基于SMRT测序技术的塔里木马鹿冬季肠道菌群多样性分析  

Analysis of Gut Microbiota Diversity of Tarim Red Deer in Winter Based on the SMRT Sequencing

作　　者：祁程 姜李欢 阿卜杜萨拉木·努尔麦麦提 王开彦 单文娟 钟林强 QI Cheng;JIANG Lihuan;ABDUSALAMU Nurmamati;WANG Kaiyan;SHAN Wenjuan;ZHONG Linqiang(Xinjiang Key Laboratory of Biological Resources and Genetic Engineering,College of Life Science and Technology,Xinjiang University,Urumqi,830017,China;Forestry and Grassland Bureau of Shaya County,Shaya,842200,China)

机构地区：[1]新疆大学生命科学与技术学院,新疆生物资源基因工程重点实验室,乌鲁木齐830017 [2]新疆沙雅县林业和草原局,沙雅842200

出　　处：《野生动物学报》2024年第1期58-66,共9页CHINESE JOURNAL OF WILDLIFE

基　　金：新疆维吾尔自治区自然科学基金项目(2022D01C657);新疆大学科研启动项目(620321053);新疆大学自治区级大学生创新训练计划项目(S202210755079)。

摘　　要：为探究塔里木河流域塔里木马鹿(Cervus elaphus yarkandensis)冬季肠道菌群群落结构、多样性与功能,采用PacBio平台的单分子实时测序技术(single molecule realtime sequencing,SMRT)对塔里木河上游湿地自然保护区采集并筛选的25份塔里木马鹿粪便样本的16S rRNA基因全长进行测序,共获得298578个clean reads,clean reads聚类获得28026个OTU,包括25门684属。Alpha多样性分析结果显示,塔里木马鹿冬季肠道菌群Shannon指数为(7.764±0.044),Simpson指数为(0.015±0.001),Chao1指数为(12242.668±695.106),ACE指数为(9366.423±407.612)。塔里木马鹿优势菌门为厚壁菌门(Firmicutes,60.51%)、拟杆菌门(Bacteroidetes,26.02%)、变形菌门(Proteobacteria,3.61%)、疣微菌门(Verrucomicrobia,1.57%)和浮霉菌门(Planctomycetes,1.46%)。相对丰富度在前10的菌属为Papillibacter(5.48%)、拟杆菌属(Bacteroides,5.12%)、Muribaculum(4.69%)、Phocaeicola(4.49%)、Lawsonibacter(4.31%)、瘤胃球菌属(Ruminococcus,4.09%)、Intestinimonas(3.06%)、普氏菌属(Prevotella,2.87%)、克里斯滕森菌属(Christensenella,2.71%)和弯曲杆菌属(Campylobacter,2.54%)。PICRUSt 16S功能预测结果表明,塔里木马鹿肠道菌群基因功能主要富集于新陈代谢(48.58%)、遗传信息处理(19.04%)和环境信息处理(12.08%);其中新陈代谢主要以碳水化合物代谢(9.47%)、氨基酸代谢(9.93%)为主,并且环境信息处理的膜转运(9.96%)基因相对丰富度最高。研究揭示了野生塔里木马鹿冬季肠道菌群特征和功能,为塔里木马鹿野生种群的保护提供基础数据。The Tarim red deer(Cervus elaphus yarkandensis) is the only subspecies of red deer that has adapted to the desert habitat in China.However,there is limited knowledge about how the gut microbiota's structure and function of wild Tarim red deer adapted to desert plants.This study analyzed the gut microbiota of 25 fecal samples obtained from Tarim red deer located in the Upper Tarim River Nature Reserve using the PacBio single molecule real-time sequencing(SMRT) technique.A total of 298,578 clean reads were obtained and clustered into 28,026 OTU,belonging to 25 phyla and 684 genera.Alpha diversity analysis yielded Shannon index of(7.764±0.044),Simpson index of(0.015±0.001),Chao1 index of(12,242.668±695.106),and ACE index of(9,366.423±407.612).The dominant phyla in the gut microbiota of Tarim red deer were Firmicutes(60.51%),Bacteroidetes(26.02%),Proteobacteria(3.61%),Verrucomicrobia(1.57%),and Planctomycetes(1.46%).At the genus level,Papillibacter(5.48%),Bacteroides(5.12%),Muribaculum(4.69%),Phocaeicola(4.49%),Lawsonibacter(4.31%),Ruminococcus(4.09%),Intestinimonas(3.06%),Prevotella(2.87%),Christensenella(2.71%),and Campylobacter(2.54%) were the top 10 bacteria.PICRUSt analysis revealed that the predicted gene functions of the Tarim red deer gut microbiota were mainly in metabolism(48.58%),genetic information processing(19.04%),and environmental information processing(12.08%).Carbohydrate metabolism(9.47%) and amino acid metabolism(9.93%) were the main categories of metabolism,while membrane transport(9.96%) was the most enriched gene category of environmental information processing.This study provided the first insight into the characteristics and functions of the gut microbiota of wild Tarim red deer,which may serve as a basis for wild population conservation.

关 键 词：塔里木马鹿 肠道菌群 单分子实时测序(SMRT) PICRUSt功能预测 

分 类 号：Q938[生物学—微生物学]