AD-IMDB Documentation

User Guide for the Annotated Genomes of the 3xTg AD Mouse Gut Microbiota

Getting Started

The AD-IMDB database is a curated resource dedicated to the reconstruction and annotation of microbial genomes from a catalogue of shotgun metagenomic data related to Alzheimer's disease mouse models. The original dataset relative to 3xTg-AD mice was published and described in Favero et al., Biol Direct, 2024 (PMID: 39478626). Here, we implemented a computational pipeline for the ab initio reconstruction of both known and unknown genomes from raw sequencing data, followed by a targeted computational analysis of the annotated proteins. The AD-IMDB database provides access to the complete set of genomes and proteins, along with their functional annotations.

The AD-IMDB database provides 3 main functionalities:

  • Explore Genomes
  • Explore Protein Annotations
  • Access Downloads
Homepage Overview
Explore Genomes

This interface allows filtering of genomic data based on biological and quality parameters.

Genome Filter UI

Available Filters:

  • Experimental Group: All, Wild Type, Alzheimer
  • Sampling Time: 2, 6, 12 months
  • Contamination (<=): e.g., 5
  • Completeness (>=): e.g., 90
Example Query: Alzheimer + 2 months + ≤ 5 % contamination + ≥ 50 % completeness
Example Filtered Search

Genome Results:

  • Color-coded by quality
  • Sortable & filterable table
Genome Table
Genome Details View

Click a Genome Label to view detailed information:

  • General Info
  • Assembly Quality Metrics
  • Predicted Sequences
  • MAG Downloads
General Info Assembly Metrics Predicted Sequences Genome Download
Taxonomy Search

Use taxonomic levels to filter genomes:

  • Levels: Kingdom, Phylum, Class, Order, Family, Genus, Species
  • Search term must match database classification
Example: Select "Phylum" and enter "Bacillota (Synonym of Firmicutes)". NB: You may need to use synonyms.
Taxonomy Search UI
Protein Annotations

Sequence Annotations Search

This page allows users to query annotated genomic sequences by protein domains, metabolic pathways, and gene ontologies.

How to Use the Search

  1. Enter a Search Term
    • Examples: PASTA, ko00550, GO:0003674
  2. Select Search Type
    • PFAMs – Protein family domains
    • KEGG Pathway – Metabolic/signaling pathways
    • KEGG Ontology – Functional gene groupings
    • GO Terms – Gene Ontology categories
  3. Click the Search Button
Annotation Search UI
Make sure your search term format matches the selected search type.

Search Results Table

Query Sequence Description KEGG Pathway KEGG Ontology GO Terms PFAMs Action
Example_01 Hypothetical Protein ko00550 K03456 GO:0003674 PF03793
Downloads

Downloads

This section provides access to key datasets including genomic assemblies, annotations, and supporting material.

  • File Name – A descriptive title
  • Description – Brief summary of contents
  • Size – For estimating download time
  • Download – A direct download link
⚠️ This list may be updated as new datasets are added.
Data Downloads Page Screenshot