基于宏基因组和转录组挖掘淮猪耐粗饲的肠道微生物特征及其特异性受体基因

Huai pig, one of Chinese old native pig breeds, is tolerant to forage. Even with only 25% ancestry of Huai pig, Suhuai pig still appeared its tolerance to high fiber diet. Reports showed a higher apparent crude fiber (CF) digestibility of indigenous pig breeds than that of exotic lean pigs. This was speculated to be related to the development of the intestinal tract and the flora of the large intestine. However, the underlying mechanism remains unclear. In this experiment, Huai pigs, controlled with Large white pigs similar in age to them, Large white pigs similar in body weight to them, 18 of each, were selected and allocated into three different groups and fed with two different diets (Low fiber diet or high fiber diet). The apparent digestibility of dietary fiber and intestinal development of these animals will be determined. Related functional gene receptor of Huai pig was searched from intestinal microorganisms (and metabolites) combined with the technology of RNAseq. Characteristics of the intestinal microbial population with crude fiber digestibility of high fiber diet in Huai pig will be determined by 16S rRNA gene sequencing. We will also characterize the functions of microbes and identify the specific gut bacteria that encoding the cellulolytic enzyme in Huai pig through metagenome de novo sequencing. The interaction between gene expression difference, host microbial abundance and their functional specificity will also be analyzed through bioinformatics analysis. We will also systematically analyze the molecular mechanism of combined action of the host and the intestinal microflora of Huai pig on its crude fiber digestibility. The results will provide a theoretical basis for dissecting the molecular basis of the crude fiber tolerance mechanism and genetic characteristics of Chinese indigenous pig breeds.

淮猪是我国优秀的耐粗饲地方猪遗传资源，即使仅含25%淮猪血统的苏淮猪，仍能耐受高纤维水平日粮。研究表明淮猪比国外瘦肉型猪对高纤维日粮粗纤维消化能力更强，且可能源于其肠道发育和大肠微生物区系特征，但机制不清。本研究以淮猪为试验动物，以同日龄和同体重大白猪为对照，分别饲喂高、低纤维日粮，分析淮猪粗纤维消化率和肠道发育特征，结合RNAseq技术挖掘淮猪肠道内特有微生物（及代谢物）受体功能基因；利用16S rRNA基因测序技术分析淮猪高粗纤维日粮消化能力的肠道微生物菌群特性，并利用宏基因组学技术挖掘淮猪与纤维消化相关的特异功能微生物；最后利用生物信息学技术分析宿主肠道基因表达特性与微生物特性的互作关系，及其互作影响粗纤维消化率的机制，为最终解析中国地方猪种耐粗饲机制与遗传特性奠定基础。

为初步评价和解析中国地方猪种耐粗饲特性，本试验以二花脸育肥阉公猪（Er-HL）为试验猪、与二花脸猪相同体重大白育肥阉公猪（S-LW）、与二花脸猪相同生理阶段大白猪（L-LW） 育肥阉公猪为对照猪，采用奥饲本 FIRE 种猪生产性能测定系统（简称 FIRE 系统）分别饲喂基础日粮、 7%麸皮替代基础日粮、14%麸皮替代基础日粮和 21%麸皮替代基础日粮28天后全部屠宰，检测、分析各组生产性能、表观消化率、肠道发育、微生物菌群结构、多样性、纤维降解菌丰度及微生物代谢、酶活特征及微生物功能特征。结果如下：.1、随着日粮纤维水平的升高， 二花脸猪的平均日采食量和日增重不受影响，且料重比显著下降（P＜0.05），但H-LW 的平均日采食量和日增重均显著降低（P＜0.05）。.2、7%麸皮替代基础日粮情况下，二花脸猪的纤维表观消化率（NDF, ADF, CL, ADS, TDF, IDF）最高，且显著高于L-LW和S-LW（P＜0.05）。.3、二花脸猪的相对大肠长度、相对盲肠、结直肠长度均极显著高于相同体重和相同生理阶段大白猪（P＜0.01）。7%麸皮替代基础日粮组和14%麸皮替代基础日粮组，二花脸猪的纤维素内切酶活力显著高于相同体重大白猪和相同生理阶段大白猪（P＜0.05）。二花脸猪高纤维消化能力的原因可能是由于其大肠发育优势和其大肠内容物具有更高的纤维素酶活力。.4、盲肠共有58个差异微生物可能为影响二花脸猪7%麸皮替代基础日粮组与其他组产生差异的关键微生物。其中Ruminococcaceae_UCG_002，Ruminococcaceae_UCG_005，Ruminococcaceae_UCG_010，Ruminococcus_1均为已知纤维分解菌。盲肠微生物差异功能包括碳水化合物运输与代谢。结肠共有15个差异微生物可能为影响二花脸猪7%麸皮替代基础日粮组与其他组产生差异的关键微生物。其中，Ruminococcaceae_UCG_009和Cellulosilyticum为已知纤维降解菌。结肠微生物的差异功能主要为碳水化合物运输与代谢。二花脸猪高纤维消化能力的原因可能是由于其特有大肠纤维分解菌和具有碳水化合物运输与代谢的功能微生物有关。