BaseClear offers complete solutions to analyse the human gut microbiome. This analysis can help create a better understand the role of gut microbes in human health and disease. BaseClear offers a complete package for gut microbiome analysis, including sampling, logistics, sample preparation, collection of metadata, downstream bioinformatics and statistical analysis.

BaseClear also provides expert consultancy and can help with your project design. Our product managers can advise you for instance about standardised sampling methods, DNA or RNA extraction, sample preparation and the best technical approach to use.

Analysis of the Human Gut Microbiome

The human gut microbiota have been considered as the most important microecosystem living in symbiosis with the body. The human gut is home to billions of bacteria, fungi and viruses, that make up the gut microbiota. Traditionally, studying samples from human stool (faeces) relied on time consuming and labour intensive microbiology techniques. These included growing and isolating individual organisms followed by phenotypic or genotypic analysis. Microbial community analysis within a single sample was not possible with these methods.

With next-generation sequencing (NGS) technology we have the tool to analyse the human gut microbiome. With this high-throughput technology we can perform complete metagenomics studies capable of surveying the genomes of entire communities, including those of unculturable organisms.

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Gut microbiome analysis

We translate gut microbiome data to clear results

The BaseClear team includes a number of experienced PhD-level molecular biologists, microbiome specialists and bioinformatics experts. Get in touch with one of our experts to discuss your project or to learn more about our microbiome analysis solutions.

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Sampling and logistics for gut microbiome analysis projects

BaseClear can help you with the logistics of your gut microbiome analysis project, including sampling and storage solutions for faecal samples. Sampling and storage are critical steps for gut microbiota analysis. Sampling must be standardized and samples should be completely stabilised during storage to prevent bias in the results.

We offer sampling collection kits that contain all the necessary materials to collect faecal samples. Our kit contains specific instructions for sampling, making sure the sampling is done correctly and in uniform. The samples are sent directly back to us for analysis in a standardized way. Besides offering our standard sample collection kit, we can also customise the branding of the kit itself and its contents to suit the needs of your specific project.

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Sampling box

DNA AND/OR RNA EXTRACTION FROM FAECAL SAMPLES

BaseClear has optimized and validated extraction procedures to extract DNA (or RNA) from faecal samples. DNA extraction is an essential step in gut microbiome analysis projects, since the analysis has no value if the DNA of the different organisms do not represent the actual microbial community. The extraction method can have a strong influence on the quantification of the total bacteria and the abundance estimations of specific groups.

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DNA extraction with the microbiomics products from Zymo Research

Statistics of gut microbiome sequencing data

Typically, the sequencing data coming from gut microbial community studies are high-dimensional and together with associated meta-data can be used to unravel the relation between the gut microbial composition and/or function with environmental variables or sample characteristics. Using multivariate analyses BaseClear can mine data to stratify individuals in, for example, responders and non-responders based on the abundances of different microbial groups or functional identifiers as well as indicate if the different sample group are significantly different. Furthermore, this analysis facilitates identification of microbial groups or function identifiers that are important drivers of the difference between sample groups.

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Multivariate analysis

Meet Tom van den Bogert!

Tom is our metagenomics and microbiome specialist. He is responsible for the development of new and improved metagenomics and microbial profiling services, which are based on Next-Generation sequencing and related technologies. Tom completed his PhD research at the Laboratory for Microbiology at Wageningen University. He studied community and genomic analysis of the human small intestine microbiota in a project funded by TI Food and Nutrition entitled "Complex fermentations."

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