Microbial profiling of Drosophila in French Guiana reveals candidate microbial taxa associated with native and invasive host

Invasive alien species (IAS) threaten biodiversity, human health, and economies, yet host-associated microbiome differences between invasive and native species remain poorly understood in natural systems. We investigated bacterial and fungal microbiomes of IAS and native Drosophila species collected along an anthropisation gradient in French Guiana. IAS occurrence declined strongly from coastal anthropised habitats toward rainforest localities. Using bacterial 16S rRNA and fungal ITS metabarcoding of pooled flies, we assessed microbial diversity and community structure across host species, host category (invasive vs. native), and locality. IAS-associated bacterial communities showed reduced alpha diversity and differed in structure from those of native Drosophila. Bacteriome variation was also associated with host phylogeny and locality; because host category was partially confounded with these factors, differences cannot be attributed solely to invasion status. Fungal communities were primarily associated with locality and host species. We further identified core and exclusive taxa and compared bacteriome composition with global reference datasets and microbiome literature, identifying bacterial and fungal taxa preferentially or exclusively associated with invasive or native hosts. Overall, our study characterises microbiome variation between invasive and native Drosophila in French Guiana and identifies candidate taxa for future functional investigation.