Supporting clinical trials

Clinical trials bridge microbiome hypotheses to real-world benefits. Microbiome analysis takes center stage in these trials, providing insights into microbial interactions, evaluating novel (bio)therapeutics, and substantiating claims such as the efficacy of dietary supplements with pre-, pro-, post-biotics, and vitamins. BaseClear specializes in comprehensive microbial analysis, empowering trials with precision, reliability, and actionable insights, fostering therapeutic advancements and innovative solutions.

Our solutions

Pre- and clinical trials
BaseClear is your end-to-end partner, guiding you through the entire clinical trial process from study design through sample processing and data analysis to providing a comprehensive report including data interpretation and ready-to-use figures and tables for publication.

Claim substantiation
Our robust claim substantiation services ensure your product’s assertions are supported by solid scientific evidence. Leveraging advanced multi-omics techniques, including taxonomic and functional microbiome profiling, metatranscriptomics, and metabolomics, along with comprehensive data analysis, we provide the necessary support for the claims made during clinical trials.

Tracking of probiotics and quantification
Our tailored qPCR solutions ensure precise tracking and quantification of probiotics, thus enabling accurate monitoring of targeted bacterial populations. This data-driven approach accelerates lead generation, optimizing your research pipeline by identifying high-potential targets and biomarkers for future studies.

Microbiome friendly
Our solutions prioritize the delicate balance of the microbiome, defining microbiome friendliness through a science-led format. This aids regulatory bodies in validating claims and building trust with consumers.

Why BaseClear?

  • 1-Stop-Shop
    Streamlined services under one roof, eliminating the need to coordinate with multiple partners, ensuring efficiency and a seamless research experience.
  • In-house validated methods
    Rigorous in-house validation methods for bioinformatics pipelines as well as Illumina and ONT procedures, ensuring reliability, accuracy, and compliance with industry regulations.
  • Diverse analytical techniques
    Expertise in various techniques, such as qPCR, multi-omics data analysis, robust biostatistics, immune markers, amplicon profiling, and curated databases to meet diverse research needs.
  • Data interpretation by PhD scientist
    In-depth data interpretation led by experienced PhD scientists, ensuring a high level of expertise and accuracy in drawing meaningful conclusions from complex datasets.
  • Customizability
    Flexibility to incorporate commercial kits or published methods for specialized analyses, providing tailored solutions while leveraging established techniques.
  • Continuous communication and support
    Ongoing consultation throughout the entire research process, from covering critical aspects of sample management right to summarizing the study findings in comprehensive reports.

Our clinical trials process

BaseClear’s microbial genomics experts are here to support your project, including consultancy, microbial analysis, and substantiating claims.


Human Health
BaseClear is at the forefront of supporting diverse studies revealing the microbiome’s impact on human health. Our expertise covers critical areas, such as infant-mother and human gut studies, providing insights into early-life microbial interactions and overall well-being. In clinical trials, we bolster product claims with robust scientific evidence, utilizing advanced techniques like precise probiotic tracking for accurate monitoring.

Skin Health
We support the development of innovative personal care products that maintain the balance and health of the skin microbiome. Our science-led approach in defining microbiome friendliness assists regulatory validation, further fostering consumer trust. Through microbiome analysis, we provide solutions for diverse products, including cosmetics and personal care items for multiple body sites (skin, scalp, oral, vaginal).

Animal Health
Promoting sustainable agricultural practices is central to our commitments to animal health. Partnering in clinical trials on feed efficiency allows us to advance resource-efficient animal farming. Through our innovative metagenomics pipeline, BaseClear supports studies characterizing antibiotic resistance genes in the animal gut. Our in-house methane metabolism bioinformatics pipeline is ideal for studying interventions in ruminants during feeding trials.

Case study

BaseClear contributed to an exciting new research, which aimed to explore the potential benefits of probiotic supplementation in infants. The study investigated two dosing methods for probiotic supplements.

Our involvement included precise qPCR quantification to evaluate the absolute abundance of probiotic strains post-seeding, shedding light on their colonization dynamics. Furthermore, we conducted comprehensive microbiome profiling using 16S amplicon sequencing, coupled with advanced biostatistical and metabolite analyses. This approach provided valuable insights into the intricate microbial communities at play. Dividing the samples into small aliquots for microbiome and qPCR analysis or metabolite analysis, necessitated a high level of coordination and flexibility in sample handling.

Our analyses uncovered that Infant Seeding (IS) exhibited higher levels of short-chain fatty acids, with the exception of butyrate, when compared to Maternal Seeding (MS). Additionally, we identified key biomarkers including pH (which was lower in IS and inversely correlated with bifidobacteria), calprotectin (equal in IS and MS), and endotoxin (lower in IS). These findings suggest that IS expedites the colonization of beneficial strains, leading to softer stools and reduced instances of crying and fussing. Overall this study uncovers the intricate complexity of microbial interactions and their profound impact on the health of both mothers and infants.


  • S. Deyaert, F. Moens, W. Pirovano, B. Van Den Bogert, E. S. Klaassens, M. Marzorati, T. Van De Wiele, M. Kleerebezem, P. Van den Abbeele, 2023, Development of a reproducible small intestinal microbiota model and its integration into the SHIME®-system, a dynamic in vitro gut model, Frontiers in Microbiology. 10.3389/fmicb.2022.1054061
  • Van Belkum, P. Lisotto, W. Pirovano, S. Mongiat, A. Zorgani, R. Howlin, M. Gempeler, R. Bongoni, E. Klaassens, 2023, Being friendly to the skin microbiome: experimental assessment, Frontiers in Microbiomes. 10.3389/frmbi.2022.1077151
  • Melsaether C, Høtoft D, Wellejus A, Hermes GDA, Damholt A. Seeding the Infant Gut in Early Life-Effects of Maternal and Infant Seeding with Probiotics on Strain Transfer, Microbiota, and Gastrointestinal Symptoms in Healthy Breastfed Infants. Nutrients. 2023 Sep 15;15(18):4000.

Get in touch!

Get in touch with the BaseClear experts to discuss your specific project.

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Meet Eline Klaassens!

Human microbiome specialist Eline Klaassens joined BaseClear to use her expertise as Product Manager Human Health. “I’ve always had a strong interest in sustainability and human health. Many people have health problems related to gut dysbiosis. Through my studies, I’ve learnt a lot about the gut microbiome and I’d like to use my knowledge to improve people’s wellbeing through applications developed with microbial genomics,” she comments. Eline advises clients about genomics analyses for expert projects for clinical trials and the food industry. "As a human microbiome expert, customers value my contribution to interpretation of the analyses to support their projects. I make an important contribution to the success of their research due to my specialised academic background,” she notes.

Contact Eline
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