Clinical trials connect science to health benefits. Microbiome analysis is at the heart of clinical trials designed to substantiate health benefits of functional foods (e.g. dietary Supplements like Pre and Probiotics, herbal products), to assess therapeutic or prophylactic activity of new biotherapeutics (e.g. Live Biotherapeutic Products) or to prove the specificity of action of new antibiotics on the gut microbiome.

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From study design to microbiome insight


Over the past two decades, Biofortis has designed, organized and executed state-of-the-art clinical trials to help academics and sponsors from the pharma, biotech and food tech industries to substantiate their health claims.

By virtue of our unique expertise in microbiome, we help you to accelerate your microbiome-health innovation projects.

Flexible “à la carte” solutions

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Whether you require a one-stop shop to manage your entire clinical trial, or just a microbiome-specialized central laboratory to work together with your existing CRO, Biofortis offers a comprehensive range of customisable solutions.

From study design and documentationsample management and collection kits supply, NGS and microbiome biomarkers analysis, to advanced data integration and visualization, Biofortis supports hundreds of academics, sponsors, CROs and investigational sites worldwide.

Specific (pre)clinical design

When studying the human or animal microbiome, we must take into account a great variety of factors, namely the specific characteristics of each of the many microbial communities coexisting in and on the host.

The design of a study incorporating microbiome data analysis requires specific adaptations that take into account a variety of aspects, such as the inclusion and exclusion criteria, which will be largely dependent upon the specific microbiota type (gut, skin, vaginal, oral etc.). The cohort size, the duration of the study, the wash-out period or the sample collection time points are also parameters to be taken into consideration when planning your trial.

Highly specialized skills and robust experience in inter and intra individual and group variability are essential to gain valuable insights from the microbiota diversity analysis.

As a result of Biofortis’ extensive experience in both clinical and preclinical studies incorporating microbiome data analysis, our experts are in an unrivalled position to help you to quickly understand and assess the challenges and opportunities of your research project.

 Watch our webinar on Adaptive Designs in clinical trials

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Samples collection

Biofortis currently supports 100+ clinical investigational sites worldwide.

We assemble and supply sampling kits specially designed to collect human (adult or infant) or animal stool, skin, oral, and vaginal samples and we produce all the necessary study documentation (laboratory manual, technical instructions, pocket cards, etc.) in order to ensure the standardization and integrity of your samples and thus the reliability of your laboratory test results.

We have also developed our proprietary easy-to-use stool collection kit, which allows trial volunteers to easily and safely transport samples at room temperature.

NGS services

Biofortis has been providing microorganism ecosystems and bacterial isolates sequencing services to industries and academic laboratories for many years.

We offer a wide range of technologies (short and long reads) and methods (whole genome, metabarcoding and shotgun sequencing) to fit your diverse study goals, biological matrices and budgets.

16S metabarcoding

16S metabarcoding allows to profile the bacterial taxonomical composition of all types of samples and is specially recommended for low DNA content sample types and highly host-contaminated samples and is cost effective.

Shotgun metagenomics

Shotgun metagenomics allows to profile all microorganisms (Bacteria, Eukaryota, Archaea, Virus) within an ecosystem. It allows both taxonomical and functional analyses (gene ontologies, enzyme classifications and metabolic pathways).

WGS (Whole Genome Sequencing)

WGS (Whole Genome Sequencing) provides the sequence of bacterial isolates to bring phenotypic traits such as serotype, virulence or antibiotic resistance. In addition, genetic relatedness between strains can be assessed using genetic variations (wgSNP or wgMLST).

The Biofortis bioinformatics pipelines were developed and validated internally based on reference algorithms published by the Scientific community. Our highly trained and experienced Bioinformatics and Data Science team has developed dedicated validated bioinformatic pipelines for each application based on the state-of-the-art of the literature. Depending on the client’s requirements, our team is able to adapt its methods to provide customised deliverables.

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Biomarker Analyses

Some biological markers are known to be correlated to microbiota diversity and dysbiosis in various diseases, and can reflect the functional activity of the microbiome.

At Biofortis’ ISO 9001:2015 and GCP-compliant cutting-edge central laboratory facilities, we routinely perform +360 different analytical parameters, including routine and specific assays in microbiology, qPCR or biological analyses and specific biomarkers (IL, IgAs, TNF, CBC, SCFA, lipid profile, hepatic function, inflammation, etc.).

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Advanced custom data integration

Changes in the microbiome can only be interpreted in conjunction with other relevant informations, such as clinical outcomes, dietary habits, disease or biological insights obtained from multi-omics approaches.

This huge amount of information can be integrated and valued by machine learning approaches widely used to uderstand host-microbiome responses, biomarker discovery, identification of responder profiles or prediction or association studies.

In line with the “5P medicine” approach (Preventive, Predictive, Participative, Personalized and Pertinent), Machine Learning is increasingly used to assist healthcare professionals in the diagnosis, prognosis and treatment of pathologies.

During the past few years Biofortis has seen a vast increase in the number of advanced data integration projects requiring machine learning approaches.

EasyBioM®, data visualization in few clicks

EasyBioM® is a user-friendly, secured, web application to get quick insights from microbiome NGS analyses in a few clicks.

It allows to explore the taxonomic and functional content of biological samples, their richness, diversity and relatedness.

It brings autonomy to any scientist in visualization and first steps of analyses, with or without bioinformatic programing knowledge. 

From your 16S metabarcoding or Shotgun metagenomics abundance profiles, you can visualize in a few minutes customizable interactive charts and graphs, from classical plots to unique functional analysis figures. Customizable plots can be exported and included in a report.

This application has been developed and is constantly updated by Biofortis’ Bioinformatics and Data Science team.

EasyBioM® is a R shiny web-based application, securely stored in a certified Health Data Hosting server compliant with GDPR (Europe), HIPAA (USA), CSL and PHIMM (China).


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Biofortis’ Microbiome news

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