健康人血液微生物宏基因组和噬菌体组的深度挖掘分析  

Deep mining of healthy blood metagenomics and phageomes

作　　者：朱林 王琪琪 徐玉莲 黄杨 高瞻[2] 何苗[2] ZHU Lin;WANG Qiqi;XU Yulian;HUANG Yang;GAO Zhan;HE Miao(Mianyang Central Blood Station,Mianyang 621000,China;Institute of Blood Transfusion,Chinese Academy of Medical Sciences&Peking Union Medical College,Chengdu 610052,China;Sichuan College of Traditional Chinese Medicine,Mianyang 621000,China)

机构地区：[1]绵阳市中心血站,四川绵阳621000 [2]中国医学科学院北京协和医学院输血研究所,四川成都610052 [3]四川中医药高等专科学校,四川绵阳621000

出　　处：《中国输血杂志》2024年第10期1091-1100,共10页Chinese Journal of Blood Transfusion

基　　金：四川省自然科学基金面上项目(2024NSFSC0716)。

摘　　要：目的探索健康人血液中微生物和噬菌体的存在及其可能的相互作用,通过生物信息学深度挖掘探讨血液微生物生态系统的结构和功能。方法收集2012—2018年绵阳市中心血站的1600份献血者血浆标本,通过DNA提取和文库构建,使用Illumina Hiseq 4500平台进行高通量测序后进行生物信息学深度挖掘。采用Bowtie2、Trimmomatic及Kraken等宏基因组分析软件对血液标本中的微生物丰度进行分析;随后进一步使用Megahit、geNomad、CheckV和eggNOG-mapper等软件进行噬菌体组分析,包括序列质控、组装、识别、聚类和功能注释,并通过使用iTOL、BLAST和PhaBOX等软件对发现的血液噬菌体构建系统发育树、物种注释分析以及宿主分析与预测。结果宏基因组测序结果从血浆标本中识别出36个菌门、151个菌目、338个菌科、338个菌属和3757个菌种的微生物。在种的分类水平上,丰度排名前11的菌种分别是炭疽芽孢杆菌(Bacillus cereus)、鼠杆菌属乳杆菌(Lactobacillus murinus)、约翰逊乳杆菌(L.johnsonii)、普劳兹氏梭杆菌(Faecalibacterium prausnitzii)、苏云金芽孢杆菌(B.thuringiensis)、路氏乳杆菌(L.reuteri)、痤疮丙酸杆菌(Cutibacterium acnes)、海迪茨氏菌(Dietzia sp.JS16-p6b)、猪鼻炎支原体(Mycoplasma hyorhinis)、猪肺炎支原体(M.hyopneumoniae)、金黄色葡萄球菌(Staphylococcus aureus)。通过噬菌体组分析鉴定了202个噬菌体操作分类单元(vOTU),物种注释揭示了24种噬菌体类型,通过病毒宿主数据库与宿主分析,完成15个潜在的噬菌体宿主的比对,包括嗜麦芽窄食单胞菌(Stenotrophomonas maltophilia)、湖红胞菌(Rhodoferax lacus)、海洋拟变形菌(Pseudoalteromonas marina)、Thalassotalea loyana、海藻糖弧菌(Vibrio alginolyticus)、塔斯马尼亚弧菌(V.tasmaniensis)、溶血弧菌(V.vulnificus)、假单胞菌(Pseudomonas sp.)、农杆菌(Agrobacterium sp.ST15.13/040)、鸡肠球菌(Enterococcus gallinarum)、黄杆菌�Objective To explore the presence and potential interactions of microbes and bacteriophages in the blood of healthy individuals by employing in-depth bioinformatics mining to analyze the structure and function of the blood microbiome ecosystem.Methods Blood plasma samples from 1600 voluntary blood donors collected at Mianyang Central Blood Station from 2012 to 2018 were subjected to DNA extraction and library construction.High-throughput sequencing was conducted using the Illumina HiSeq 4500 platform,followed by extensive bioinformatics analysis.Microbial abundance in blood samples was analyzed using metagenomic analysis software such as Bowtie2,Trimmomatic and Kraken.Subsequent phageome analysis included sequence quality control,assembly,identification,clustering and functional annotation using software such as Megahit,geNomad,CheckV and eggNOG-mapper.Phylogenetic trees,species annotation and host analysis and prediction for the identified blood bacteriophages were constructed using iTOL,BLAST and PhaBOX software.Results Metagenomic sequencing identified microbes across 36 phyla,151 orders,338 families,338 genera and 3757 species in the plasma samples.At the species level,the most abundant species included Bacillus cereus,Lactobacillus murinus,L.johnsonii,Faecalibacterium prausnitzii,B.thuringiensis,L.reuteri,Cutibacterium acnes,Dietzia sp.JS16-p6b,Mycoplasma hyorhinis,M.hyopneumoniae and Staphylococcus aureus.Through phageome analysis,202 viral Operational Taxonomic Units(vOTUs)were identified,revealing 24 types of bacteriophages.Host analysis using the viral host database completed matches for 15 potential bacteriophage hosts,including Stenotrophomonas maltophilia,Rhodoferax lacus,Pseudoalteromonas marina,Thalassotalea loyana,Vibrio alginolyticus,V.tasmaniensis,V.vulnificus,Pseudomonas sp.,Agrobacterium sp.ST15.13/040,Enterococcus gallinarum,Flavobacterium sp.,Thermotoga naphthophila,Chryseobacterium sp.RU33C,L.acidipiscis and Neisseria mucosa.Conclusion The study of the healthy human blood microbiome and phag

关 键 词：血液微生物组 血液噬菌体组 宏基因组 高通量测序 血液微生态 

分 类 号：R457.1[医药卫生—治疗学]