Raw Illumina MiSeq sequencing reads (paired) for Screening of phytophagous and xylophagous insects guts microbiota abilities to degrade lignocellulose in bioreactor. Names used correspond the publication. 5 insects were used for screening : Beetle, Chafer, Cockroach, Cricket and Locust, with 4 samples each. Initial bacterial content (T0), end composition with blank reactor (BR) without lignocellulosic substrate, and end composition (2 biological replicates) of a wheat-straw reactor (WSR1 and WSR2). 3 insects were used for fed-batch reactors : Chefer, Cockroach and Locust. Samples are available for blank reactors (BR) and wheat straw reactors (WS) at different time points : initial reactor content (T0a and T0b for WS replicates, T0 for BR) and end content of each fed-batch cycles (SBR-Na and SBR-Nb for WS replicates, SBR-N for BR).