Experts in typing bacterial strains by whole-genome sequencing

A powerful tool to fully characterise your bacterial strain

The increasing global demand and use of microbial biocontrol agents and biofertilisers have prompted efforts in screening for candidate bacterial strains with activity against soil-borne pathogens and/or plant-growth promotion capabilities. Requirements for the registration of microbial-based products include, among others, a precise identification of the bacterial strain, as well as data on the efficacy and safety of the inoculum. Whole-genome sequencing (WGS) has become the gold standard approach for identifying bacteria at the strain level. WGS is a fast and cost-efficient way to generate high-resolution genomic data, which brings a number of advantageous applications for the biocontrol industry, including:

  • Complete characterisation of bacterial strains, to meet the requirements for product registration and patent application.
  • Accurate discrimination of closely related and/or commercial strains.
  • Identification of traits of agronomical interest (e.g., genes related to biological nitrogen fixation, phosphate solubilisation, ACC deaminase activity, and production of siderophores and phytohormones; chemotaxis and flagellar motility genes; secondary metabolic pathways).

At AllGenetics, we use high-throughput sequencing to obtain the annotated genomes of your bacterial strains. To do so we take advantage of Illumina’s MiSeq technology which enables us to obtain the genomes cost-effectively and accurately.

Please note that repetitive genomic regions may be difficult or impossible to assemble using Illumina's short reads. In this case, Illumina's MiSeq sequencing can be complemented with Oxford Nanopore’s MinION or PacBio’s RSII. These are new technologies which provide longer reads that improve genome assembly. 

How we work

Bacterial strain typing workflow

Step 1: We isolate DNA from your samples using specific DNA isolation protocols for bacterial cells.

Step 2: We prepare genomic libraries using the kits recommended by Illumina.

Step 3: We sequence the libraries using the Illumina MiSeq technology.

Step 4: We analyse the high-throughput sequencing data to obtain your annotated genomes.

Please contact us for further information and pricing.

What you receive

A species or strain identification certificate.

A report with a summary of the methods followed.

The raw high-throughput sequencing files.

The results of the bioinformatic analysis including:

  • Automatic gene annotation.
  • Average nucleotide identity between the genomes sequenced and other bacterial genomes available in reference databases.

We can also carry out on-demand bioinformatic analyses, which can be applied to investigate strain relatedness or look for specific gene sets.

At no additional cost, our project specialists will be available to you after project delivery. We offer up to five 60-min sessions per project, depending on the project size.

What we need

Your bacterial cultures appropriately preserved (fresh, frozen, or lyophilised). Please contact us if you need assistance on how to preserve and ship your cultures.

Genomic solutions for your company

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