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(ⅲ) The indexes of OTU, Shannon, Simpson and observed species were all higher in SFR group than in SEC group while in GEC group than in GFR group, with SFR group showing the greatest diversity of cecum microorganisms among the four groups. (ⅰv) The clustering result was consistent with the strain classification, with a similar composition of cecum bacteria in the two strains of laying hens. Conclusion The core microbiota was not altered by husbandry systems or strains. The free-range system increased the diversity of cecal microbes onl