Examples

Co-ocurrence Network Case Study: Clavibacter

This section provides an example of how to analyze co-occurrence networks using the Clavibacter dataset. The dataset includes various Clavibacter species, and the analysis focuses on identifying microbial genera associated with Clavibacter across plant microbiomes (chili, corn, tomato).

Input:

  • OTU tables from microbiome samples (Kraken2) aggregated at genus level.

Analysis:

  • Bray-Curtis dissimilarity and Spearman correlation.

  • Links defined by dissimilarity < 0.3 and weight > 0.7.

  • Networks built and visualized in Gephi, colored by class.

Samples:

  • Chili (n = 13)

  • Corn (n = 34)

  • Tomato (n = 18)

Findings:

  • Bifidobacterium and Curtobacterium consistently correlated with Clavibacter.

  • 6 genera negatively correlated across two hosts.

  • 65 taxa showed host-specific associations.

Includes co-occurrence graphs and Venn diagram summarizing genus overlap across hosts.

Clavibacter Co-occurrence Network