Research application
Molecular & integrative analysis
Research analysis of taxonomic/functional profiles and associations with matched immune states/metabolites over time. Scope is agreed after reviewing laboratory-generated data, study design and feasibility.
Analyses are tailored to your experimental design, data quality and research question. The workflow and deliverables are agreed following project review.
Analysis modules
Microbiome QC: review compatible sequence/count profiles and processing provenance.
Taxonomic and functional profiles: use design-appropriate compositional summaries.
Matched-host integration: associate microbial profiles with immune states and measured metabolites.
Longitudinal comparisons: account for donor, exposure, antibiotic, diet and batch metadata.
Sensitivity review: report confounding and uncertainty; associations do not establish causality.
Data and metadata
Compatible microbiome sequence/count data plus matched host data and exposure/batch metadata. Include assay and processing provenance, quality-control summaries, sample identifiers without patient identifiers, species/tissue, groups, controls, batch and relevant donor/time-point metadata.
Proposed deliverables
Compositional analyses, association tables and longitudinal comparisons. Proposed outputs include documented methods, quality-control summaries and explicit limitations; deliverables are tailored after review.
Interpretation and feasibility
Account for antibiotics/diet/batch; associations do not establish causality.
Selected scientific references
Selected methodological and research references. Methods and software are chosen for each project after feasibility and licence review. Citations do not imply affiliation or validation of an ImmunLattice pipeline.
Microbiota-driven antitumour immunity mediated by dendritic cell migration (Nature 2025). Mechanistic research context; observational associations alone do not establish causality.
MOFA+ (Genome Biology 2020). Multi-omics integration and latent-factor context.
Longitudinal gut microbiota analysis during anti-PD-1 therapy reveals stable microbial features of response in melanoma (Cell Host & Microbe 2024). Research application: jointly follows microbial functions and host immune markers during melanoma immunotherapy.
Microbiota-dependent activation of CD4+ T cells induces CTLA-4 blockade-associated colitis via Fcγ receptors (Science 2024). Research application: combines microbial profiling and single-cell immunology to investigate checkpoint-blockade-associated colitis mechanisms.
Fecal microbiota transplantation plus anti-PD-1 immunotherapy in advanced melanoma: a phase I trial (Nature Medicine 2023). Research application: illustrates strain-resolved engraftment and longitudinal host–microbiome comparisons in a phase I study.
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