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:
- How does our treatment change the overall microbiome population compared to controls?
- Do we see an increase in the abundance of fermenting species in animals who were fed by our product?
- Do we find back our probiotic species after a week of consumption?
- How does this particular diet change the alpha and beta diversity in samples?
- Are we able to eliminate the microbe of interest in the population that received the treatment?
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:
- What are the microbial functions that are significantly differentially abundant in the healthy subjects compared to those with disease?
- How does our product influence the abundance and diversity of antibiotic resistance genes?
- Which KEGG modules are found more in animals with reduced inflammation in their gut?
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.
Microbiome analysis by shallow shotgun
Our new 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 animal and human microbiome research.
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