabolism, Base Composition, Carotenoids/metabolism, Chromatiaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Peru, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA
- topic2: Metabolism
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 | |
| 22640 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-21881 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21881) | |
| 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 | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 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 | |
| 89842 | 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-ID407631.1 |