| Animals and plants are complex life systems composed of host and symbiotic microorganisms.Especially,the gastrointestinal tract of an animal is colonized by a complex and abundant ensemble of microbes.Studies suggested that the gut microbiota was mutualistic,co-metabolism,and coevolved with host genetic.In recent years,with the rapid development of next generation high-throughput sequencing technology,the goal,scope and ability of environmental microbiology research have been greatly changed and improved.Therefore,the research on intestinal microbitoa of animals,including humans,has became a hot spot.Studies have shown that gut microbitoa are affected by both environmental and genetic factors.And cognition of microbial composition and structure of the human and some of the main model animals and agricultural animals have been preliminarily completed,and on this basis,the complex relationships among host traits,genetic basis and gut microbiota were studied and discussed.Nevertheless,it is limited by many factors such as theory,technology and method,our understanding of gut microbiota is limited to the collection of phenotypic data and single-direction correlation analysis,little is known about the complex interactions between host-gut microbes and their coevolutionary relationships during long-term adaptation and evolution.In this study,we used chicken of bidirectional selection lines as model,which included two groups: chickens that had undergone long-term,bidirectional selection for a single immune trait and body weight trait that supplied by Dr.Paul seigel from Virginia Polytechnic Institute and State University.Using next generation high-throughput sequencing technology,we detected the expression of mRNA and miRNA,genomic DNA methylation modification of intestinal tissues,and composition and distribution of gut microbiota.From transcriptome,epigenomics and microbiome,we analyzed and compared the adaptive change of host and gut microbiota,in addition,from the perspective of hologenome,systematic integration and analysis of multi-omics information,aim to explore the possible internal relations among host traits,genetic basis and gut microbiota.It provides a basic reference for the study of the molecular mechanism of the symbiosis and co-evolution of host and gut microbiota.The details of results are listed below:(1)After long-term bidirectional selection,we found that the structure of gut microbitoa was significantly changed.Compared to high antibody selection(HAS)line,results indicated that there were 8 genera belonged to proteobacteria(potentially pathogenic microbe)that was enriched in low antibody selection(LAS)line.Microbial functional analysis showed that pathway of infectious disease was also enriched in LAS line.Relaxing selection enriched some microorganisms whose functions were opposite to host immunity.Particularly,Ruminococcaceae and Oscillospira enriched in high antibody relax(HAR)line and contributed to reduction in antibody response,while Lactobacillus increased in low antibody relax(LAR)and elevated the antibody response.Microbial functional analysis showed alterations were involved in pathways relating to the immune system and immune system disease.Our findings demonstrated a coadaptation relationship of host-microbiome and that gut microorganisms influenced host immunity.(2)We detected the composition of miocrobiota between high weight(HW)and low weight(LW)line and further proved that the structure of gut microbiota was altered by long-term selection stress.Results demonstrated that the composition and structure of microbiota in different intestinal segments were varied,and the composition of microbiota in cecum and small intestine was significantly changed.In addition,the cecal microbiota has the highest diversity.Enriched microorganisms of cecum have an important impact on the difference of chicken body weight,for example,the 8 genera with the ability to produce short chain fatty acid were enriched and may supply sufficient energy substrate for the HW line.The results of metagenome sequencing have also found pathways associated with host growth,such as TCA cycle,gluconeogenesis,oxidative phosphorylation and PPAR signaling pathway that all enriched in HW line.The results shown that the gut microbiota had adaptive changes under severe pressure of artificial selection and may contribute to the difference of host traits.(3)Comparative analysis of the gene expression profile between HW and LW lines.There were 327 differentially expressed genes between the two lines.The growth-related gene IGF2BP1 was the most significantly upregulated gene in the HW line.In addition,it was found that the expression levels of Myl2,MYBPC3 and CASQ2 were significantly up-regulated in HW line.The three genes are involved in the development of cardiac muscle and heart.Conversely,the GAL2,GAL6 and GAL7 related to defensins were all up-regulated in the LW line.The results indicated that the genes related to host growth,cardiac development and innate immunity cecum were differentially expressed after long-term selection bidirectional.(4)We identified 4,779 differential methylation regions(DMR)between HW and LW line.There were 641 differential methylation genes(DMG)that were identified.Through integrated analysis with mRNA profile,we found that the growth-related gene IGF2BP1 was hypermethylated in LW line and up-regulated expression in HW line.The DMR involved in IGF2BP1 occurred in CpG island and the distance to transcription initiation site is only 388 bp.The results illuminated that the epigenetic structure of host genome also changed under the selection pressure and the change of methylation level may have an important regulatory effect on the expression of related genes.(5)According to integrated analysis by multi-omics data of cecum,there was a high positive correlation between host cecum gene expression,miRNA expression and the abundance of some microorganisms.Such as the expression of ENSGALG00000026130 and Flavobacteriaceae,the expression of gga-miR-1682 and Ruminococcus,and the correlation coefficient is greater than 0.8.To some extent,it indicated the interaction relationship between host and gut microbiota.To sum up,under the selection pressure,the gut microbiota respond rapidly to changes in host genomes and undergo adaptive changes,and the variation may have an important impact on the difference of host traits,for example,the changed microbes may be involved in the regulation of host immune responses,or provide sufficient energy substrates and promote the growth of the host.Besides,transcriptional expression and epigenetics of genes in host cecum were significantly altered,in which,growth related genes such as IGF2BP1 and SMAD1 showed significant changes in transcriptional expression and methylation modification.These results not only reflect the host’s response to the selection of weight traits,but also suggest that chicken cecum may be widely involved in the physiological processes of host growth,immunity and heart and its regulation.Thus,we hypothesized that under the selection pressure,both host genome and gut microbiota have adaptive changes,and the sum of these effects may have important influence on host traits. |
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