利用宏基因组学方法分析健康人群肠道微生物与其生理指标的关系

目的探究亚洲健康人群的肠道菌群组成特征及其与血压和年龄相关生理指标的关系。方法应用WGCNA分析,对22个健康个体肠道微生物细菌基因组进行解析。结果亚洲健康人肠道微生物相对丰度最高的细菌门水平分别是Firmicutes(厚壁菌门)、 Bacteroidetes(拟杆菌门)以及Proteobacteria(变形菌门),并且在Proteobacteria中显示高差异性。WGCNA分析结果表明两个模块(yellow,green)中微生物物种丰富度分别与收缩压和舒张压以及年龄呈正相关(t=3.098 1,P=0.005 6;t=3.015 9,P=0.006 8;t=2.390 8,P=0.026 7)。其中Ruminococcus sp.(瘤胃球菌)、Oscillospiraceae sp.(颤螺菌)、Clostridium hathewayi(哈氏梭菌)与血压呈现显著正相关;Intestinibacter(肠杆菌)、Clostridium(梭菌)、Blautia(劳特菌)以及Veillonella(韦荣球菌)属下的Aypic、Tobetsuensis rogosae与年龄呈现正相关。抗性基因注释结果表明,年龄和血压相关核心菌群均富集有较多的大环内酯-林可酰胺-链霉素类、杆菌肽类以及四环素类抗生素抗性基因。其中多黏菌素类抗性基因仅存在于年龄相关核心菌群而氯霉素抗性基因仅存在于血压相关核心菌群。结论健康人肠道微生物物种丰度与血压以及年龄相关,肠道菌群可能在心血管疾病以及衰老过程中发挥重要影响。     

沙门菌感染后0至5岁婴幼儿肠道微生物群落

目的比较0至5岁沙门菌感染和健康婴幼儿的肠道菌群分布特点,研究沙门菌感染导致的婴幼儿肠道菌群微生态失调情况,为腹泻病的发病机制和防治提供微生态学理论依据。方法采集9例沙门菌腹泻婴幼儿(腹泻组)与11例健康婴幼儿(健康组)的粪便样本,通过16S扩增子测序分析肠道菌群的多样性,并比较2组样本的群落结构差异,研究沙门菌对婴幼儿肠道微生态的影响。结果腹泻组婴幼儿粪便样本的Shannon指数显著低于健康组(2.261 1 vs 4.069 9,t=-4.892 0,P=0.001 0),Simpson指数也显著低于健康组(0.562 9 vs 0.873 3,t=-3.721 0,P=0.006 0)。腹泻组婴幼儿粪便样本的变形菌门(Proteobacteria)丰富度显著高于健康组(t=0.035 7,P=0.009 2),而厚壁菌门(Firmicutes)和拟杆菌门(Bacteroidetes)丰富度显著低于健康组(t=0.115 4,P=0.044 6;t=0.035 7,P=0.007 0)。腹泻组婴幼儿粪便样本的人类疾病(human diseases)功能的基因丰富度显著高于健康组(t=0.131 5,P=0.026 0),而新陈代谢(metabolism)功能和生物体系统(organismal systems)功能的基因丰富度显著低于健康组(t=0.099 1,P=0.009 8;t=0.142 9,P=0.046 3)。结论沙门菌降低了婴幼儿肠道菌群的多样性,改变了肠道菌群的群落结构,并调控机体功能的基因表达。细菌性腹泻与病原菌侵袭、肠道微生态失衡及机体功能密切相关。     

健康与腹泻林麝肠道菌群的多态性

目的分析圈养状态下正常林麝和腹泻林麝粪便菌群的组成差异,找到能够影响肠道总菌群稳态的标志菌,为减少林麝腹泻提供防治新策略。方法测序分析54只健康林麝(正常组)和18只有腹泻症状的林麝(腹泻组)肠道菌群总DNA中16S rRNA基因V3-V4区,注释微生物种类和数量。计算Chao1、Ace、Shannon和Simpson等多样性指数,进行聚类分析。结果正常组和腹泻组之间共有的可操作分类单元(OTUs)2 366个,正常组特有的OTUs 409个,腹泻组特有的OTUs 150个。按组计算α多样性指数,结果表明腹泻组Chao1指数(1 352.766±75.497,t=10.798 7,P0.000 1)、Ace指数(1 381.480±75.937,t=11.037 5,P0.000 1)均高于正常组(1 126.655±81.090,1 149.175±81.370),Shannon指数(6.839±0.546,t=1.810 3,P=0.053 0)、Simpson指数(0.937±0.041,t=3.644 4,P0.000 1)均低正常组(7.097±0.448,0.974±0.025)。通过Wilcoxon秩和检验,MRPP分析计算比较值A为0.072 4,组间差异大于组内差异(Significance=0.01),差异有统计学意义。2组门水平上比较,找到5个差异物种,分别为拟杆菌门(Bacteroidetes)、螺旋体门(Spirochaetes)、放线菌门(Actinobacteria)、广古菌门(Euryarchaeota)和黑水仙菌门(Melainabacteria)。属分类水平上,找到差异物种23个,其中有代表性的物种为拟杆菌属(Bacteroides)、另枝菌属(Alistipes)、不动杆菌属(Agathobacter)、甲烷短杆菌属(Methanobrevibacter)、根瘤菌属(Rhizobiaceae)和黄金杆菌属(Chryseobacterium)。结论腹泻发生时,林麝的肠道菌群丰富度和多样性有所下降,菌群总量显著增加。拟杆菌门物种丰富度极显著性减少的同时,作为潜在致病菌标志的变形菌门(Proteobacteria)比例上升,Chryseobacterium数量极显著升高,研究结果丰富了对林麝腹泻基于肠道菌群变化的认识。     

干燥综合征患者肠道微生物菌落的分析

目的通过检测干燥综合征(Sj9gren′s syndrome,SS)患者粪便标本的微生物种群分布及外周血Treg细胞绝对计数,分析SS患者肠道菌群变化状态及其与Treg细胞的相关性,为临床诊疗提供新思路。方法通过采用Illumina HiSeq 2500高通量测序平台对29例干燥综合征患者粪便标本中的16S rRNA V3区进行定性分析,与83例健康人粪便标本中菌群的多样性与丰富度统计数据进行比较,分析SS患者中差异性菌群丰富度及其与Treg细胞绝对计数的关系。结果两组研究对象性别、年龄比较差异均无统计学意义(P0.05)。与健康人对比,SS患者粪便菌群中细菌多样性低于健康对照组(P0.05),肠道菌群丰富度在门(Phylum)水平上厚壁菌门(Firmicutes)细菌数量较正常对照组减少(P0.05),变形菌门(Proteobacteria)和放线菌门(Actinobacteria)较健康对照组明显增加(均P0.05)。在科(Family)水平上链球菌科(Streptococcaceae)、肠杆菌科(Enterobacteriales)和乳杆菌科(Lactobacillaceae)细菌数量较正常对照组明显升高(均P0.05),普雷沃菌科(Prevotellaceae)和Paraprevotellaceae较对照组明显减少(均P0.05)。在属(Genus)水平上Blautia、颤螺旋菌属(Oscillospira)、链球菌属(Streptococcus)和韦荣球菌属(Veillonella)细菌数量较正常对照组明显升高(均P0.05),而Roseburia、粪杆菌属(Faecalibacterium)和普氏菌属(Prevotella)较正常对照组明显减少(均P0.05)。其中,SS患者粪便中韦荣球菌属的百分比与其外周血Treg细胞绝对计数呈显著负相关(P0.05)。结论 SS患者肠道微生态环境中细菌群落的多样性和均衡性与正常人群存在明显差异,且韦荣球菌属水平的升高与外周血Treg细胞绝对计数呈显著负相关,肠道菌群紊乱或许参与了SS的发病过程。     

维持性血液透析终末期肾病患者肠道优势菌群多样性变化研究

目的探讨维持性血液透析终末期肾病患者肠道优势菌群多样性及其与炎症因子的相关性。方法采集维持性血液透析的稳定终末期肾病患者和健康对照受试者的血液和粪便样本,采用荧光实时定量PCR(real-time quantitative PCR,QPCR)检测肠道优势菌群的变化情况,应用酶联免疫吸附技术(enzymelinked immunosorbent assay,ELISA)检测患者血液中的白介素1β(interleukin 1β,IL-1β)、白介素6(interleukin 6,IL-6)、肿瘤坏死因子α(tumor necrosis factor-α,TNF-α)和内毒素(lipoposaccharide,LPS)。结果维持性血液透析终末期肾病患者肠道菌群总菌量差异无统计学意义,但肠道内有益菌群如双歧杆菌属细菌、乳酸杆菌属细菌和粪杆菌属细菌显著降低,而肠道内有害菌如肠杆菌科细菌和肠球菌属细菌均显著升高(P0.05)。维持性血液透析终末期肾病患者血液中IL-6、TNF-α和LPS显著升高,均与双歧杆菌属细菌有显著负相关,与肠杆菌科细菌有显著正相关。肠道内乳酸杆菌属细菌和粪杆菌属细菌与IL-6呈显著负相关,肠球菌属细菌与其呈显著正相关。此外,乳杆菌属细菌与TNF-α呈显著负相关,肠球菌属细菌和LPS呈显著正相关。结论维持性血液透析终末期肾病患者肠道优势菌群多样性发生了显著变化,且与患者炎症因子有密切的相关性。     

链球菌与香菇多糖联用对PM_(2.5)暴露肺癌小鼠呼吸道菌群的影响CSCD

目的观察潜在益生菌链球菌C17、D19株与香菇多糖联合应用对PM_(2.5)暴露肺癌荷瘤小鼠呼吸道菌群多样性的影响。方法尾静脉注射A549细胞悬液构建荷瘤SCID小鼠模型,气管滴注40μL 20mg/mL的PM_(2.5)溶液,每周1次,持续4周。实验组(LS组)给予链球菌C17、D19株混合菌液喷雾给药,每周2次,同时腹腔注射3mg/kg香菇多糖。对照组(PM组)仅喷雾生理盐水。比较组(LE组)喷雾生理盐水同时给予香菇多糖。全部小鼠均持续处理4周。利用高通量测序对咽拭子样本中的菌群进行16SrDNA序列检测,进行OTU统计、物种组成分析、指示物种分析、Alpha多样性分析、Beta多样性分析。结果PM组小鼠OTU数量大于LE组、LS组。各组主要优势菌为厚壁菌门、变形菌门、放线菌门、蓝细菌门、拟杆菌门。与PM组比较,LE组(t=3.2064,P=0.0071)、LS组(t=3.4061,P=0.0098)放线菌门丰度增加显著,LE组蓝细菌门丰度减少显著(t=2.7316,P=0.0340)。属水平上,LS组与LE组各优势菌属总丰度显著高于PM组。与PM组比较,LS组小鼠呼吸道嗜气杆菌属(t=7.1686,P=0.0008)和普雷沃菌属(t=2.2702,P=0.0230)丰度显著增加,LE组嗜气杆菌属(t=2.5238,P=0.0429)、加德纳菌属(t=2.4720,P=0.0445)、奇异菌属(t=4.8123,P=0.0030)、弧菌属(t=2.4597,P=0.0210)、普雷沃菌属(t=2.6076,P=0.0319)丰度差异显著。种水平上,与PM组比较,LS组小鼠呼吸道酸性链球菌(t=2.4456,P=0.0450)、Rodentibacter_heylii(t=7.1686,P=0.0008)增加显著,LE组普雷沃菌(t=2.2751,P=0.0462)、Rodentibacter_heylii(t=2.5238,P=0.0340)增加显著。Alpha多样性分析显示,LE组与PM组间、LS组与PM组间菌群Chao指数(t=2.3867,P=0.0388;t=5.8780,P=0.0006),Ace指数(t=2.8267,P=0.0192;t=6.1316,P=0.0009)差异有统计学意义。Beta多样性分析显示,LS组与PM组间(t=2.9994,P=0.0056)、LE组与PM组间(t=4.8938,P<0.0001)OTU水平比较差异有统计学意义。结论潜在益生菌C17、D19株与香菇多糖联合应用可调节PM_(2.5)暴露肺癌小鼠呼吸道的菌群多样性。     

老年房颤患者肠道菌群变化及其影响因素

目的探讨老年房颤患者肠道菌群变化及影响菌群变化的相关因素。方法回顾性收集20例老年房颤患者作为房颤组,并选取性别、年龄与患者匹配的30例老年健康体检者作为对照组,分析两组对象肠道优势菌的特点。同时收集房颤组患者C反应蛋白(CRP)、总胆汁酸(TBA)、同型半胱氨酸(Hcy)、B型纳尿肽(BNP)、左室射血分数数值(LVEF)等检测结果,分析上述因素与肠道优势菌群的关系。结果房颤组患者直肠真杆菌数量为(4.66±1.62)lg copies/g粪便,低于对照组的(6.10±1.44)lg copies/g粪便,差异有统计学意义(t=-3.286,P=0.002)。房颤组患者肠道普拉梭菌、肠球菌、类杆菌、乳杆菌、双歧杆菌、柔嫩梭菌、酪酸梭菌、Atopobium cluster(Ato)、肠杆菌数量及双歧杆菌/肠杆菌(B/E)值与对照组比较差异无统计学意义(均P0.05)。在房颤组中,CRP升高患者肠道双歧杆菌数量和B/E值显著高于CRP正常患者,CRP升高与双歧杆菌数量呈正相关(r=0.651,P=0.002);Hcy升高患者肠道肠杆菌数量显著高于Hcy正常患者,Hcy升高与肠杆菌数量呈正相关(r=0.567,P=0.009)。BNP、TBA、LVEF与优势菌群无显著相关性。结论老年房颤患者存在肠道菌群失调。CRP、Hcy和老年房颤患者肠道菌群具有一定的相关性。     

幽门螺杆菌感染对正常胃部菌群多样性和组成的影响

目的通过高通量测序分析,探讨幽门螺杆菌(Helicobacter pylori)感染在正常胃部菌群多样性和组成中的差异。方法选择2017年10月-2018年1月在本院就诊的胃镜体检受试者40例,其中H.pylori阳性20例,阴性20例,均无阳性体征,收集胃液样本行胃部菌群MiSeq高通量测序分析。结果 H.pylori感染组α-多样性指数Shannon(t=-6.690,P0.001)和Simpson(t=-3.673,P=0.002)显著改变,显示胃部菌群多样性降低;菌群丰富度指数如PD Whole tree(t=-2.282,P=0.008),Chao1(t=-2.173,P=0.036)和Observed species(t=-2.627,P=0.012)在H.pylori阳性受试者中显著降低;β-多样性指数PCA分析可显著区分两组,结果显示H.pylori感染胃部菌群显著改变。LEfSe组成差异分析发现,胃部菌群组成亦发生了显著改变,H.pylori感染阳性组中变形菌门细菌显著升高,而厚壁菌门、拟杆菌门、放线菌门等显著降低;在属水平上,螺杆菌属(Helicobacter)、盐单胞菌属(Halomonas)、希瓦内拉菌属(Shewanella)和葡萄球菌属(Staphylococcus)等显著富集,而普氏菌属(Prevotella)、假单胞菌属(Pseudomonas)、芽胞杆菌属(Bacillus)等显著降低(LDA2,P0.05)。PiCRUSt菌群功能预测分析发现,H.pylori阳性的胃部菌群细菌分泌系统、脂多糖合成蛋白、脂多糖合成、细菌毒素、癌症信号通路的表达显著升高,而氨基酸代谢通路显著降低,这与胃癌的发生发展具有密切的联系。结论 H.pylori感染是影响正常胃部菌群多样性和组成的重要因素,这些改变可能与胃癌发生发展及预后密切相关。     

基于高通量测序的精神分裂症患者 肠道菌群多样性

目的探讨精神分裂症患者肠道菌群多样性变化。方法收集16例精神分裂症患者(schizophrenia,Sch)与18例健康者(healthy donor,HD)的粪便样本,提取肠道菌群基因组,扩增16SrRNA基因,运用Illumina平台进行测序。对测序结果进行多样性和物种组成差异分析。结果精神分裂症患者组肠道菌群在门、纲、目、科、属、种、分类操作单元(operational taxonomic units,OTUs)水平的群落种类数目少于健康对照组。Alpha多样性指标中患者组的Ace指数(226.58±31.67)、Chao1指数(222.29±34.45)和Shannon指数(2.66±0.69)明显低于健康对照组(293.63±56.07、302.2±57.99、3.59±0.36),差异均有统计学意义(Ps0.001),而Simpson指数(0.20±0.17)明显高于健康对照组(0.07±0.03),差异有统计学意义(P0.01);Beta多样性分析显示两组研究对象肠道菌群样本可被鉴别区分。精神分裂症患者组与健康对照组样本在门和属水平上肠道菌群组成和含量有差异,其中患者组拟杆菌门和软壁菌门占比明显低于健康组,差异有统计学意义(21.76%vs.27.05%,P=0.008;0.00%vs.0.20%,P=0.033),而放线菌门明显高于健康组(13.52%vs.2.88%,P=0.020),差异有统计学意义;患者组拟杆菌属和柔嫩梭菌属占比明显低于健康组(9.15%vs.20.60%,P=0.031;3.29%vs.9.58%,P=0.005),差异有统计学意义,而双歧杆菌属、普雷沃菌属和巨单胞菌属明显高于健康组(10.89%vs.1.78%,P=0.025;10.88%vs.1.98%,P=0.046;10.78%vs.2.69%,P=0.026),差异有统计学意义。结论基于16SrRNA的高通量测序有助于分析精神分裂症患者肠道菌群多样性变化,为研究肠道菌群与精神分裂症的关系提供新的思路和理论依据。     

高通量 16S rRNA 标签测序法比较人与不同动物肠道微生物组多样性

收集人、大猪、小猪、大鼠、小鼠以及鸡五个不同个体的粪便样品 , 每个个体取两个平行样 , 提取总 DNA;PCR 扩增 , 获得 16S rRNA V6 标签片段 ; Illumina 测序 ; 经 BIPES 以及 QIIME 分析并比较菌群结构及多样性。研究结果发现 , 不同物种之间肠道菌群差异较大。五类物种肠道菌群均以厚壁菌门、拟杆菌门、以及变形菌门为主 , 但鸡的厚壁菌门显著减少 , 而变形菌门显著增加。从α多样性角度来看 , 猪肠道菌群种属丰富度及 Shannon 指数均显著高于人及鸡肠道菌群。从β多样性角度 , 尽管不同人之间的肠道菌群相似度较低 , 但不同物种之间相比较 , 小猪与大鼠肠道菌群与人相似性高于小鼠和鸡肠道菌群。与人类相比 , 小猪的肠道微生物组最相近 , 而鸡的肠道菌群相似度最低。     

Recent advances in the study of Kaposi's sarcoma-associated herpesvirus replication and pathogenesis

It has now been over twenty years since a novel herpesviral genome was identified in Kaposi's sarcoma biopsies. Since then, the cumulative research effort by molecular biologists, virologists, clinicians, and epidemiologists alike has led to the extensive characterization of this tumor virus, Kaposi's sarcoma-associated herpesvirus(KSHV; also known as human herpesvirus 8(HHV-8)), and its associated diseases. Here we review the current knowledge of KSHV biology and pathogenesis, with a particular emphasis on new and exciting advances in the field of epigenetics. We also discuss the development and practicality of various cell culture and animal model systems to study KSHV replication and pathogenesis.     

A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility

正Dear Editor,In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia(Coronavirus Disease 2019,COVID-19) in Wuhan, Hubei, China(Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases     

Curcuminoids as inhibitors of thioredoxin reductase: A receptor based pharmacophore study with distance mapping of the active site

Curcumin is the yellow pigment of turmeric that interacts irreversibly forming an adduct with thioredoxin reductase (TrxR), an enzyme responsible for redox control of cell and defence against oxidative stress. Docking at both the active sites of TrxR was performed to compare the potency of three naturally occurring curcuminoids, namely curcumin, demethoxy curcumin and bis-demethoxy curcumin. Results show that active sites of TrxR occur at the junction of E and F chains. Volume and area of both cavities is predicted. It has been concluded by distance mapping of the most active conformations that Se atom of catalytic residue SeCYS498, is at a distance of 3.56 from C13 of demethoxy curcumin at the E chain active site, whereas C13 carbon atom forms adduct with Se atom of SeCys 498. We report that at least one methoxy group in curcuminoids is necessary for interation with catalytic residues of thioredoxin. Pharmacophore of both active sites of the TrxR receptor for curcumin and demethoxy curcumin molecules has been drawn and proposed for design and synthesis of most probable potent antiproliferative synthetic drugs.     

The structure, reproduction and taxonomy of Vidalia and Osmundaria (Rhodophyta, Rhodomelaceae)

Comprises species occurring mostly in subtidal habitats in tropical, subtropical and warm-temperate areas of the world. An analysis of the type species, V. spiralis (Sonder) Lamouroux ex J. Agardh, a species from Australia, establishes basic characters for distinguishing species in the genus. These characters are (1) branching patterns of thalli, (2) flat blades that may be spiralled on their axis, (3) width of the blade, (4) primary or secondary derivation of sterile and fertile branchlets and (5) position of sterile and fertile branchlets on the thalli. Application of the latter two characters provides an important basic method for separation of species into three major groups. Osmundaria , a genus known only in southern Australia, was studied in relation to Vidalia , and its separation from the Vidalia assemblage is not accepted. Species of Vidalia therefore are transferred to the older genus name, Osmundaria. Two new species, Osmundaria papenfussii and Osmundaria oliveae are described from Natal. Confusion in the usage of the epithet, Vidalia fimbriala Brown ex Turner has been clarified, and Vidalia gregaria Falkenberg, described as an epiphyte on Osmundaria pro/ifera Lamouroux, is revealed to be young branches of the host, Osmundaria prolifera.     

New or rare chromosome counts in Artemisia L. (Asteraceae, Anthemideae) and related genera from Kazakhstan

Fifteen chromosome counts of six Artemisia taxa and one species of each of the genera Brachanthemum, Hippolytia, Kaschgaria, Lepidolopsis and Turaniphytum are reported from Kazakhstan. Three of them are new reports, two are not consistent with previous counts and the remainder are confirmations of very scarce (one to four) earlier records. All the populations studied have the same basic chromosome number, x = 9, with ploidy levels ranging from 2x to 6x. Some correlations between ploidy level, morphological characters and distribution are noted.