培菌白蚁菌圃和粪便微生物多样性分析

【背景】培菌白蚁是属于白蚁科的一类与鸡枞菌属真菌共生的高等白蚁,其与体内肠道微生物和体外菌圃微生物形成三维共生体系。【目的】分析培菌白蚁菌圃和粪便的微生物多样性,并与肠道微生物进行比较。【方法】通过Illumina MiSeq高通量测序方法对培菌白蚁菌圃和粪便样品进行细菌16S rRNA基因和真菌ITS测序分析。【结果】高通量测序获得培菌白蚁菌圃和粪便样品细菌和真菌的有效序列和OTU数目。5个样品细菌OTU数目在90-199之间,而真菌OTU在10-58之间,细菌的种类多样性明显大于真菌。不论是细菌还是真菌,粪便样品的OTU数目多于菌圃样品。经物种分类分析,菌圃样品主要优势细菌是变形菌门(Proteobacteria),其相对含量超过82.4%;其次是拟杆菌门(Bacteroidetes)和厚壁菌门(Firmicutes);粪便样品中优势细菌为拟杆菌门,其次是变形菌门,粪便优势菌属为别样杆菌属和营发酵单胞菌属,这与培菌白蚁肠道菌多样性组成一致。培菌白蚁菌圃和粪便样品共生真菌主要为担子菌门(Basidiomycota)和子囊菌门(Ascomycota)。菌圃优势真菌为鸡枞菌属(Termitomyces),相对含量在51.83%以上,菌圃中还鉴定到炭角菌属(1%,Xylaria)。【结论】为今后培菌白蚁-体内外微生物共生关系研究以及微生物的分离培养提供了依据和参考。     

基于Illumina MiSeq高通量测序技术分析硇洲岛海星共附生微生物多样性

【背景】海星作为海洋生物中的一类比较高级的棘皮类动物,其体内蕴藏着丰富且具有生物活性的共附生微生物资源。【目的】分析湛江硇洲岛海星中共附生微生物的多样性。【方法】采用IlluminaMiSeq高通量测序技术分别对硇洲岛海星进行共附生细菌16SrRNA基因V3-V4区和共附生真菌18S rRNA基因ITS1-ITS2区的测序,并根据测序结果进行OTU聚类分析、α多样性分析及物种分类分析等。【结果】高通量测序获得细菌和真菌Filtered的数目分别为61992和71196个,OTU数目分别为2384和529个。经物种分类分析,共附生细菌主要为变形菌门(Proteobacteria),其平均相对含量高达77.37%;其次是厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidetes)、放线菌门(Actinobacteria)和梭杆菌门(Fusobacteria);其中优势细菌属为嗜冷杆菌属(Psychrobacter)和乳球菌属(Lactococcus)。共附生真菌主要为子囊菌门(Ascomycota),其相对含量高达92.33%;其次是霉菌门(Fungi)、担子菌门(Basidiomycota)、被孢菌门(Mortierellomycota)和罗兹菌门(Rozellomycota);优势真菌属以毕赤酵母属(Pichia)为主,未经分类的(unclassified)假丝酵母属(Candida)次之;【结论】硇洲岛海星体内蕴藏着丰富的共附生微生物资源,该研究为今后从事海星微生物资源持续开发和挖掘生物活性物质的研究提供一定的参考依据。     

基于PCR-DGGE和高通量测序分析白云边酒窖泥细菌群落结构与多样性

【目的】探索白云边酒不同窖龄窖泥细菌群落结构及其多样性,分析窖泥细菌群落特征对兼香型白酒风格形成的影响。【方法】分别提取2年和23年窖泥样品总DNA,采用PCR-DGGE、基因克隆以及高通量测序技术,研究窖泥细菌的分布情况。【结果】白云边窖泥细菌归属于变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、放线菌门(Actinobacteria)4个菌门。2、23年窖泥共同的优势菌属(≥1.0%)包括棒状杆菌属(Corynebacterium)、香味菌属(Myroides)、鞘氨醇杆菌属(Sphingobacterium)、乳杆菌属(Lactobacillus)、梭菌属(Clostridium)、醋杆菌属(Acetobacter)、产碱杆菌属(Alcaligenes)、肠杆菌属(Enterobacter)和不动杆菌属(Acinetobacter)。2年窖泥特有优势菌属为Dysgonomonas、Fluviicola、变形杆菌属(Proteus)和Wohlfahrtiimonas,而23年窖泥特有优势菌属为葡萄球菌属(Staphylococcus)、Hazenella、魏斯氏菌属(Weissella)、葡糖醋杆菌属(Gluconacetobacter)和摩根氏菌属(Morganella)。【结论】2年窖泥细菌群落多样性高于23年窖泥。比较了白云边两种窖龄窖泥主要细菌组成情况,为研究微生物对白云边酒浓酱兼香型独特风味形成的影响提供依据。     

基于16S rRNA基因序列分析法比较苏尼特双峰驼和阿拉善双峰驼自然发酵酸驼乳的微生物多样性

【目的】传统发酵乳制品是一类未经任何处理自然发酵而成的,其微生态环境未遭破坏,从而乳酸菌的生物学特性和基因多样性得到了很好的保留,具有开发和利用价值。自然发酵酸驼乳常用来治疗多种疾病且效果良好,与其中丰富的乳酸菌资源有着密不可分的联系。然而,目前有关自然发酵酸驼乳微生物菌群及多样性相关研究甚少。因此进一步挖掘内蒙古地区双峰驼自然发酵酸驼乳微生物群落结构和多样性是至关重要的。【方法】本研究采用IlluminaMiseq测序技术,测定了苏尼特和阿拉善双峰驼的自然发酵酸驼乳中微生物16S rRNA V3–V4区序列,并对群落结构和多样性进行了比较分析。【结果】多样性分析表明,苏尼特双峰驼酸驼乳中微生物群落丰富度和种群差异性比阿拉善双峰驼酸驼乳大,细菌多样性也高。在门水平上,苏尼特和阿拉善双峰驼酸驼乳中的菌群均以厚壁菌门(Firmicutes)和变形菌门(Proteobacteria)为主。在属水平上,苏尼特双峰驼酸驼乳主要以乳杆菌属(Lactobacillus)和乳球菌属(Lactococcus)为优势菌群,阿拉善双峰驼酸驼乳以乳杆菌属(Lactobacillus)和醋酸杆菌属(Acetobacter)为优势菌属。此外,肠杆菌属(Enterobacter)、拉乌尔菌属(Raoultella)和明串珠菌属(Leuconostoc)等的含有食源性致病菌和环境污染菌的菌属被检出。综上所述,不同地区不同品种酸驼乳的乳酸菌种类及优势菌群有较大差异,存在显著的地理差异。【结论】通过本研究,不仅对苏尼特和阿拉善双峰驼自然发酵酸驼乳乳酸菌的组成和种类有了明确的认知,为评估发酵酸驼乳微生物群落对消费者身体健康的影响提供了数据基础的同时为今后筛选优势菌群和挖掘新型益生菌奠定基础。     

液固工艺山西陈醋发酵微生物群落组成、互作网络及溯源分析

【背景】传统山西陈醋是在开放环境下由多菌种固态发酵酿制而成,解析酿造过程中微生物群落的组成、互作网络及来源对认识和调控食醋发酵过程都具有重要意义。【目的】揭示山西陈醋酿造微生物群落的组成、演替、互作网络及来源。【方法】基于高通量测序技术揭示山西陈醋酿造过程中微生物群落的组成、演替和多样性;采用SPSS数据统计软件计算物种间的斯皮尔曼相关系数并利用Gephi软件对微生物群落互作网络进行可视化分析;采用快速期望最大化微生物源跟踪(fast expectation-maximization microbial source tracking, FEAST)方法解析发酵微生物群落的来源。【结果】山西陈醋酿造过程中有6个优势细菌属和5个优势真菌属(平均相对丰度大于1%);醋酸杆菌属(Acetobacter)、乳酸杆菌属(Lactobacillus)和复膜孢酵母属(Saccharomycopsis)的平均相对丰度较高,分别为20.76%、30.38%和46.24%;醋酸杆菌属(Acetobacter)的相对丰度在醋酸发酵阶段逐渐增加,而乳酸杆菌属(Lactobacillus)在此阶段的趋势则相反。微生物群落互作网络结果显示魏斯氏菌属(Weissella)、乳球菌属(Lactococcus)、季也蒙酵母属(Meyerozyma)、Loigolactobacillus、Schleiferilactobacillus和地杆菌属(Geobacter)具有较高的连接度(连接度≥7);此外,醋酸杆菌属(Acetobacter)与魏斯氏菌属(Weissella)、Schleiferilactobacillus、Loigolactobacillus、乳球菌属(Lactococcus)、季也蒙酵母属(Meyerozyma)具有显著的拮抗作用。来源追溯结果显示糖化发酵第2天样品中有1.02%的细菌群落和77.04%的真菌群落来源于大曲;在醋酸发酵第1天样品中有0.93%的细菌群落和52.82%的真菌群落来源于火醅。【结论】为了解山西陈醋酿造过程中微生物群落的组成、演替、互作网络和解释酿造微生物来源提供了重要的理论数据。     

基于高通量测序研究青藏高原茶卡盐湖微生物多样性

【目的】茶卡盐湖(Chaka Salt Lake,CSL)是青藏高原有名的天然结晶盐湖,具有独特的石盐盐湖矿床,盛产青盐。盐湖卤水环境中存在丰富的嗜盐菌资源和潜在的新种,细菌和古菌的群落结构特征和物种多样性尚不明确。【方法】采用Illumina高通量测序平台对茶卡盐湖水样和底泥混合物中的细菌和古菌群落进行16S r RNA基因(V3-V5区)高通量测序,检测4个样本的群落结构差异和微生物多样性。【结果】获得细菌和古菌总有效序列分别为117 192和110 571条。结果分析表明细菌和古菌的物种注释(Operational taxonomic unit,OTU)数目分别为421和317,获得分类地位明确的细菌种类为14门28纲170属,古菌为5门4纲34属。细菌的优势类群是厚壁菌门(Firmicutes),所占比例为68.37%,其次为变形菌门Proteobacteria(20.49%);优势种属依次为芽孢杆菌属Bacillus(41.94%)、海洋芽孢杆菌属Oceanobacillus(8.03%)、假单胞菌属Pseudomonas(7.67%)、盐厌氧菌属Halanaerobium(7.42%)和乳球菌属Lactococcus(7.38%);古菌的优势类群以广古菌门(Euryarchaeota)盐杆菌纲(Halobacteria)为主,优势菌是Halonotius(17.21%)和盐红菌属Halorubrum(16.23%)。【结论】揭示了茶卡盐湖中细菌和古菌的群落结构及物种多样性,为嗜盐菌的开发及后续微生物资源的挖掘提供了理论依据。     

基于高通量测序的褐飞虱肠道微生物多样性分析

【目的】探明褐飞虱Nilaparvata lugens成虫肠道微生物群落结构和多样性。【方法】分离褐飞虱成虫完整肠道并提取总DNA,利用Illumina MiSeq(PE300)技术对其肠道细菌16S rRNA的V3-V4变异区和真菌ITS2序列进行测序,统计肠道微生物的操作分类单元(operational taxonomic unit, OTU)数量,分析其物种组成、丰度及Alpha多样性。并通过qPCR技术验证随机挑选注释到的4种肠道菌的高通量测序数据的有效性。【结果】分别获得褐飞虱成虫肠道细菌16S rRNA和真菌ITS2优质序列32 395和24 986条,根据序列相似性进行聚类分析分别获得235和128个OTUs。其中,细菌共注释到7个门, 15个纲, 26个目, 45个科和73个属;真菌共鉴定到3个门, 9个纲, 12个目, 15个科和18个属。在门分类水平上,细菌以变形菌门(Proteobacteria)、拟杆菌门(Bacteroidetes)和厚壁菌门(Firmicutes)为优势门类;真菌以子囊菌门(Ascomycota)为绝对优势菌门。在属分类水平上,细菌的优势属为不动杆菌属Acinetobacter以及紫单胞菌科(Porphyromonadaceae)未确定属和毛螺菌科(Lachnospiraceae)未确定属,其丰度分别为36.37%, 17.22%和15.01%;真菌的优势属为粪壳菌纲(Sordariomycetes)未确定属,丰度为95.77%。Alpha多样性分析结果显示,褐飞虱肠道细菌(真菌)的观测物种数、Chao1指数、Shannon指数和Simpson 指数分别为235(128), 262.64(165.40), 3.90(0.91)和0.62(0.75)。4种肠道菌的qPCR结果显示高通量测序数据具有较高的有效性。【结论】褐飞虱成虫肠道细菌和真菌群落整体多样性比较丰富。研究结果为从共生微生物角度解析褐飞虱的环境适应性以及开发基于微生物防治的新技术等方面提供了依据。     

日本弓背蚁颊下囊微生物的组成及多样性

【目的】本研究旨在调查日本弓背蚁Camponotus japonicus颊下囊中微生物(放线菌、细菌、真菌)组成、分布规律及细菌的多样性水平,以揭示其可能在蚂蚁食物利用、群体免疫等方面发挥的潜在功能。【方法】综合采用传统的微生物分离培养和Hi Seq高通量测序方法,对在陕西杨凌采集获得的日本弓背蚁工蚁的颊下囊内含物、消化道、体表的微生物进行了分析比较。【结果】采用传统分离培养方法从日本弓背蚁工蚁颊下囊内含物分离到10株放线菌,其中5株为链霉菌属Streptomyces,其平均分离频率达到73.3%~96.7%;分离到7株细菌,其中4株为芽孢杆菌Bacillus,菌株N-B1和N-B4分离频率均达70%以上;分离到3株真菌,其中菌株P-F1(拟威克酵母菌属Wickerhamiella)为优势类群,分离频率达96.7%。从嗉囊、中肠及体表中分离到的菌株均可在颊下囊中发现,从颊下囊中分离到的菌株种类和菌落数量明显高于体表、嗉囊和中肠。Hi Seq高通量测序结果表明,颊下囊中的优势菌门为变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)和放线菌门(Actinobacteria),嗉囊和中肠的优势菌门为变形菌门和厚壁菌门;颊下囊和嗉囊样品中丰度较高的细菌类群明显高于中肠,中肠细菌组成相对较为简单;颊下囊中的优势属包括嗜果糖乳酸细菌属Fructobacillus、杆菌属Bacterium、假单胞菌属Pseudomonas、不动杆菌属Acinetobacter和鞘氨醇单胞菌属Sphingtomonas;颊下囊中微生物物种丰度和多样性均高于嗉囊和中肠。【结论】日本弓背蚁工蚁颊下囊中普遍存在放线菌、芽孢杆菌和酵母菌及其他优势菌群,且微生物的丰度和多样性水平明显高于嗉囊和中肠,这些微生物在蚂蚁食物利用、营养物质消化以及群体免疫中的潜在功能有待于深入研究。     

传统醋曲储存过程中的微生物多样性

【背景】醋曲是我国传统谷物醋酿造中的重要微生物来源,通常一次制备分批使用。【目的】解析传统醋曲储存过程中微生物群落结构变化规律。【方法】从山西晋南一家百年老醋坊分别采集大曲原料、新制醋曲、储存7个月和12个月的醋曲,利用高通量测序技术分析微生物多样性。【结果】从4组样品中共找到610个真菌可操作分类单元(operational taxonomic unit, OTU)和747个细菌OTU。子囊菌门(Ascomycota,占比95%)和厚壁菌门(Firmicutes,占比81%)分别为优势的真菌和细菌类群。醋曲成品中约1/3的真菌OTU和约95%的细菌OTU可在醋曲原料中找到,说明原料是醋曲的重要微生物来源。相较于新制醋曲,储存7个月和12个月醋曲中的真菌和细菌多样性均显著降低。醋曲贮存过程中微生物群落结构发生明显改变,并且相较于真菌群落结构,细菌群落结构更易波动。相较于醋曲原料,醋曲成品中显著富集扣囊复膜孢酵母(Saccharomycopsis fibuligera)、东方伊萨酵母(Issatchenkiaorientalis)等真菌,以及克罗彭斯特菌属(Kroppenstedtia)...     

芝麻香型白酒发酵过程中乳酸菌多样性及其演替规律

【背景】乳酸菌是白酒发酵过程中一类非常重要的微生物,其种类及动态变化对于白酒品质具有重要影响。然而,目前对于芝麻香型白酒发酵过程中乳酸菌群落结构及其演替规律的认识并不全面。【目的】揭示芝麻香型白酒发酵过程中乳酸菌的多样性及菌群的演替规律,为更好地探索白酒酿造机理和控制白酒品质提供生物学依据。【方法】利用高通量测序技术对芝麻香型白酒发酵过程中乳酸菌菌群演替进行跟踪分析,同时采用实时荧光定量PCR对发酵过程中乳酸菌的生物量进行定量分析。【结果】高通量测序结果显示,芝麻香型白酒发酵过程涉及5个属的乳酸菌:魏斯氏菌属(Weissella)、片球菌属(Pediococcus)、乳杆菌属(Lactobacillus)、明串珠菌属(Leuconostoc)和乳球菌属(Lactococcus),共计43种乳酸菌。其中,在发酵过程中平均相对丰度大于0.5%的乳酸菌有10种,分别是类肠膜魏斯氏菌(Weissella paramesenteroides)、食窦魏斯氏菌(Weissella cibaria)、融合魏斯氏菌(Weissella confusa)、戊糖片球菌(Pediococcus pentosaceus)、假肠膜明串珠菌(Leuconostoc pseudomesenteroides)、发酵乳杆菌(Lactobacillus fermentum)、植物乳杆菌(Lactobacillus plantarum)、副干酪乳杆菌(Lactobacillus paracasei)、耐酸乳杆菌(Lactobacillus acetotolerans)和Lactobacillus sp.。在堆积发酵过程中,Weissella属占细菌总量的50%以上,其次是Pediococcus属和Lactobacillus属,而Leuconostoc属和Lactococcus属相对较少。在窖池发酵过程中Lactobacillus属的乳酸菌逐渐成为优势细菌,尤其是Lactobacillus sp.在窖池发酵中后期相对丰度达到80%以上。实时荧光定量PCR结果显示,在堆积发酵和窖池发酵前期乳酸菌总量变化不大;从窖池发酵5 d开始,乳酸菌总量迅速上升,30 d时达到最大值。【结论】对白酒发酵过程中乳酸菌种类及动态变化的研究有助于探究白酒酿造过程中乳酸菌功能,进而解析白酒酿造机理,最终达到控制白酒品质的目的。     

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.     

Comparative morphology of the carpel in the Liliaceae: Hewardieae, Petrosavieae, and Tricyrteae

The young pistils in the melanthioid tribes, Hewardieae, Petrosavieae and Tricyrteae, are uniformly tricarpellate and syncarpous. They lack raphide idioblasts. All are multiovulate, with bitegmic ovules. The Petrosavieae are marked by the presence of septal glands and incomplete syncarpy. Tepals and stamens adhere to the ovary in the Hewardieae and the Petrosavieae but not in the Tricyrteae. Two vascular bundles occur in the stamens of the Hewartlieae and Tricyrtis latifolia. Ventral bundles in the upper part of the ovary of the Hewardieae are continuous with compound septal bundles and placental bundles in the lower part. Putative ventral bundles occur in the alternate position in the Tricyrteae and putative placental bundles in the opposite. position in the Petrosavieae. The dichtomously branched stigma in each carpel of the Tricyrteae is supplied by a bifurcated dorsal bundle.     

Enterovirus 71 3C proteolytically processes the histone H3 N-terminal tail during infection

Highlights
1. The N-terminal tail of histone H3 is specifically cleaved during EV71 infection.
2. Viral protease 3C is identified as a protease responsible for proteolytically processing the N-terminal H3 tail.
3. Our finding reveals a new epigenetic regulatory mechanism for Enterovirus 71 in virus-host interactions.     

Detection of EBV and HHV6 in the Brain Tissue of Patients with Rasmussen’s Encephalitis

Rasmussen’s encephalitis (RE) is a rare pediatric neurological disorder, and the exact etiology is not clear. Viral infection may be involved in the pathogenesis of RE, but conflicting results have reported. In this study, we evaluated the expression of both Epstein-Barr virus (EBV) and human herpes virus (HHV) 6 antigens in brain sections from 30 patients with RE and 16 control individuals by immunohistochemistry. In the RE group, EBV and HHV6 antigens were detected in 56.7% (17/30) and 50% (15/30) of individuals, respectively. In contrast, no detectable EBV and HHV6 antigen expression was found in brain tissues of the control group. The co-expression of EBV and HHV6 was detected in 20.0% (6/30) of individuals. In particular, a 4-year-old boy had a typical clinical course, including a medical history of viral encephalitis, intractable epilepsy, and hemispheric atrophy. The co-expression of EBV and HHV6 was detected in neurons and astrocytes in the brain tissue, accompanied by a high frequency of CD8⁺ T cells. Our results suggest that EBV and HHV6 infection and the activation of CD8⁺ T cells are involved in the pathogenesis of RE.     

Perinatal Vertical Transmission of Chikungunya Virus in Ruili,a Town on the Border between China and Myanmar

正Dear Editor,Chikungunya virus (CHIKV), an arbovirus in the family of Togaviridae, genus Alphavirus, is transmitted by the A.aegyptii or A. albopictus mosquito, and causes disease in humans characterized by fever, rash, and arthralgia (Silva and Dermody 2017; Suhrbier 2019). It was first reported in 1953 in Tanzania, and caused only a few outbreaks and sporadic cases in Africa and Asia in last century. However, in the epidemic in 2004, CHIKV acquired mutations that conferred enhanced transmission by the A. albopictus mosquito(Schuffenecker et al. 2006). Since then, it has successively caused outbreaks in Africa, the Indian Ocean, South East Asia, the South America, and Europe (Zeller et al. 2016).     

Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2

In conclusion, the novel visual RT-LAMP assay is a simple, rapid, and sensitive approach for detection of SARS-CoV-2, and it is ready for application in primary care and community hospitals or health care centers, and even patients' own houses in response to the current SARS-CoV-2 epidemic because the assay does not require sophisticated equipment and skilled personnel. Furthermore, it is also ready to be used in fields for screening samples from wild animals and environments to facilitate the identification of potential intermediate hosts that mediate the cross-species transmission of SARS-CoV-2 from bats to humans.