Whole Bacterial / Fungal Genome Sequencing is an advanced sequencing method that determines an organism's complete genome sequence. This technique enables analysis of the entire DNA content.
Bacterial/Fungal WGS workflow
01DNA extraction: Sample collection and extraction of high-quality genomic DNA from a bacterial sample. Various methods are used, such as DNA extraction kits that remove contaminants and provide pure genetic material.
02Library preparation: DNA fragmentation and addition of sequencing adapters and indexes.
03Sequencing: Sequencing on Illumina, PacBio, or ONT (Oxford Nanopore Technologies) platforms.
04Bioinformatics analysis: Genome assembly to reconstruct the whole-genome sequence from short reads, followed by gene annotation and comparison with a reference genome.
Applications of Bacterial/Fungal WGS
01Medical diagnostics:
- Identification of pathogens responsible for bacterial infections.
- Analysis of antibiotic resistance, including the detection of resistance genes such as bla, mecA, van).
- Characterisation of bacterial strains to determine their pathogenic potential.
- Diagnosis of fungal pathogens such as Candida albicans, Aspergillus fumigatus. Analysis of strains resistant to antifungal agents.
02Epidemiology:
- Tracing infection sources during outbreaks, such as Salmonella, E. coli and Listeria.
- Determining the genetic relatedness of strains across time and geographical locations.
- Analysis of the relatedness of fungal strains in hospital and environmental infection outbreaks.
03Research:
- Characterisation of novel bacterial species and their genomes.
- Understanding adaptive mechanisms, for example in the environment or in response to antibiotic exposure.
- Understanding fungal biology, including life cycles and mechanisms of pathogenesis. Investigation of genes involved in the production of secondary metabolites, such as antibiotics.
04Food safety:
- Monitoring bacteria in the food supply chain, including the detection of pathogenic bacteria in the food industry.
- Quality control and tracing of strains responsible for product contamination.
- Detection of mycotoxin-producing fungi in food and animal feed, such as Aspergillus species that produce aflatoxins.
05Agriculture and animal health:
- Analysis of bacterial pathogens affecting livestock.
- Studies of the soil microbiome and the impact of bacteria on crop yields.
- Analysis of fungal plant pathogens such as Fusarium, Phytophthora).
- Studies of symbiotic fungi that improve plant health.
06Environmental microbiology:
- Studies of microorganism diversity in ecosystems.
- Analysis of the role of bacteria in biotechnological processes such as environmental remediation.
- Applications in the pharmaceutical industry, such as penicillin production by Penicillium, the food industry, including fermentation, and the biofuel industry, such as cellulolytic enzymes.
- Analysis of the role of fungi in nutrient cycling, including biomass degradation, and in bioremediation.
Technical specifications of Bacterial/Fungal WGS
- Sequencing mode:
- Illumina: 2 x 150 bp
- ONT: 20kb
- PacBio Revio: 10 kb-HiFi
- Recommended genome coverage / amount of data per sample:
- Bacterial WGS
- Illumina (Draft map): 100 X
- Nanopore: ≥ 100X ONT + 100X Illumina - gapless genome assembly
- PacBio: 30X HiFi + 100X Illumina - gapless genome assembly
- Fungal WGS
- Illumina: 100X (Survey: 50X)
- Nanopore: ≥ 100X ONT + 50X Illumina
- PacBio: 30X HiFi + 50X Illumina
- Bacterial WGS
Sample Requirements
Minimum Sample Requirements - DNA/RNA (Illumina):
- Sample type: gDNA
- Amount: > 60 ng
- Concentration (NanoDrop): >1 ng/μL
- Volume: >20 μL
Minimum Sample Requirements - DNA/RNA (PacBio):
- Sample type: gDNA
- Amount: > 2μg
- Concentration (NanoDrop): >20 ng/μL
- Volume: >20 μL
Minimum Sample Requirements - DNA/RNA (ONT):
- Sample type: gDNA
- Amount: > 2μg
- Concentration (NanoDrop): >50 ng/μL
- Volume: >20 μL
We recommend submitting samples at quantities and concentrations above the minimum requirements.
DNA extraction from submitted samples is also available. Details here.
Bacterial/Fungal WGS bioinformatics analysis
- Whole-genome resequencing of fungi (WGS):
- Detection of single-nucleotide polymorphisms (SNPs).
- Genome assembly de novo:
BIOINFORMATICS ANALYSIS SCOPE3 analysesFungal/bacterial genome analysis (Illumina) Genome size estimation.Draft fungal/bacterial genome (Illumina) Analysis of genome components and functional annotation.High-quality fungal/bacterial genome (Illumina + ONT/PacBio) Analysis of genome components and functional annotation. Bacteria - genome visualisation using a Circos plot.
Example figures
Selected projects and client publications
See which institutions we perform next-generation sequencing (NGS) for and explore scientific publications that draw on the data we have supplied.
Selected projects (6 orders)
INSTITUTION
SCOPE OF WORK
PROJECT YEARS
PROJECT YEARS
2026
PROJECT YEARS
2025
PROJECT YEARS
2024
SCOPE OF WORKWhole Bacterial/Fungal Genome Sequencing
PROJECT YEARS
2026
SCOPE OF WORKWhole Bacterial/Fungal Genome Sequencing
PROJECT YEARS
2023
SCOPE OF WORKWhole Bacterial/Fungal Genome Sequencing
PROJECT YEARS
2026
To protect client confidentiality, we show only selected projects for public-sector institutions that are not covered by non-disclosure agreements (NDAs).
Last updated: 12 November 2026
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bacterial genomefungal genomeisolatesmicrobe WGSbacterial genome sequencing
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