The All In One In Vitro Human Gut Microbiome Analysis Platform

Standard cultivation of HUMAN microbiome

Analytic and bioinformatic platform


Our Platform allows to rapidly assess the effect of compounds (e.g. drugs, supplements, foods, probiotics) on the composition and the function of the human microbiome.

By combining an in-house Human Gut Microbiome Sample Bank, a standardized in vitro Human Gut Microbiome Cultivation System and our Multi-Omic and Functional Platform we provide a unique all in one solution to discover, screen and understand your product’s impact on the human gut microbiome. 

Human Microbiome

Human Gut Microbiome

Our samples are anonymised from the beginning to ensure anonymity of the donors. 


Our Cultivation System

Our in-vitro culture conditions ensure a stable population over the cultivation time. Our system allows a fast and parallel analysis of your product(s) on the HUMAN microbiome.

The Multi-Omic and Functional Analysis Platform

Our Microbiome Specific Multi-Omic & Functional Platform allows analysing the effect of your product(s) on the composition and the function of the human microbiome.

The flexibility of our platform allows modulating the output of the study depending on your specific needs.

ACARYON's integrative multi-omics and functional platform allows to assess any aspect of the microbiome compound relationship.

Our platform allows integrating analysis aspects of:

Microbiome Profiling

Microbiome Profiling

The functional properties of the microbiome are directly related to its taxonomical composition. Based on qRT-PCR and Next Generation Sequencing the composition of the microbiome can be analysed at any level.

Quantitative PCR

Quantitative PCR (qPCR) is a first analysis level that allows determining changes in whole bacteria as well as in specific groups of bacteria like Bacteroides spp etc.

Species specific qRT-PCR is the tool of choice for quick and affordable detection of changes in one or a restricted number of species over time or in response to treatment.

16S RNA Metagenomic

16S rRNA gene sequencing (16S amplicon sequencing) helps evaluating the relative abundance of main bacterial taxa composing the microbiome. This analysis is dedicated to identifying changes in the overall microbial profile over time, or between treatments.

Shotgun Metagenomic

Our shotgun metagenomics services facilitate detailed taxa profiling with high coverage at species level as well as more advance functional profiling of the microbiome without PCR amplification bias.

ITS2 rRNA Sequencing

ITS2 rRNA gene sequencing (ITS2 amplicon sequencing) helps evaluating the relative abundance of main fungal taxa in the microbiome. This analysis is dedicated to identifying changes in the overall microbial profile over time or between treatments.

Functional Profiling

Functional Profiling

Functional profiling or functional predictive profiling aims identifying protein (e.g. enzymatic) functions present in the microbiome. This may deliver information complementing the microbiome profiling.

16S RNA Predictive Functional Profiling (PFP)

This approach combines taxonomic information from 16S rRNA gene data with functional information (e.g., metabolic pathways) derived from closely related taxa with sequenced genomes.

PFP is a powerful and cost-efficient alternative to shotgun metagenomics for the human gut microbiome.


Shotgun metatranscriptomics allows determining microbial activity, differential expression of genes across species, and active metabolic pathways.


Liquid chromatography–mass spectrometry (LC–MS) allows the analysis of specific protein content.

Metabolite Profiling

Metabolite Profiling

The microbiome generates a variety of metabolites that influence the composition of the microbiome as well as the host’s health and pathophysiological functions.

As the vast majority of microbial taxa belonging to the human gut microbiome remain unknown, metabolite analysis allows to bypass the unknown between tax composition and metabolite production.

Based on LC-MS, we provide a wide range of metabolic analysis including content of short chain fatty acids, vitamins, bile salt metabolites, neurotransmitters etc..

Short chain fatty acids

SCFAs like propionate, butyrate and acetate are mainly produced by the microbiome and are involved in regulating the composition of the microbiome as wells as the host‘s immunity and metabolisms.

Bile salt metabolites

Primary bile acids are further metabolized by the gut microbiota to secondary bile acids. These metabolites strongly impact the gut barrier function and the immune system.


The microbiome can produce several neurotransmitters (e.g., acetylcholine, GABA, dopamine, and serotonin) and modulate the metabolism of others.


The microbiome is directly involved in the production of vitamines like vitamine B12 and others.

Intestinal & Immuno Profiling

Intestinal & Immuno Profiling

The microbiome and substances it is producing (like polysaccharides, metabolites etc.) influence the integrity of the intestinal barrier, modulate the local and the systemic immune system and impact the development and colonisation of pathogen microorganisms.

Some mechanisms involved in these functions include:

  • induction and/or suppression of cytokines, chemokines
  • induction of antimicrobial peptides
  • recruitment or activation of immune cell populations in the gut mucosa
  • stimulation of mucosal antibody production
  • enhancement of epithelial repair and barrier functions etc.

Based on different cellular intestinal models (human intestinal cell lines Caco2, HT29 or HT29-MTX etc..) we analyse the effect of your products on the microbiome’s intestinal and immunomodulatory properties.

Anti-Microbial Properties

The microbiome directly supports the immune system through avoiding growth and colonization of pathogen microorganisms. Two of the main mechanisms are:

  • the production of antimicrobial substances,
  • limiting the binding of pathogens to intestinal cells.

Based on established assays, we test the effect of your product(s) on the anti-microbial and anti-adhesion properties of the microbiome.


The microbiome is in continuous cross-talk with the immune system. This complex network of innate and adaptive components has to be kept in balance to ensure defence against harmful external agents and to avoid aberrant immune responses that may lead to a variety of diseases.

Based on established assays, we can assay the effect of your product(s) on the immunomodulatory properties of the microbiome (e.g. the induction of cytokine production, macrophage proliferation or polarization etc).

Gut Barrier Integrity

The microbiome is strongly involved in regulating the gut barrier integrity. Thus, the microbiome impacts:

  • the mucus production,
  • the permeability of the gut wall and
  • the proliferation/differentiation of intestinal cells.

Based on established assays, we can assay the effect of your product(s) on the immunomodulatory properties of the microbiome (e.g. permeability of the gut under different conditions, mucus production, cell proliferation etc.).

Co-founded project

One of the most important and recent paradigm shifts in medicine is the recognition of the central role that the gut microbiome plays in human health. However, the implementation of research findings in concrete applications is limited by the lack of specific analysis systems. Mainly, there is a lack of reliable and standardized in vitro platforms allowing to run high throughput analysis on the human microbiome. With the financial support of the EU and the state of Berlin, ACARYON develops a new in vitro human microbiome model that aims mimicking the natural gut conditions, thereby allowing to ensure a stable composition of the human microbiome in the system for more than 48 hours.