Laboratory of Biomonitoring and Bioprospecting

The Laboratory of Biomonitoring and Bioprospecting offers scientific and research services in the fields of bioinformatics, environmental microbiology, molecular biology, and bioprospecting.

For many years, we have worked with environmental bacterial isolates, including strains from extreme environments, such as the Arctic, Antarctica, and highly contaminated areas. By combining classical microbiology, molecular microbiology, and bioinformatics, we are able to improve cultivation efficiency and further characterise these strains. We assess, among others, their safety profile, including the presence of antibiotic resistance genes and virulence factors, as well as their metabolic and biotechnological potential.

We can also effectively characterise microbial diversity in the environment using qualitative amplicon and metagenomic analyses, as well as quantitative qPCR analyses. Bioinformatic tools developed by our team, including MAISEN and UniPriVal, allow us to efficiently and precisely characterise individual genomes or selected features in metagenomic data. These methods can be used to monitor microorganisms or selected traits, such as antibiotic resistance genes, both in laboratory cultures and in environmental samples.

The Laboratory provides services to research institutions, service organisations, and industrial partners as part of its scientific and research activities.

Scope of Services

BIOINFORMATICS

• use of computational infrastructure for large-scale computing,
• comprehensive analysis of bacterial and fungal amplicons, including total DNA isolation, amplicon preparation, DNA sequencing, and bioinformatic analysis,
• comprehensive genomic characterisation of bacterial strains, including cultivation, DNA isolation, DNA sequencing, and bioinformatic analysis,
• comprehensive metagenomic analysis, including total DNA isolation, DNA sequencing, and bioinformatic analysis,
• automatic and/or manual annotation of bacterial genomes and mobile genetic elements, including plasmids and bacteriophages,
• deposition of sequencing data in public repositories, including bacterial genomes, bacteriophage genomes, plasmids, amplicons, and metagenomes,
• design of PCR and qPCR primers and TaqMan probes,
• in silico validation of PCR/qPCR primers.

ENVIRONMENTAL MICROBIOLOGY

• isolation of environmental DNA from complex matrices,
• molecular identification of bacteria using one or more molecular markers,
• determination of DNA concentration in environmental samples using fluorescence-based methods,
• determination of DNA concentration in environmental samples using spectrophotometric methods,
• determination of the genetic antibiotic resistance profile of bacterial strains,
• enrichment and selective cultivation of environmental samples.

MOLECULAR BIOLOGY

• Western blotting using monoclonal primary antibodies, including anti-His-tag, anti-c-Myc, anti-HA, and others,
• Western blotting using polyclonal primary antibodies provided by the client,
• SDD-AGE analysis (semi-denaturing detergent agarose gel electrophoresis) of amyloidogenic proteins.

BIOPROSPECTING

• protein purification, from de novo gene synthesis to purified protein, at a scale of <0.1 mg,
• protein purification, from de novo gene synthesis to purified protein, at a scale of >0.1 mg,
• identification of proteins, including selected enzymes, in genomic and metagenomic data,
• preparation of highly specialised microbiological media,
• selection of environmental strains showing traits that can be directly detected on solid microbiological media.

Equipment

• computing cluster:
  • 3 × CPU units: AMD EPYC 7443P 24C/48T, 128 GB RAM, 12 TB HDD
  • 1 × CPU unit: AMD EPYC 7551P 32C/64T, 512 GB RAM, 12 TB HDD
  • 1 × GPU unit: AMD EPYC 7443P 24C/48T, 512 GB RAM, 12 TB HDD, 2 × NVIDIA A4000 16 GB VRAM
  • workload management system: Slurm
• FastPrep-24^™ homogeniser (MP Biomedicals)
• NanoReady F-2100 spectrophotometer for microvolume and cuvette measurements (LifeReal)
• Qubit^™ 2.0 Fluorometer for measuring nucleic acid and protein concentrations (Thermo Fisher Scientific)
• CFX OPUS 96 Real-Time PCR System (Bio-Rad)
• lake and soil microcosm systems