Microbiota consisting of various fungi and bacteria have a significant impact on the physiological functions of the host. In the wild, the presence of microbes is crucial for the developmental growth of Drosophila larvae. D. melanogaster in its natural habitat feeds on fruits fermented by its associated microbes. Germ-free larvae cannot grow on fresh fruits alone, while inoculation with certain species of yeasts or bacteria promotes pupariation. However, it is unclear which species play a central role in food microbiota and how they affect the host. To address these questions, we sampled fermented bananas that had been fed upon by wild Drosophila species. We collected the foods at two different timepoints, referred to as "early-stage" and "late-stage" foods, and demonstrated a dramatic shift in fungal and bacterial taxonomic compositions during fermentation. Regarding fungi, we observed that yeasts predominated in both stages, but the dominant species changed between the stages. Among bacterial species, Enterobacterales accounted for a large proportion in the early stage, whereas lactic acid bacteria and acetic acid bacteria dominated in the late stage. We then isolated yeast and bacterial strains from the food samples and tested their ability to support larval development. Hanseniaspora uvarum, the predominant yeast species in the early stage, was able to support larval growth by itself. In contrast, most of the late-stage microbes tested did not efficiently promote larval growth when inoculated individually. However, we found that when the acetic acid bacteria Acetobacter orientalis coexisted with either lactic acid bacteria or late-stage yeast species, it effectively promoted larval growth. Our analyses of larvae under different microbial environments strongly suggest that A. orientalis is potentially able to promote larval growth, although it requires interactions with other late-stage microbes. Finally, we investigated the molecular basis underlying the distinct larval growth-promoting effects among yeast species. Surprisingly, all the yeast species strongly promoted larval growth upon heat killing. This and additional results indicate that all species produce sufficient nutrients for larval development, but larvae cannot utilize those produced by the live non-supportive species. Our metabolomic analysis and metabolite supplementation assay suggest that only the supportive yeast cells can release critical metabolites for larval growth. Collectively, our findings detail the key microbial species, their interactions, and the yeast species-dependent supply of nutrients that contribute to the development of Drosophila larvae in nature (Mure et al. eLife, 2023).