Table 1. Bacterial community samples used in this study.

Naturally Collected Flies
Library Name	Species	Diet	Location
ELA	D. elegans	Alpinia Flowers	Hsinchu, Taiwan
ELD	D. elegans	Brugmansia Flowers	Hsinchu, Taiwan
FLV	D. flavohirta	Syzigium Flowers	NSW, Australia
FNS	D. falleni	Mushroom, Russula sp.	Stony Brook, NY
HCF	D. hydei	Citrus Fruit	Winters, Ca
HPM	D. hydei	Pomegranate Fruit	Winters, Ca
HPP	D. hydei	Opuntia Fruit	Arboretum, Davis, Ca
ICF	D. immigrans	Citrus Fruit	Winters, Ca
IMH	D. sp. aff. immigrans	Hibiscus flowers	Captain Cook, Hawaii
MAG	D. sulfurigaster	Mango Fruit	Waimanu, Hawaii
MAH	D. melanogaster	Grapes	Mahoney Winery, Napa, Ca
MAW	D. melanogaster	Grapes	Mahoney Winery, Napa, Ca
MIC	Microdrosophila sp.	Shelf Mushroom	Malaysia
MOV	D. mojavensis + D. arizonae	Agria Cactus	Sonora, Mexico
POM	Unidentified Drosophila	Ipomoea Flowers	Waimanu, Hawaii
PON	Unidentified Drosophila	Pandanus Fruit	Waimanu, Hawaii
SCA	Scaptodrosophila hibiscii	Hibiscus Flowers	Queensland, Australia
SEC	D. sechellia	Morinda Fruit	Seychelles, Africa
TBB	D. melanogaster	Citrus Fruit	Winters, Ca
TKM	D. takahashii	Morinda Fruit	Captain Cook, Hawaii

All 20 naturally collected samples were obtained without the use of artificial baits. All samples represent either externally washed whole bodies or dissected intestines, unless otherwise noted. All laboratory samples are from the University of California, Davis. Further details, including media composition, are provided in Dataset S1 and Text S1.