Microbiome–Metabolomics Integration & Network Mapping — Hands-on

Connect microbial community structure and function to small-molecule readouts. This hands-on module builds end-to-end metabolomics (LC–MS/MS & GC–MS) pipelines, then fuses them with amplicon/shotgun microbiome profiles for mechanistic insight. You'll perform rigorous QC and normalization, annotate metabolites with MS/MS evidence, build GNPS molecular networks, and link taxa↔metabolites using modern multi-omics methods (mmvec, MixOmics, MOFA) . Deliverables include reproducible notebooks, figures, and a concise report.

Microbiome–Metabolomics Integration & Network Mapping

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Session Index

Session 1 — MS Workflows, QC & Preprocessing Session 2 — Feature Tables, ID & GNPS Networks Session 3 — Fusion: Taxa↔Metabolites (mmvec/MixOmics) Session 4 — Pathways, Causal Hints & Reporting

Session 1

Fee: Rs 8800

MS Workflows, QC & Preprocessing

Acquisition & formats

LC–MS/MS (DDA/DIA) & GC–MS mzML/mzXML, vendor→open chromatography basics

QC & drift control

pooled QC / blanks / S&N RT alignment checks batch correction (ComBat/LOESS)

Peak picking & alignment

XCMS / MZmine centroiding / deconvolution missingness handling

Session 2

Fee: Rs 11800

Feature Tables, Identification & GNPS Networks

Normalization & scaling

internal standards TIC/probabilistic quotient log/pareto scaling

Annotation & ID evidence

MS/MS libraries (GNPS/MoNA) SIRIUS+CSI:FingerID / MetFrag confidence levels (MSI)

Molecular networking (GNPS)

spectral clustering analog discovery library propagation

Session 3

Fee: Rs 14800

Fusion: Taxa↔Metabolites (mmvec/MixOmics/MOFA)

Compositional data awareness

CLR/rCLR & balances confounders & blocking FDR control

Association learning

mmvec (conditional co-occurrence) MixOmics (sPLS, DIABLO) MOFA/CCA (overview)

Network & module discovery

co-occurrence graphs hub taxa & key metabolites stability & permutation tests

Session 4

Fee: Rs 18800

Pathways, Causal Hints & Reproducible Reporting

Pathway mapping & enrichment

MSEA / mummichog / GSEA KEGG/MetaCyc context link to HUMAnN outputs

Causal hints & validation design

mediation & SEM (overview) gnotobiotic/perturbation ideas target selection

Reporting & dashboards

Quarto notebooks network/heatmap/sankey panels data dictionary & env files

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Microbiome–Metabolomics Integration & Network Mapping Training | XCMS/MZmine, GNPS, mmvec/MixOmics & Pathways

Microbiome–Metabolomics Integration & Network Mapping — Hands-on