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A case study of the effects of rearing yellow mealworm (Tenebrio molitor L.) in a closed artificial ecosystem on their associated microbial communities is presented. Two groups of T. molitor larvae were reared, one in a controlled environment agricultural ecosystem and another one in an open environment (as a control). Microbial community structures of larval midgut, larval homogenate and frass samples of both groups, and a sample of feed, which was made through the fermentation of plant wastes, were tested by 16S rRNA gene sequencing on the Illumina MiSeq platform. Microbiota differences among the two groups and the feed revealed that the diversities of microbial communities in all samples of both groups decreased compared with the feed, with the lowest in midgut of the both groups. Compared with the three samples from the closed ecosystem, those from the open environment had higher abundances of Bacillus, Lactococcus, Weissella, Escherichia and Clostridiaceae. Enterococcus and some unclassified Enterobacteriaceae were identified as the predominant bacteria in samples from the closed ecosystem. The classes Acidobacteria, Planctomycetacia and Sphingobacteria were found in feed, but almost disappeared in the samples of both groups. Possible metabolic and immune effects of the above differences in associated microbial communities on larval growth are discussed. With the aim of improving the rearing efficiency of T. molitor in such a controlled environment agricultural ecosystem, follow-up study would focus on microbial isolation from the midgut of T. molitor for the preparation of probiotics as well as measures of microbial pathogen control.