microorganisms Article New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome Elias Asimakis 1 , Panagiota Stathopoulou 1 , Apostolis Sapounas 2, Kanjana Khaeso 1, Costas Batargias 2 , Mahfuza Khan 3 and George Tsiamis 1,* 1 Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, 2 Seferi St., 30100 Agrinio, Greece;
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[email protected]; Tel.: +30-264-107-4149 Abstract: Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the Citation: Asimakis, E.; Stathopoulou, highest relative abundance across populations. Network analysis indicated variable interactions P.; Sapounas, A.; Khaeso, K.; between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain Batargias, C.; Khan, M.; Tsiamis, G.