Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China
Characterization of the Pig Gut Microbiome and Antibiotic Resistome in Industrialized Feedlots in China
复制标题
中国工业化饲养场猪肠道微生物组和抗生素耐药性的特征
DOI：
10.1128/msystems.00206-19
复制
发表时间：
2019-11-01
期刊：
影响因子：
6.4
通讯作者：
Liu, Siguo
中科院分区：
文献类型：
--
作者：
Wang, Chunlai;Li, Peng;Liu, Siguo
肠道菌群被认为与宿主的许多重要生理功能密切相关。关于哺乳动物肠道宏基因组的全面数据促进了宿主-微生物组相互作用机制的研究，但与人类微生物组相比，对猪肠道微生物组，特别是工业化饲养场猪的肠道微生物组知之甚少。另一方面，作为重要的食物来源，生猪生产被认为加剧了人类的抗生素耐药性，原因是世界各地在生猪生产中滥用抗生素。这项研究描绘了工业化饲养场中猪肠道微生物组和抗生素耐药组的复杂图景，并可能为养猪业提供见解。摘要为了表征普通养猪场猪肠道微生物组和抗性组的多样性和丰富性，并探索其功能和结构，我们对来自中国四个偏远省份的四个不同工业化饲养场的猪粪便进行了采样和宏基因组测序。令人惊讶的是，与先前发表的猪肠道微生物组参考基因目录（RGC）相比，当前目录中超过一半的非冗余基因（1，937，648，54.3%）是新发现的。此外，通过分析每个饲养场的优势物种，获得了16个高完整性的基因组草图。值得注意的是，其中七种经常出现在人体部位。尽管非冗余基因的数量较少，但我们的研究确定了比RGC中可用的更多的抗生素抗性基因。四环素类、氨基糖苷类和多药耐药基因占目前目录中相对丰度的近70%。工业化饲养场猪肠道微生物组和人类肠道微生物组之间的共享率略高于RGC和人类对应物之间的共享率（基因为14.7%对12.6%，功能组为94.1%对87.7%）。此外，发现猪、人和小鼠耐药组共有大量抗生素耐药蛋白（n =141），这表明耐药基因有水平转移的潜力。在猪和人共有的抗生素耐药蛋白中，50个蛋白与四环素耐药相关，49个与氨基糖苷类耐药相关。肠道微生物群被认为与宿主的许多重要生理功能密切相关。关于哺乳动物肠道宏基因组的全面数据促进了宿主-微生物组相互作用机制的研究，但与人类微生物组相比，对猪肠道微生物组，特别是工业化饲养场猪的肠道微生物组知之甚少。另一方面，作为重要的食物来源，生猪生产被认为加剧了人类的抗生素耐药性，原因是世界各地在生猪生产中滥用抗生素。这项研究描绘了工业化饲养场中猪肠道微生物组和抗生素耐药组的复杂图景，并可能为养猪业提供见解。
The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry. ABSTRACT To characterize the diversity and richness and explore the function and structure of swine gut microbiome and resistome in common pig-farming feedlots, we sampled and metagenomic sequenced the feces of pigs from four different industrialized feedlots located in four distant provinces across China. Surprisingly, more than half of the nonredundant genes (1,937,648, 54.3%) in the current catalogue were newly found compared with the previously published reference gene catalogue (RGC) of the pig gut microbiome. Additionally, 16 high-completeness draft genomes were obtained by analyzing the dominant species on each feedlot. Notably, seven of these species often appeared in the human body sites. Despite a smaller number of nonredundant genes, our study identified more antibiotic resistance genes than those available in the RGC. Tetracycline, aminoglycoside, and multidrug resistance genes accounted for nearly 70% of the relative abundance in the current catalogue. Slightly higher sharing ratios were shown between the industrialized feedlot pig gut microbiomes and human gut microbiomes than that between the RGC and human counterpart (14.7% versus 12.6% in genes and 94.1% versus 87.7% in functional groups, respectively). Furthermore, a remarkably high number of the antibiotic resistance proteins (n =141) were identified to be shared by the pig, human, and mouse resistome, indicating the potential for horizontal transfer of resistance genes. Of the antibiotic resistance proteins shared by pigs and humans, 50 proteins were related to tetracycline resistance, and 49 were related to aminoglycoside resistance. IMPORTANCE The gut microbiota is believed to be closely related to many important physical functions in the host. Comprehensive data on mammalian gut metagenomes has facilitated research on host-microbiome interaction mechanisms, but less is known about pig gut microbiome, especially the gut microbiome in industrialized feedlot pigs, compared with human microbiome. On the other hand, pig production, as an important source of food, is believed to exacerbate the antibiotic resistance in humans due to the abuse of antibiotics in pig production in various parts of the world. This study delineates an intricate picture of swine gut microbiome and antibiotic resistome in industrialized feedlots and may provide insight for the pig producing industry.