Based on a number of factors including study design and budgets, researchers need to decide the approach to use in human, animal and environmental microbiome studies. Generally this choice is between the low-cost microbial profiling (amplicon/16S sequencing) and the high-cost approach of complete metagenome sequencing (shotgun metagenomics). BaseClear offers a service that combines benefits of both approaches. With our shallow shotgun sequencing service, we offer a thoroughly tested workflow for cost-efficient species-level community profiling and functional analysis for human, animal and environmental microbiome studies.
Many applications in today’s human and animal microbiome research require species-level characterisation of gut microbiome (faecal) samples. Questions that require reliable and complete species-level microbiome analyses include:
Functional microbiome analysis, on the other hand, provides essential information on the abundance of microbial gene groups and pathways. This information is key for a good understanding of the molecular microbial mechanisms that are associated with a certain group of samples or subjects. Questions that can only be answered by functional microbiome analysis include:
From a method point of view, species-level community profiles and functional microbiome analyses require one thing in common: shotgun metagenome sequencing of samples. In short, shotgun-based approaches allow species-level community profiling, cross-domain coverage (bacteria, fungi, archaea, phages and other viruses in one experiment) and insight into active microbial functions and pathways. Deep shotgun microbiome sequencing can have a high cost, especially for large-scale (e.g. clinical) studies with hundreds or even thousands of samples are analysed. Especially for such studies, shallow shotgun microbiome sequencing is an attractive option.
Our shallow shotgun microbiome analysis workflow is based on state-of-the-art experimental and computational methods and customised databases. With a limited sequencing depth, our approach delivers robust and complete profiles for species-level community profiles and functional characterisation of microbiome samples for environmental, animal and human microbiome research.
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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.
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