AUTHOR=Qin Weiyun , Xie Yunxiao , Ren Zhanshi , Xu Chao , Sun Ming-an , Yin Zongjun , Bao Wenbin 

TITLE=Integrative ATAC-seq and RNA-seq analyses of IPEC-J2 cells reveals porcine transcription and chromatin accessibility changes associated with Escherichia coli F18ac inhibited by Lactobacillus reuteri

JOURNAL=Frontiers in Microbiology

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1101111

DOI=10.3389/fmicb.2023.1101111

ISSN=1664-302X

ABSTRACT=<p><italic>Escherichia coli</italic> is the main cause of postweaning diarrhea in pigs, leading to economic loss. As a probiotic, <italic>Lactobacillus reuteri</italic> has been used to inhibit <italic>E. coli</italic> in clinical applications; however, its integrative interactions with hosts remain unclear, especially in pigs. Here, we found that <italic>L. reuteri</italic> effectively inhibited <italic>E. coli</italic> F18ac adhering to porcine IPEC-J2 cells, and explored the genome-wide transcription and chromatin accessibility landscapes of IPEC-J2 cells by RNA-seq and ATAC-seq. The results showed that some key signal transduction pathways, such as PI3K-AKT and MAPK signaling pathways, were enriched in the differentially expressed genes (DEGs) between <italic>E. coli</italic> F18ac treatment with and without <italic>L. reuteri</italic> groups. However, we found less overlap between RNA-seq and ATAC-seq datasets; we speculated that this might be caused by histones modification through ChIP-qPCR detection. Furthermore, we identified the regulation of the actin cytoskeleton pathway and a number of candidate genes (<italic>ARHGEF12</italic>, <italic>EGFR</italic>, and <italic>DIAPH3</italic>) that might be associated with the inhibition of <italic>E. coli</italic> F18ac adherence to IPEC-J2 cells by <italic>L. reuteri</italic>. In conclusion, we provide a valuable dataset that can be used to seek potential porcine molecular markers of <italic>E. coli</italic> F18ac pathogenesis and <italic>L. reuteri</italic> antibacterial activity, and to guide the antibacterial application of <italic>L. reuteri</italic>.</p>