Sequencing
Shotgun metagenomic sequencing of faecal samples.
Overview
The AD-IMDB database currently contains 1,959 curated metagenome-assembled genomes (MAGs) reconstructed from shotgun metagenomic data of 3xTg-AD and wild-type mice. MAGs were retained after quality control based on completeness and contamination, followed by taxonomic and functional annotation.
Processing Overview
The pipeline combines metagenomic assembly, binning, quality control, taxonomic assignment, and functional annotation to generate a curated collection of microbial genomes of the transgenic 3xTg-AD and Wild-type mouse gut microbiome.
Microbiome Processing Pipeline
Schematic overview of the main processing steps used to derive curated MAGs and their annotations.
Quality Control
Ensuring adapter are trimmed.
Host DNA Removal
Identification and removal of host (mouse-derived) reads.
Genome Assembly
Per-sample metagenomic assembly to contigs.
Genome Binning
Clustering contigs into draft MAGs.
Coverage Estimation
Read mapping and coverage estimation per MAG.
Assembly QC
Completeness and contamination-based curation (1,959 MAGs retained).
Taxonomic Assignment
Mash-based classification of curated MAGs.
Gene Calling
Prediction of protein-coding genes on MAG assemblies.
Protein Annotation
Functional annotation using eggNOG-mapper.
Quality Metrics for Curated MAGs
Summary metrics computed from retained MAGs (N = 1,959). Values below are derived directly from the PostgreSQL database.
Total curated MAGs
1,959
Mean completeness
79.17%
Range: 50.00–100.00%>
Mean contamination
1.54%
Range: 0.00–9.73%
Mean genome length
2.29 Mb
Average: 2,293,366 bp
Quality Assessment
Distributions of Completeness, Contamination, and Genome Length
Histograms show the distributions across all curated MAGs.
Completeness Distribution
Binned across the 50–100% range.
Contamination Distribution
Binned across the 0–10% range.
Genome Length Distribution
Genome length distribution in base pairs.
Taxonomic Composition of Curated MAGs
A total of 1,805 MAGs have mash_distance ≤ 0.05, corresponding approximately to ≥95% ANI (Known genomes).
Taxonomy
Phylum Composition
Counts from all curated MAGs (N = 1,959).
Top 10 Families
Families with the largest number of MAGs.
Top 10 Species
Most frequently observed species-level assignments among curated MAGs.