Aim
To characterize the fecal microbiota of dogs receiving a 30-day dietary supplementation of Artemisia annua using shotgun metagenomic sequencing. Beyond simple taxonomic identification, the goal was to understand how the gut community functioned by exploring both compositional and functional shifts associated with the treatment. Ultimately, the research sought to understand how the microbiome’s collective metabolism might adapt to the supplement and what these changes could mean for animal health.
Challenge
The research team aimed to characterize the gut microbiota of dogs at the species level, while accurately capturing both within- and between-sample diversity before and after supplementation. They needed a workflow capable of revealing both meaningful taxonomic and functional differences from raw reads to annotated pathways, all within a single coherent framework. Additionally, full traceability and standardization were crucial across every analytical stage, from quality control to taxonomic classification and pathway-level profiling.
Solution
Sequentia Biotech deployed GAIA®, its versatile, high-precision metagenomic analysis platform, to conduct a comprehensive end-to-end analysis. From rigorous quality control and filtering to taxonomic profiling, diversity analyses, and differential abundance analyses, the workflow delivered a unified view of the microbiome, revealing not only which species were present but also how their abundance fluctuated across individuals and time points following supplementation. For deeper, functional insights, Sequentia’s expert consulting team performed targeted functional profiling, annotating microbial genes and metabolic pathways to reveal subtle shifts in microbial activity, even when overall composition remained stable.
The results revealed a story of balance and subtlety. Overall, the canine gut microbiota remained remarkably stable throughout the 30-day supplementation. Species diversity and composition showed no significant changes — a sign that Artemisia annua did not disrupt the microbial equilibrium.
Yet beneath this apparent stability, shotgun metagenomics uncovered variations invisible to standard methods. Three Bacteroides species displayed a consistent decrease in relative abundance after treatment, suggesting a selective modulation rather than a broad disturbance of the microbiome. On a functional level, genes involved in butanol biosynthesis pathways were enriched after supplementation, hinting at a metabolic adaptation within the microbial community — one potentially linked to the plant’s bioactive compounds.
Impact
This study demonstrated how shotgun metagenomics can illuminate the subtle interplay between diet and the microbiome — even when the overall microbial landscape remains unchanged. By combining rigorous data processing with functional insight, the project delivered a scientifically validated, high-resolution picture of how Artemisia annua interacts with the canine gut ecosystem.
For the client, this meant more than just results — it meant confidence. Every step of the workflow was standardized, transparent, and reproducible, enabling the transformation of complex sequencing data into meaningful biological insights. The findings now serve as a foundation for further research into the functional effects of phytogenic supplements and their potential to promote animal health naturally.
