Microbial genomics, metagenomics & physiology

We offer:

• Genome sequencing, genome interpretation & comparative genomics
• Microbiome profiling platform
• Shotgun Metagenomics analysis platform
• Bacterial genome safety assessment

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.

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

Microbiome analyses

Microbiome analysis provides a highly sensitive, cost-effective way to characterize the microbiota of clinical, environmental, or food samples. NIZO offers 16S rRNA gene or shotgun sequencing-based microbiome analysis services as a one-stop shop, from sample logistics and preparation to advanced bioinformatics and multivariate statistical analyses with biological interpretation by our experts.

These analyses can aid in your understanding of the role of microbial communities in health and disease.

Why NIZO

• Long-standing experience in in silico, in vitro and in vivo microbiological research: strong focus on GI tract, food, personal care and health.
• NIZO acts as one-stop-shop with its partners hereby guaranteeing high quality experimental designs, execution, project management and NIZO reporting, no need to interact with multiple service providers.
• Proven track record in microbiota analyses, bioinformatics, and biological interpretation using dedicated metagenomic pipelines for profiling the gut and skin microbiota in health and disease.

Deliverables

• Overview of the microbiome composition by 16S rRNA sequencing, or high-resolution composition and functionality by shotgun metagenomic sequencing, with in-depth analyses and visualizations.
• Overview of the relationships between microbial composition (and functions) and phenotypes of interest or clinical responses using multivariate statistics and Machine Learning.
• During and/or and at the end of the project a teleconference will be organized to go over the main results and discuss potential follow-up in the form of in-depth analysis and interpretation.
• A confidential, concisely written report.

Our approach

A. Sample registration & processing

Samples will be either collected by NIZO, or shipped to NIZO by the customer. As soon as the samples arrive they will be processed for DNA isolation with our optimized protocols for each sample type.

B. 16S rRNA-based microbiome composition profiling

Microbiome profiling has become a standard technique to include in clinical trials and in vitro fermentation studies we perform for our clients.

The 16S rRNA gene will be amplified from the isolated DNA using specific primers targeting the V3-V4 hypervariable regions. After quality control, the DNA libraries will be sequenced with Illumina MiSeq, 300bp PE reads.

Raw sequencing data will be processed using our in-house developed pipeline:

• QC and removal of low quality reads and chimeric sequences
• Inference of Amplicon Sequence Variants (ASVs) for single-nucleotide resolution, microbial counts determination and taxonomy assignment
• Genus-level (species-level where possible) resolution of sufficiently abundant microbes
• Multivariate statistics: alpha- and beta-diversity, RDA, (multilevel) PCA, linear mixed models with longitudinal measurements and/or covariate inclusion
• Machine Learning models, phenotype association, biomarker discovery.
• Visualizations of composition, diversity, and differences between sample groups
• Expert biological translation of results, e.g. links to human health parameters

C. Microbiome profiling based on shotgun metagenomic sequencing

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.

Shotgun DNA libraries will be prepared from isolated microbial DNA before sequencing on Illumina HiSeq / NovaSeq with 150bp PE reads.

Shotgun metagenomic sequencing allows for deeper insights into microbial species and the genetic functions of the microbiome compared to amplicon sequencing:

• Unbiased inference of microbial community composition based on metagenomic assembly and profiling
• Characterization of microbial functional potential (microbial gene families and metabolic pathways)
• Species/Strain-level resolution of sufficiently abundant microbes
• Screening for specific genes or pathways of interest using in-house developed/custom made profile Hidden Markov Models (e.g. microbial genes linked to health benefits for the host, see below)
• Multivariate statistics: alpha-diversity, beta-diversity, RDA, (multilevel) PCA, linear mixed models with longitudinal measurements and/or covariate inclusion
• Machine Learning models, phenotype association, biomarker discovery.
• Visualizations of composition, diversity, and differences between sample groups
• Expert biological translation of results, e.g. links to human health parameters

The (custom) gene functional analyses by the use of HMMs provides extended output of NIZO’s metagenomics bioinformatics pipeline, for in-depth analysis of specific functionality:

• In addition to the generic functional overview as provided by the standard bioinformatics pipeline, we can zoom in on functionality of particular interest.
• Sequencing reads will be assembled into contigs. Afterwards, particular (sets of) genes of interest can be identified by utilizing different (manually curated) databases and gene screening methods. This functional data (i.e. protein coding sequences) will be analyzed by NIZO’s Microbiomics experts using bivariate and multivariate statistical methods, including in-depth biological data interpretation.

Such focused analyses allow to ask specific and relevant research questions with regarding to functionality and provide a more detailed overview of the impact of intervention on functionality of interest compared to the generic function overviews as provided by standard bioinformatics pipelines that depend on generic databases.

Examples of gene functions that NIZO has screened for are:

• Antibiotics resistance
• Virulence
• Human Milk Oligosacharide (HMO) utilization
• Short Chain Fatty Acid (SCFA) metabolism
• Various gut-brain axis related gene functions

Note that we always can look into the possibility of building new dedicated bioinformatics modules for the gene functions of your specific interest. Would you like to know more? Contact us!