Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong Universitygrid.16821.3c, Shanghai, People's Republic of China.
Department of Animal and Poultry Sciences, Virginia Techgrid.438526.e, Blacksburg, Virginia, USA.
mSystems. 2022 Feb 22;7(1):e0126121. doi: 10.1128/msystems.01261-21. Epub 2022 Jan 11.
Multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts and variation in DNA methylation, mRNA expression, and microRNA profiles in the ceca. Insulin-like growth factor 2 mRNA-binding protein 1 () was the most upregulated gene in HWS ceca with its expression likely affected by the upregulation of expression of gga-miR-2128 and a methylated region near its transcription start site (388 bp). Correlation analysis showed that expression was associated with an abundance of microbes, such as and These findings suggest that was regulated in the hologenome in adapting to long-term artificial selection for body weight. Our study provides evidence that adaptation of the holobiont can occur in the microbiome as well as in the epigenetic profile of the host. The hologenome concept has broadened our perspectives for studying host-microbe coevolution. The multiomic analyses reported here involved two lines of chickens, from a common founder population, that had undergone long-term selection for high (HWS) or low (LWS) 56-day body weight. In these lines that differ by around 15-fold in body weight, we observed different compositions of intestinal microbiota in the holobionts, and variation in DNA methylation, mRNA expression, and microRNA profiles in ceca. The insulin-like growth factor 2 mRNA-binding protein 1 () was the most upregulated gene in HWS ceca with its expression likely affected by a methylated region near its transcription start site and the upregulation of expression of gga-miR-2128. Correlation analysis also showed that expression was associated with the abundance of microbes, such as Lactobacillus and . These findings suggest that was regulated in the hologenome in response to long-term artificial selection for body weight. Our study shows that the holobiont may adapt in both the microbiome and the host's epigenetic profile.
多组学分析涉及两条来自共同创始人群的鸡系，它们经历了长期的高（HWS）或低（LWS）56 日体重选择。在这些体重差异约 15 倍的鸡系中，我们观察到了肠道微生物群落的不同组成，以及盲肠中 DNA 甲基化、mRNA 表达和 microRNA 谱的变化。胰岛素样生长因子 2 mRNA 结合蛋白 1（）是 HWS 盲肠中上调最明显的基因，其表达可能受到gga-miR-2128 表达上调和其转录起始位点附近甲基化区域的影响。相关性分析表明，表达与微生物丰度相关，如和。这些发现表明，在适应长期人工体重选择时，在全息基因组中对进行了调节。我们的研究提供了证据，表明全息生物可以在微生物组以及宿主的表观遗传特征中适应。全息基因组概念拓宽了我们研究宿主-微生物共同进化的视角。这里报告的多组学分析涉及两条来自共同创始人群的鸡系，它们经历了长期的高（HWS）或低（LWS）56 日体重选择。在这些体重差异约 15 倍的鸡系中，我们观察到了肠道微生物群落的不同组成，以及盲肠中 DNA 甲基化、mRNA 表达和 microRNA 谱的变化。胰岛素样生长因子 2 mRNA 结合蛋白 1（）是 HWS 盲肠中上调最明显的基因，其表达可能受到其转录起始位点附近甲基化区域和 gga-miR-2128 表达上调的影响。相关性分析还表明，表达与微生物丰度相关，如和。这些发现表明，在适应长期人工体重选择时，在全息基因组中对进行了调节。我们的研究表明，全息生物可能在微生物组和宿主的表观遗传特征中都适应。
