Discussions compared 16S rRNA profiling with shotgun and long-read metagenomics, outlining a best-practice pipeline from quality control and host read removal through taxonomic profiling, de novo assembly, MAG binning, contamination checks, gene calling, and pathway mapping (including SCFA synthesis, bile acid metabolism, and polyphenol catabolism), followed by compositional statistics, confounder control, longitudinal modeling, replication across cohorts, and rigorous reproducibility via containerized workflows and versioned databases; metatranscriptomics and metabolomics were highlighted as complementary layers that capture activity and metabolic outputs to validate function rather than taxonomy alone.
A dedicated segment examined the correlation between the microbiome and nutrition—how dietary patterns (fiber diversity, fat quality, protein sources, and polyphenol intake) shape microbial community structure and functions, and how microbially derived metabolites (e.g., butyrate, propionate, secondary bile acids, indoles) in turn modulate host metabolic and inflammatory pathways; this bidirectional relationship was extended into nutrigenomics, emphasizing that host genetic variation (e.g., FUT2 secretor status, FADS1/2, AMY1 copy number, LCT) can influence baseline microbiome composition, substrate availability, and responsiveness to dietary interventions, while microbial metabolites can affect host gene expression and epigenetic programs relevant to glycemic control, lipid handling, and appetite signaling.
The group concluded that sequencing alone largely yields associations and that nutrition decisions require causal levers, motivating microbiome engineering approaches such as designed microbial consortia for targeted functions, precision probiotics at the strain level with genomic safety dossiers, phage- and CRISPR-based modulation to address pathobionts and AMR determinants, and metabolite-level tuning via prebiotic substrates, food matrices, and controlled co-cultures, all underpinned by safety and ethics (GRAS/QPS considerations, horizontal gene transfer risks, biocontainment), transparent regulation, and equitable access.
An international perspective was provided by Assoc. Prof. Gabriela Tenea (Universidad Técnica del Norte, Ecuador), who presented perspectives for beneficial strains, considerations for strain selection and validation in resource-variable settings, and the impact of dietary diversity on functional microbiome profiles; Key translation messages were to prioritize function over taxonomy in nutrition trials, apply strain-aware and genotype-aware evidence, standardize sampling and metadata capture (including diet and relevant host genotypes), and plan validation layers (e.g., metabolomics, targeted qPCR) when claiming functional change.
