Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, RDA, Wanju 55365, Korea.
Swine Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Korea.
Genes (Basel). 2019 May 20;10(5):382. doi: 10.3390/genes10050382.
The microbial composition in the cecum of pig influences host health, immunity, nutrient digestion, and feeding requirements significantly. Advancements in metagenome sequencing technologies such as 16S rRNAs have made it possible to explore cecum microbial population. In this study, we performed a comparative analysis of cecum microbiota of crossbred Korean native pigs at two different growth stages (stage L = 10 weeks, and stage LD = 26 weeks) using 16S rRNA sequencing technology. Our results revealed remarkable differences in microbial composition, α and β diversity, and differential abundance between the two stages. Phylum composition analysis with respect to SILVA132 database showed to be present at 51.87% and 48.76% in stages L and LD, respectively. Similarly, were present at 37.28% and 45.98% in L and LD, respectively. The genera , , , were differentially enriched in stage L, whereas , , were enriched in stage LD. Functional annotation of microbiome by level-three KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis revealed that glycine, serine, threonine, valine, leucine, isoleucine arginine, proline, and tryptophan metabolism were differentially enriched in stage L, whereas alanine, aspartate, glutamate, cysteine, methionine, phenylalanine, tyrosine, and tryptophan biosynthesis metabolism were differentially enriched in stage LD. Through machine-learning approaches such as LEfSe (linear discriminant analysis effect size), random forest, and Pearson's correlation, we found pathways such as amino acid metabolism, transport systems, and genetic regulation of metabolism are commonly enriched in both stages. Our findings suggest that the bacterial compositions in cecum content of pigs are heavily involved in their nutrient digestion process. This study may help to meet the demand of human food and can play significant roles in medicinal application.
盲肠中的微生物组成极大地影响宿主的健康、免疫、营养消化和饲养需求。16S rRNA 等宏基因组测序技术的进步使得探索盲肠微生物种群成为可能。在这项研究中,我们使用 16S rRNA 测序技术对两个不同生长阶段(L 期=10 周和 LD 期=26 周)的杂交韩国本地猪的盲肠微生物群进行了比较分析。我们的结果表明,两个阶段的微生物组成、α和β多样性以及差异丰度存在显著差异。基于 SILVA132 数据库的门组成分析表明,L 期和 LD 期的分别为 51.87%和 48.76%。同样,L 期和 LD 期的分别为 37.28%和 45.98%。属 、 、 、 、 、 、 在 L 期差异丰富,而 、 、 则在 LD 期富集。通过三级 KEGG(京都基因与基因组百科全书)途径分析对微生物组进行功能注释表明,L 期差异丰富的代谢途径包括甘氨酸、丝氨酸、苏氨酸、缬氨酸、亮氨酸、异亮氨酸、精氨酸、脯氨酸和色氨酸代谢,而 LD 期差异丰富的代谢途径包括丙氨酸、天冬氨酸、谷氨酸、半胱氨酸、蛋氨酸、苯丙氨酸、酪氨酸和色氨酸生物合成代谢。通过 LEfSe(线性判别分析效应大小)、随机森林和 Pearson 相关等机器学习方法,我们发现氨基酸代谢、运输系统和代谢的遗传调控等途径在两个阶段都普遍富集。我们的研究结果表明,盲肠内容物中猪的细菌组成在其营养消化过程中起着重要作用。本研究可能有助于满足人类食品的需求,并在医学应用中发挥重要作用。