16S rRNA Microbiota Profiling of <i>Heligmosomoides polygyrus</i>-Infected Mice and Their Offspring and HUMAnN 3.0 Functional Re-analysis of Orang Asli Metagenomes

Description This dataset comprises two complementary microbiome analyses: 16S rRNA gene sequencing data from a controlled murine model of maternal helminth infectionFunctional metagenomic pathway analysis (HUMAnN 3.0) of publicly available human microbiome data from the Orang Asli cohortTogether, these datasets support the investigation of microbiota-driven metabolic pathways, with emphasis on microbial tryptophan biosynthesis and its potential role in host immune regulation. 16S rRNA Analysis 16S rRNA gene sequencing was performed on fecal samples from mice exposed or not to Heligmosomoides polygyrus infection. Experimental design K05–K10: Maternal samples (K01-05 control vs. K06-10 infected)K11–K20: Offspring samples derived from these mothers (K11-15 control vs. K16-20 infected)This design enables assessment of: Microbiota alterations induced by maternal helminth infectionPotential vertical transmission of microbiota features to offspringBioinformatics processing Raw sequencing data were processed using the dada2 pipeline in R, including: Quality filtering and trimmingError modeling and ASV inferenceChimera removalTaxonomic classification using the SILVA database (v138)Downstream analyses were conducted using phyloseq and vegan, including: Alpha diversity (Observed richness, Shannon, Simpson)Beta diversity (Bray–Curtis dissimilarity and ordination)Taxonomic composition at multiple ranksDifferential abundance testing was performed using DESeq2. HUMAnN 3.0 Functional Analysis (Orang Asli Cohort) Functional profiling was performed on publicly available shotgun metagenomic data from the Orang Asli population, originally described in Gut microbiome of helminth-infected indigenous Malaysians is context dependent. Pathway abundance tables generated using HUMAnN 3.0 were analyzed using custom R scripts. Analytical workflow Filtering of samples based on metadata (e.g., removal of urban individuals)Extraction of pathway-specific abundance profilesSeparation of stratified (taxon-resolved) and unstratified pathwaysAggregation of pathway contributions at the genus levelIntegration of pathway abundance (CPM) with sample metadataPathways of interest PWY-6629: superpathway of L-tryptophan biosynthesisTRPSYN-PWY: L-tryptophan biosynthesisThese pathways were selected due to their relevance in microbiota-derived metabolite production (indole-3-propionic acid) and host immune modulation. Files Included: 16S rRNA analysis ASV count tables (raw and filtered)Taxonomy assignmentsPhyloseq objectDiversity metrics and summary tablesHUMAnN analysis Filtered pathway abundance tables (non-urban samples)PWY-6629-specific datasetGenus-level contribution tablesPer-sample CPM values for selected pathwaysProcessed datasets integrated with metadataScripts: R scripts for 16S processing and analysisR scripts for HUMAnN pathway filtering and summarizationNotes The HUMAnN analysis is a secondary analysis of publicly available data, and no new human sequencing data are generated in this dataset.Functional pathway abundances are normalized to CPM and reflect inferred metabolic potential.Relative abundances do not represent absolute microbial load.