Additional file 8 of Integrative analysis of the mouse cecal microbiome across diet, age,

Supplementary Material 8 from a study of the diverse BXD mouse population integrates multiple data layers on the cecal environment. The 12.5 MB ZIP file contains nine tables, including raw RNA-Seq counts, log-transformed gene expression, and relative bacterial abundances from MetaPhlAn 4 and Kraken2 pipelines. Ziyun Zhou published this dataset on figshare in May 2026 under a CC-BY-4.0 license.

Use Cases

• Correlate host gene expression with microbiome composition based on paired mRNA and metagenomic data.
• Investigate the influence of diet, age, and weight on gut microbial communities using the provided metadata.
• Perform functional pathway analysis of microbial communities using the HUMAnN 3.8 pipeline outputs.
• Cross-reference bacterial taxonomic names across MetaPhlAn4, SGB_ID, and GTDB databases.
• Compare relative abundance profiles from different bioinformatics pipelines (MetaPhlAn 4 vs. Kraken2).

Strengths

• Integrates multiple data types: host gene expression (RNA-Seq), microbiome composition, and functional pathways.
• Provides data from two established bioinformatics pipelines (MetaPhlAn 4 and Kraken2) for cross-validation.
• Includes a cross-reference table for taxonomic names across three major databases.
• Released under a permissive CC-BY-4.0 license for broad reuse.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment for large-scale analyses.
• Data may reflect biases inherent to the specific BXD mouse population and experimental design.

Provenance

Source

figshare, author Ziyun Zhou.

Collection Method

Likely generated from laboratory experiments on BXD mouse strains, with sequencing data processed through standard bioinformatics pipelines (MetaPhlAn 4, HUMAnN 3.8, Kraken2).

Freshness

Last updated 2026-05-14 04:35:41; freshness should be verified.