Microbial community structure and diversity of fructus gardenia before and after infection

<bold>Objective</bold> This study aims to investigate the microbial community structure variation between diseased and healthy <italic>Gardenia jasminoides</italic> fruits，and identify potential pathogens. <bold>Method</bold> Metagenome was employed to analyze microbial community structures in three types of infected fruits versus healthy controls.Pathogen prediction was conducted through alignment with PHI and VFDB databases. <bold>Result</bold> （1）The overall microbial community diversity of the three diseased Gardenia jasminoides fruit samples was lower than that of the healthy ones，However，the abundance and species number of the fungal community in them increased significantly，while the abundance ratio of bacterial to fungal communities（B/F）decreased.（2）At the fungal level，<italic>Ascomycota</italic> predominated in both diseased and healthy fruits.The relative abundance of <italic>Ramularia collo-cygni</italic> and <italic>Fusarium torreyae</italic> in scab（SC）samples was significantly higher than that in other samples.The relative abundance of <italic>Zasmidium</italic> and <italic>Talaromyces</italic> in dry rot（DR）samples was significantly higher than other samples.（3）At the bacteria level，<italic>Pseudomonadota</italic> was predominantly dominant in both infected and healthy fruits，and the <italic>Methylobacterium</italic> in the three diseased samples was relatively higher than that in the healthy samples.The samples of scab also contained high relative abundance of <italic>Brevibacillus parabrevis</italic> and <italic>Bacillus amyloliquefaciens</italic>.（4）Comparison with the Pathogen-Host Interaction Database（PHI-base）and the Virulence Factor Database of Pathogenic Bacteria（VFDB）revealed that Aspergillus fumigatus，Magnaporthe oryzae，Fusarium graminearum，Zymoseptoria tritici，Pantoea dispersa，and Pantoea dispersa B may be potential pathogens of Gardenia jasminoides fruit disease. <bold>Conclusion</bold> Fungal abundance elevation correlates with Gardenia fruit disease.<italic>R.collo-cygni</italic> and <italic>F.torreyae</italic> are potential scab pathogens，while <italic>Z.cellare</italic> may cause gardenia fruit dry rot.<italic>Aspergillus fumigatum</italic>，<italic>Macrophyllum oryzae</italic>，<italic>Fusarium graminis</italic>，<italic>Zymoseptoria tritici</italic>，<italic>Pantoea dispersa</italic> and <italic>Pantoea dispersa B</italic> may be the candidate pathogens of gardenia fruit disease.<italic>Brevibacillus parabrevis</italic> and <italic>Bacillus amyloliquefaciens</italic> may be involved in the biological control of Gardenia fruit diseases.