基于高通量测序技术分析中国荷斯坦奶牛瘤胃纤毛虫的物种多样性

摘要：

瘤胃纤毛虫是反刍动物瘤胃微生态系统的重要组成部分，在调控瘤胃微环境及参与其宿主动物的生理功能等方面具有重要作用，然而，家养反刍动物瘤胃中的瘤胃纤毛虫物种多样性及不同动物个体间瘤胃纤毛虫群落结构的差异仍不清楚。采用基于 18S rRNA 基因的高通量测序技术，解析了中国荷斯坦奶牛瘤胃内纤毛虫的物种多样性和宿主不同个体间的差异，选取3头成年健康中国荷斯坦奶牛共采集了9个瘤胃液样品，提取样品总DNA后，采用瘤胃纤毛虫 18S rRNA 基因 V5~V8 区特异性引物进行扩增，扩增产物使用 lon S5™ XL平台测序。去除低质量序列和嵌合体后，共获得 721250条高质量有效序列，基于97%的序列一致性聚类获得38个操作分类单元(operational taxonomic units,OTU)。不同个体样品间在a多样性 Chaol,ACE,Shannon和 Simpson 指数上，差异不显著。OTUs的物种分布属于纤毛门裂口纲毛口亚纲，在属水平分类上，它们主要分布于 10 个已知的瘤胃纤毛虫的属，其中内毛属是相对丰度最高的属,同时还检测到一些未被分类和鉴定的瘤胃纤毛虫，同一牧场同一饲喂条件下的不同个体之间，瘤胃纤毛虫的物种多样性没有显著差异，但不同个体之间在均匀度上存在一定的差异，研究结果将为瘤胃纤毛虫的高通量测序分析和综合分类学研究提供参考。

Rumen ciliates, the dominant protozoa in rumen, are integral part of the rumen eco-system and important to the rumen ecosystem and their host animal physiology, However, the full spectrum of rumen ciliate community diversity and individual variability in domesticated ruminant rumen is still elusive, Here, using 18S rRNA gene high-throughput sequencing technique, we deciphered the rumen ciliate community diversity and individual variability in Chinese Holstein dairy cow rumen.The special primer set of the ciliate 18S rRNA gene were used, A total of 721 250 high-quality effective sequences were obtained after sequence filtering and chimera removal, and 38 operational taxonomic units(OTUs) were obtained at 97% sequence iden-tity, The differences in alpha diversity indices, including Chaol, ACE, Shannon, and Simpson indices, among samples from different individuals were not statistically significant. Taxonomy assignments revealed that the identified O'TUs were assigned to the Litostomatea class Trichostomatia subelass, At the genus level, ten genera were assigned, of which Enodinium is the most predominant one, and a few unclassified and unidentified rumen ciliates were also detected, No significant diferent of rumen ciliate community diversity among different individuals fed on the same diet on the same farm, while little evenness difference was found between different individuals, This work would provide a reference basis for further study on metagenome analyses and integrated taxonomy of rumen ciliates in the future.

作者：

何金英，徐勤辉，王字嘉，江奕希，黄一菲，李曼，熊杰，冯金梅

Zhang Meizhen, Yin Chao, Zhang Zeyi, Yang Yimin, Zhang Zhenlong

机构地区：

江汉大学医学部病原生物学教研室；中国科学院水生生物研究所；淡水生态与生物技术国家重点实验室

引用本文：

何金英，徐勤辉，王字嘉等，基于高通量测序技术分析中国荷斯坦奶牛瘤胃纤毛虫的物种多样性[J].河南师范大学学报(自然科学版),2025,53(4):132-140,(He Jinying,Xu Qinhui, Wang Yujia,et al. High-throughput sequencing deciphering diversity and individual variability of rumen ciliate protozoa in Chinese Holstein dairycows[ J ]. Journal of Henan Normal University(Natural Science Edition),2025,53(4):132-140.D01;10.16366/j.cnki.1000-2367.2024.06.13.0001.)

基金：

国家自然科学基金；国家重点研发计划项目

关键词：

瘤胃纤毛虫；原生生物;多样性；18S rRNA基因测序；分类学

rumen ciliates; protozoa; diversity; 18S rRNA gene sequencing; taxonomy

分类号：

Q939

基于高通量测序技术分析中国荷斯坦奶牛瘤胃纤毛虫的物种多样性.pdf