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Background  The microbiota in the cecum of laying hens is crucial for host digestion, metabolism, and odor gas production. The results of recent studies have suggested that host microRNAs (miRNAs) can regulate gene expression of the gut microbiota. In the present study, the expression profiles of host-derived miRNAs in the cecal content of two laying hen breeds; Hy-line Gray and Lohmann Pink, which have dissimilar H 2 S production, were characterized; and their effects on H 2 S production by regulating the expression of gut microbiota-associated genes were demonstrated.    Results  The differential expression of microbial serine O-acetyltransferase, methionine synthase, aspartate aminotransferase, methionine-gamma-lyase, and adenylylsulfate kinase between the two hen breeds resulted in lower H 2 S production in the Hy-line hens. The results also revealed the presence of miRNA exosomes in the cecal content of laying hens, and an analysis of potential miRNA-target relationships between 9 differentially expressed miRNAs and 9 differentially expressed microbial genes related to H 2 S production identified two methionine synthase genes,  Odosp_3416  and  BF9343_2953 , that are targeted by gga-miR-222a. Interestingly, in vitro fermentation results showed that gga-miR-222a upregulates the expression of these genes, which increased methionine concentrations but decreased H 2 S production and soluble sulfide concentrations, indicating the potential of host-derived gga-miR-222a to reduce H 2 S emission in laying hens.    Conclusion  The findings of the present study reveal both a physiological role by which miRNAs shape the cecal microbiota of laying hens and a strategy to use host miRNAs to manipulate the microbiome and actively express key microbial genes to reduce H 2 S emissions and breed environmentally friendly laying hens.Video AbstractSupplementary Information  The online version contains supplementary material available at 10.1186/s40168-021-01098-7.

microbiome

Breed differences in the expression levels of gga-miR-222a in laying hens influenced H2S production by regulating methionine synthase genes in gut bacteria