Fusarium oxysporum
f.sp.
cubense
(Foc) is a soil-borne pathogen causing fusarium wilt banana disease. Management of soil-borne disease generally required the application of toxic pesticides or fungicides strongly affect the soil microbiomes ecosystem. Suppressive soil is a promising method for controlling soil-borne pathogens in which soil microbiomes may affect the suppressiveness. The comparative analysis of microbial diversity was conducted from suppressive and conducive soils by analyzing whole shotgun metagenomic DNA data. Two suppressive soil samples and two conducive soil samples were collected from a banana plantation in Sukabumi, West Java, Indonesia. Each soil sample was prepared by mixing the soil samples collected from three points sampling sites with 20 cm depth. Analysis of microbial abundance, diversity, co-occurrence network using Metagenome Analyzer 6 (MEGAN6) and functional analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed. Data showed the abundance of
Actinobacteria, Betaproteobacteria, Rhizobiales, Burkholderiales, Bradyrhizobiaceae, Methylobacteriaceae, Rhodopseudomonas palustri
s, and
Methylobacterium nodulans
were higher in the suppressive than conducive soils. Interestingly, those bacteria groups are known functionally as members of Plant Growth Promoting Rhizobacteria (PGPR). The co-occurrence analysis showed
Pseudomonas, Burkholderia
, and
Streptomyces
were present in the suppressive soils, while
Bacillus
and more
Streptomyces
were found in the conducive soils. Furthermore, the relative abundance of
Pseudomonas
,
Burkholderia
,
Bacillus
, and
Streptomyces
was performed. The analysis showed that the relative abundance of
Pseudomonas
and
Burkholderia
was higher in the suppressive than conducive soils. Therefore, it assumed
Pseudomonas
and
Burkholderia
play a role in suppressing Foc based on co-occurrence and abundance analysis. Functional analysis of
Pseudomonas
and
Burkholderia
showed that the zinc/manganese transport system was higher in the suppressive than conducive soils. In contrast, the phosphate transport system was not found in conducive soils. Both functions are may be responsible for the synthesis of a siderophore and phosphate solubilization. In conclusion, this study provides information that PGPR may be contributing to Foc growth suppressing by releasing secondary metabolites.