Strain identifier
BacDive ID: 158834
Type strain: 
Species: Agrobacterium sp.
Strain Designation: H13-3
Strain history: <- J. Wittmann, DSMZ and R. Schmitt, Uni Regensburg <-
NCBI tax ID(s): 361 (species)
version 8.1 (current version)
General
@ref: 65656
BacDive-ID: 158834
DSM-Number: 110110
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Agrobacterium sp. H13-3 is a mesophilic bacterium that was isolated from rhizosphere of Lupinus luteus.
NCBI tax id
- NCBI tax id: 361
- Matching level: species
strain history
- @ref: 65656
- history: <- J. Wittmann, DSMZ and R. Schmitt, Uni Regensburg <-
doi: 10.13145/bacdive158834.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Hyphomicrobiales
- family: Rhizobiaceae
- genus: Agrobacterium
- species: Agrobacterium sp.
- full scientific name: Agrobacterium Conn 1942 (Approved Lists 1980)
@ref: 65656
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Hyphomicrobiales
family: Rhizobiaceae
genus: Agrobacterium
species: Agrobacterium sp.
full scientific name: Agrobacterium sp.
strain designation: H13-3
type strain: no
Culture and growth conditions
culture medium
- @ref: 65656
- name: TRYPTONE YEAST EXTRACT AGAR (TYG) (DSMZ Medium 680)
- growth: yes
- link: https://mediadive.dsmz.de/medium/680
- composition: Name: TRYPTONE YEAST EXTRACT AGAR (TYG) (DSMZ Medium 680) Composition: Agar 20.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Tryptone 3.0 g/l Distilled water
culture temp
- @ref: 65656
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 65656
- sample type: rhizosphere of Lupinus luteus
- host species: Lupinus luteus
- geographic location: unknown
- country: Hungary
- origin.country: HUN
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Rhizosphere |
taxonmaps
- @ref: 69479
- File name: preview.99_376.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_6;97_6;98_6;99_376&stattab=map
- Last taxonomy: Agrobacterium
- 16S sequence: CP002248
- Sequence Identity:
- Total samples: 88
- soil counts: 7
- aquatic counts: 6
- animal counts: 33
- plant counts: 42
Sequence information
16S sequences
- @ref: 65656
- description: Agrobacterium sp. H13-3 circular chromosome, complete sequence
- accession: CP002248
- length: 2823930
- database: ena
- NCBI tax ID: 861208
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Agrobacterium sp. H13-3 | 861208.11 | plasmid | patric | 1183401 |
| 66792 | Agrobacterium sp. H13-3 | 861208.3 | complete | patric | 1183401 |
| 66792 | Agrobacterium sp. H13-3 | 650716007 | complete | img | 861208 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 85.015 | no |
| flagellated | no | 68.13 | no |
| gram-positive | no | 98.11 | no |
| anaerobic | no | 97.659 | no |
| halophile | no | 85.821 | no |
| spore-forming | no | 96.86 | no |
| thermophile | no | 99.521 | yes |
| glucose-util | yes | 90.407 | no |
| aerobic | yes | 89.385 | no |
| glucose-ferment | no | 89.842 | no |
External links
@ref: 65656
culture collection no.: DSM 110110
straininfo link
- @ref: 111353
- straininfo: 399074
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Genetics | 21329740 | Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid. | Wibberg D, Blom J, Jaenicke S, Kollin F, Rupp O, Scharf B, Schneiker-Bekel S, Sczcepanowski R, Goesmann A, Setubal JC, Schmitt R, Puhler A, Schluter A | J Biotechnol | 10.1016/j.jbiotec.2011.01.010 | 2011 | Agrobacterium/classification/*genetics/physiology, *Chromosomes, Bacterial, Genes, Bacterial, *Genome, Bacterial, Lupinus/microbiology, Phylogeny, Plasmids/*genetics, Polymerase Chain Reaction, Rhizosphere, Sequence Analysis, DNA | Phylogeny |
| Genetics | 22650361 | Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3. | Kropinski AM, Van den Bossche A, Lavigne R, Noben JP, Babinger P, Schmitt R | Virol J | 10.1186/1743-422X-9-102 | 2012 | Agrobacterium/*virology, Bacteriophages/*genetics/isolation & purification, DNA Viruses/genetics/isolation & purification, DNA, Viral/chemistry/*genetics, Gene Order, *Genome, Viral, Microscopy, Electron, Molecular Sequence Data, Open Reading Frames, Proteome/*analysis, Sequence Analysis, DNA, Viral Proteins/*analysis, Virion/ultrastructure | Proteome |
| 22865074 | Minimum requirements of flagellation and motility for infection of Agrobacterium sp. strain H13-3 by flagellotropic bacteriophage 7-7-1. | Yen JY, Broadway KM, Scharf BE | Appl Environ Microbiol | 10.1128/AEM.01082-12 | 2012 | Agrobacterium/*physiology/*virology, Bacterial Proteins/genetics, Bacteriophages/*growth & development/physiology, Flagella/*physiology/*virology, Flagellin/genetics, Gene Deletion, *Locomotion, Mutation, Missense, Rhizobium, Virus Attachment | ||
| Pathogenicity | 29204058 | Diversity of bacterial lactase genes in intestinal contents of mice with antibiotics-induced diarrhea. | Long CX, He L, Guo YF, Liu YW, Xiao NQ, Tan ZJ | World J Gastroenterol | 10.3748/wjg.v23.i42.7584 | 2017 | Animals, Anti-Bacterial Agents/*adverse effects, Diarrhea/*chemically induced/microbiology, Female, Gastrointestinal Microbiome/*drug effects, *Genes, Bacterial, Lactase/genetics/*metabolism, Male, Mice, Random Allocation | Metabolism |
| Metabolism | 30012730 | More than Rotating Flagella: Lipopolysaccharide as a Secondary Receptor for Flagellotropic Phage 7-7-1. | Gonzalez F, Helm RF, Broadway KM, Scharf BE | J Bacteriol | 10.1128/JB.00363-18 | 2018 | Agrobacterium/genetics/*virology, Bacterial Proteins/genetics/*metabolism, Caudovirales/*physiology, DNA Transposable Elements, DNA, Viral/genetics, Flagella/genetics/*metabolism, Genetic Complementation Test, Lipopolysaccharides/*metabolism, Mutagenesis, Receptors, Virus/genetics/*metabolism, Virus Attachment |
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 | |
| 65656 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-110110 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 110110) | |
| 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/ | |
| 111353 | 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-ID399074.1 |