基于QIIME2平台扩增子测序分析探究肉牛瘤胃和直肠中厌氧真菌区系结构的差异

Amplicon Sequencing Analysis Based on QIIME2 Platform Evaluates Difference in Anaerobic Fungal Structure between Ruminal and Rectal Content of Beef Cattle

本研究旨在介绍一种适用于肠道厌氧真菌扩增子测序数据的处理流程,并比较肉牛瘤胃和直肠中厌氧真菌区系结构差异。6头具永久性瘤胃瘘管的晋南牛饲喂相同的试验饲粮15 d后,于次日晨饲前分别经瘤胃瘘管和直肠采集肠道内容物样品,提取全基因组DNA后进行内转录间隔区1(ITS1)扩增子测序。结果表明:直肠粪便中厌氧真菌费氏系统发育学多样性指数显著高于瘤胃内容物(P<0.05),但采样位点对其他alpha多样性指标均无显著影响(P>0.05);beta多样性的组间差异分析表明厌氧真菌群落结构在肉牛瘤胃和直肠内容物之间具有显著差异(P<0.05);菌群差异丰度分析表明,相较于瘤胃内容物,直肠粪便中盲肠真菌属(Caecomyces)和未归类真菌(unclassified fungi)的相对丰度有升高的趋势(0.05≤P<0.10)。由此可见,厌氧真菌群落在肉牛瘤胃和直肠之间产生了生态位分化,这可能是由盲肠真菌属等单中心厌氧真菌导致的。

This study aimed to introduce a processing pipeline for amplicon sequencing data of gastrointestinal anaerobic fungal community,and to investigate the difference in anaerobic fungal composition between ruminal and rectal content of beef cattle.Six Jinnan cattle fitted with permanent rumen cannula were offered the same experimental diet for 15 days,and then ruminal and rectal content samples were collected through the rumen fistulas and rectum respectively before morning feeding on the next day.The whole genomic DNA was extracted from all samples and used to internal transcribed spacer 1(ITS1)amplicon sequencing.Results showed that the Faith phylogenetic diversity of fungal community in rectal content was higher than that in ruminal content(P<0.05),while the other alpha diversity indices were not affected by the gastrointestinal regions(P>0.05).The differential analysis of beta diversity metrics revealed a significant difference in anaerobic fungal profiles between ruminal and rectal content of beef cattle(P<0.05).Fungal differential abundance analysis indicated that the relative abundance of Caecomyces and unclassified fungi in rectal content had an increasing tendency compared with that in ruminal content(0.05≤P<0.10).In conclusion,there is a niche differentiation within anaerobic fungal community between rumen and rectum of beef cattle,which could be attributed to monocentric anaerobic fungal genus Caecomyces.