Understanding the diversity and functions of (your) microorganisms is essential for improving your food or other products influencing human health. NIZO offers you complete solutions for all your bacterial genomics & metagenomics questions, to obtain information for you about identity, safety and functionality of your culture or microbiome.

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We offer:

  • Genome sequencing, genome interpretation & comparative genomics
  • Microbiome profiling platform
  • Shotgun Metagenomics analysis platform
  • Bacterial genome safety assessment
  • Validation of genomic hypotheses with genetic tools such as CRISPR/Cas
  • Production of desired components in microorganisms that are safe for human use (health/pharmaceutical applications only)

Genome sequencing, genome interpretation & comparative genomics

At NIZO, we have long term experience in detailed functional characterization by genome research of lactic acid bacteria and Bacillus and, more recently also in characterization of gut and skin commensal organisms. We offer our customers:

  • Whole genome sequencing of single bacterial strains, strain collections and bacterial communities.
  • Genome assembly and annotation on single genome level, using our software pipeline and visualization tools tuned towards the interpretation of genomics data.
  • Analyzing phylogenetic relationships and gene content between strains using our comparative genomics software pipeline to compare multiple genomes combing from, for example, culture collections.
  • Studying/Indentifying genotype (gene) to phenotype (function) associations using our in-house developed gene trait matching algorithms.
  • Predicting possible intervention strategies to influence the population with compounds obtained from comparing strains with different in vivo behavior (e.g. pathogens vs. commensals).
  • Functional interpretation of genome sequences with respect to properties such as probiotic function, spoilage behavior (e.g. bacteriospores) or metabolic functionality using dedicated genomics tools and databases.
  • Validating strain functionality using transcriptomics (analysis of gene expression) and proteomics (analysis of protein production).
  • Safety assessment of a strain with respect to virulence and antibiotic resistance, using our in-house databases and search tools.
  • Identification of new strain functionalityand mechanistic understanding of food and health processes, using our expertise on microbiology, food processing, nutrition and immunology.

Microbiome profiling platform

At NIZO we aid customers to assess the microbiome composition in a clinical, environmental or food niche, by profiling the target microbiome for them. Combined with the expert knowledge in food, (gut) health and personal care, microbiome profiling of the gut and skin microbiota has become a standard technique to include in the clinical trials and challenge model studies we perform for our clients.
We offer our microbiome profiling platform as a one stop shop, comprising:

  • Sample preparation also in challenging environments such as faecal matter, skin or milk.
  • Determining the microbiome composition of a sample highly sensitive, cost effective.
  • Sample interpretation with advanced multivariate statistical analyses in our dedicated bioinformatics pipeline and including domain knowledge from our experts.

Shotgun metagenomics analysis platform

For customers who are looking for a functional relationship between microbiome and health, to get to mechanistic understanding of microbe-host interactions or strengthen their health claims dossier, we can, next to providing information on the composition of a microbiome, provide information about functionality as well. We do this by full sequencing the microbiobial DNA sample known as (shotgun) metagenomics.
Our metagenome analysis platform allows for a more specific or more in-depth analysis than the microbiome profiling platform.

  • It provides functional insights on the microbiome in clinical, environmental or food samples.
  • It pinpoints at key processes underlying the changes in the microbiome, related to the studied health issues and associate the processes and altered functions with specific microbes in the microbiome.

Bacterial genome safety assessment

The bacterial genome can reveal a lot about its actual behaviour in your product: whether it has the potential to produce toxic products, survive treatments with antibiotics or produce antimicrobial compounds. Before subjecting your probiotic strains to expensive and lengthy experimentation on health benefit substantiating properties, an in silico genome assessment can provide you with the most important first insight: is the strain safe for application? 

NIZO offers a fast and automated genome assessment service, specifically designed to provide you with a clear overview of genomic potential of your strains, in the areas of: 

  • Antibiotic resistance
  • Virulence
  • Production of animicrobial compounds
Any questions?

Ioana Iorga is happy to answer all your questions.

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