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Background    Escherichia coli  F18 is mainly responsible for post-weaning diarrhea (PWD) in piglets. The molecular regulation of  E. coli  F18 resistance in Chinese domestic weaned piglets is still obscure. We used Meishan piglets as model animals to test their susceptibility to  E. coli  F18. Small RNA duodenal libraries were constructed for  E. coli  F18-sensitive and -resistant weaned piglets challenged with  E. coli  F18 and sequenced using Illumina Solexa high-throughput sequencing technology.    Results  Sequencing results showed that 3,475,231 and 37,198,259 clean reads were obtained, with 311 known miRNAs differently expressed in resistant and sensitive groups, respectively. Twenty-four miRNAs, including 15 up-regulated and 9 down-regulated, demonstrated more than a 2-fold differential expression between the F18-resistant and -sensitive piglets. Stem-loop RT-qPCR showed that miR-136, miR-196b, miR-499-5p and miR-218-3p significantly expressed in intestinal tissue ( p  < 0.05). KEGG pathway analysis for target genes revealed that differently expressed miRNAs were involved in infectious diseases, signal transduction and immune system pathways. Interestingly, the expression of miR-218-3p in intestinal tissue had a very significant negative correlation with target  DLG5  ( P  < 0.01).    Conclusions  Based on the expression correlation between miRNA and target genes analysis, we speculate that miR-218-3p targeting to  DLG5 , appears to be very promising candidate for miRNAs involved in response to  E. coli  F18 infection. The present study provides improved database information on pig miRNAs, better understanding of the genetic basis of  E. coli  F18 resistance in local Chinese pig breeds and lays a new foundation for identifying novel markers of  E. coli  F18 resistance.    Reviewers  This article was reviewed by Neil R Smalheiser and Weixiong Zhang.    Electronic supplementary material  The online version of this article (doi:10.1186/s13062-016-0160-3) contains supplementary material, which is available to authorized users.

Identification of microRNAs regulating Escherichia coli F18 infection in Meishan weaned piglets