利用宏基因组组装基因组揭示猪肠道微生物组的新见解。
Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes.
机构信息
Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada.
Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta, Canada.
出版信息
Microbiol Spectr. 2022 Aug 31;10(4):e0238022. doi: 10.1128/spectrum.02380-22. Epub 2022 Jul 26.
Pigs are among the most numerous and intensively farmed food-producing animals in the world. The gut microbiome plays an important role in the health and performance of swine and changes rapidly after weaning. Here, fecal samples were collected from pigs at 7 different times points from 7 to 140 days of age. These swine fecal metagenomes were used to assemble 1,150 dereplicated metagenome-assembled genomes (MAGs) that were at least 90% complete and had less than 5% contamination. These MAGs represented 472 archaeal and bacterial species, and the most widely distributed MAGs were the uncultured species sp002391315, sp004557565, and sp000434975. Weaning was associated with a decrease in the relative abundance of 69 MAGs (e.g., Escherichia coli) and an increase in the relative abundance of 140 MAGs (e.g., sp000435835, ). Genes encoding for the production of the short-chain fatty acids acetate, butyrate, and propionate were identified in 68.5%, 18.8%, and 8.3% of the MAGs, respectively. Carbohydrate-active enzymes associated with the degradation of arabinose oligosaccharides and mixed-linkage glucans were predicted to be most prevalent among the MAGs. Antimicrobial resistance genes were detected in 327 MAGs, including 59 MAGs with tetracycline resistance genes commonly associated with pigs, such as (44), (Q), and (W). Overall, 82% of the MAGs were assigned to species that lack cultured representatives indicating that a large portion of the swine gut microbiome is still poorly characterized. The results here also demonstrate the value of MAGs in adding genomic context to gut microbiomes. Many of the bacterial strains found in the mammalian gut are difficult to culture and isolate due to their various growth and nutrient requirements that are frequently unknown. Here, we assembled strain-level genomes from short metagenomic sequences, so-called metagenome-assembled genomes (MAGs), that were derived from fecal samples collected from pigs at multiple time points. The genomic context of a number of antimicrobial resistance genes commonly detected in swine was also determined. In addition, our study connected taxonomy with potential metabolic functions such as carbohydrate degradation and short-chain fatty acid production.
猪是世界上数量最多、集约化养殖的食用动物之一。肠道微生物群在猪的健康和性能中起着重要作用,并且在断奶后迅速变化。在这里,从 7 到 140 天龄的 7 个不同时间点采集了猪的粪便样本。这些猪的粪便宏基因组用于组装 1150 个去重复的宏基因组组装基因组 (MAG),这些 MAG 至少 90%完整,污染小于 5%。这些 MAG 代表了 472 种古菌和细菌物种,分布最广的 MAG 是未培养的物种 sp002391315、sp004557565 和 sp000434975。断奶与 69 个 MAG(例如大肠杆菌)的相对丰度降低和 140 个 MAG(例如 sp000435835、)的相对丰度增加有关。在 68.5%、18.8%和 8.3%的 MAG 中分别鉴定出编码产生短链脂肪酸乙酸盐、丁酸盐和丙酸盐的基因。预测 MAG 中最普遍存在的是与阿拉伯糖寡糖和混合链葡聚糖降解有关的碳水化合物活性酶。在 327 个 MAG 中检测到了抗微生物药物抗性基因,包括 59 个具有与猪常见的四环素抗性基因,如 (44)、(Q) 和 (W)。总体而言,82%的 MAG 被分配到缺乏培养代表的物种,这表明猪肠道微生物组的很大一部分仍未得到很好的描述。这里的结果还表明 MAG 可以为肠道微生物组增加基因组背景。由于许多在哺乳动物肠道中发现的细菌菌株由于其各种生长和营养需求而难以培养和分离,这些需求通常是未知的。在这里,我们从多个时间点从猪粪便中收集的短宏基因组序列(所谓的宏基因组组装基因组(MAG))组装了菌株水平的基因组。还确定了在猪中经常检测到的许多抗微生物药物抗性基因的基因组背景。此外,我们的研究将分类学与潜在的代谢功能(如碳水化合物降解和短链脂肪酸产生)联系起来。