Mouse and Human Microbiome Data for Tryptophan Pathway Analysis

Two complementary datasets support investigation of microbiota-driven metabolic pathways, particularly microbial tryptophan biosynthesis. The first contains 16S rRNA sequencing data from 20 mouse samples in a maternal helminth infection model, processed with dada2 and analyzed with phyloseq. The second is a HUMAnN 3.0 functional re-analysis of shotgun metagenomic data from the Orang Asli human cohort, focusing on specific biosynthesis pathways.

Use Cases

• Assess microbiota alterations from maternal helminth infection based on the 16S rRNA mouse cohort design.
• Investigate potential vertical transmission of microbiota features to offspring using the control vs. infected offspring sample groups.
• Analyze functional pathway abundance, specifically L-tryptophan biosynthesis (PWY-6629, TRPSYN-PWY), in human microbiome data.
• Perform differential abundance testing on taxonomic data using the described DESeq2 methodology.
• Integrate pathway abundance data with sample metadata for cohort-specific analysis, as described in the Orang Asli workflow.

Strengths

• Includes a controlled experimental design with 20 mouse samples (10 maternal, 10 offspring) split into control and infected groups.
• Data processing is detailed, using the dada2 pipeline, SILVA v138 database, and established R packages (phyloseq, vegan, DESeq2).
• Functional analysis focuses on specific, biologically relevant pathways (L-tryptophan biosynthesis) linked to host immune regulation.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count for both datasets is unknown, which may limit suitability assessment.
• The human cohort data is a re-analysis of publicly available data, so original sample collection biases may persist.

Provenance

Source

figshare, author Krist Antunes Fernandes.

Collection Method

16S rRNA gene sequencing of murine fecal samples and computational re-analysis (HUMAnN 3.0) of existing human shotgun metagenomes.

Time Range

null

Freshness

Last updated 2026-04-08 18:45:41; freshness should be verified.

Geography

Mouse model (laboratory setting) and human data from the Orang Asli population in Malaysia.