人体肠道4 644株代表菌次级代谢产物生物合成基因簇挖掘与耐药及毒力基因分析

为了更好地从肠道微生物组中挖掘新的次级代谢产物、了解肠道微生物组编码的抗生素耐药基因和毒力因子情况,本研究基于4 644株人体肠道微生物代表菌的基因组序列,对其编码的次级代谢产物基因簇、抗生素耐药基因和毒力因子进行了预测分析。经antiSMASH预测分析发现,超过60%的代表菌编码至少1个次级代谢产物基因簇,并从8个未可培养菌中发现了8个潜在的新颖次级代谢产物基因簇。人体肠道中的次级代谢产物主要由梭菌纲（Clostridia）、芽孢杆菌纲（Bacilli）、γ-变形菌纲（Gammaproteobacteria）、拟杆菌纲（Bacteroidia）、放线菌纲（Actinobacteria）和厚壁菌纲（Negativicutes）6类细菌编码的非核糖体多肽合成酶（nonribosomal peptide synthetase,NRPS）、细菌素、芳基多烯类化合物、萜烯、β-丙内酯、NRPS-样蛋白组成。经PathoFact预测分析发现,抗生素耐药基因和毒力因子在代表性菌株中分布广泛,但潜在病原菌编码频率更高。潜在病原菌中编码外膜蛋白、PapC N-端结构域、PapC C-端结构域、肽酶M16失活结构域等分泌型毒素和硝基还原酶家族、AcrB/AcrD/AcrF家族、PLD-样结构域、Cupin结构域、假定溶血素、S24-样肽酶、磷酸转移酶家族、内切核酸酶/外切核酸酶/磷酸酶家族、乙二醛酶/博莱霉素抗性等非分泌型毒素的频率较高。该研究将为进一步从肠道微生物组中挖掘新的微生物天然产物、了解肠道微生物的定殖与感染机制,为肠道微生物相关疾病提供靶向防治策略等奠定基础。     

退耕对民勤绿洲土壤碳氮循环关键微生物及功能基因的影响

采用时空互代法,以巴丹吉林沙漠东南缘民勤绿洲不同退耕年限样地土壤为研究对象,利用微生物宏基因组测序技术,以KEGG数据库碳固定、氮代谢途径为工具,研究长期退耕对参与区域土壤碳固定和氮代谢途径的主要微生物群落组成及其功能基因变化的影响。试验共设置9个退耕年限梯度样地：未退耕耕地、退耕1年样地、退耕2年样地、退耕4年样地、退耕8年样地、退耕13年样地、退耕20年样地、退耕30年样地和退耕40年样地。结果表明：退耕明显改变了碳固定、氮代谢土壤微生物和功能基因丰度,细菌在碳固定和氮代谢两个过程中均起到主导作用;还原三羧酸循环途径、还原乙酰辅酶A途径以及3-羟基丙酸/4-羟基丁酸循环途径等为研究区土壤微生物主要碳固定途径,厌氧氨氧化途径、硝酸盐异化还原途径、硝酸盐同化还原途径、反硝化途径以及硝化途径等为研究区土壤微生物主要氮代谢途径;芽单胞菌属（Gemmatimonas）、未分类绿弯菌属（unclassified_Chloroflexi）和链霉菌属（Streptomyces）等是区域土壤微生物碳固定主要菌属,氮代谢则以腈基降解菌属（Nitriliruptor）、芽单胞菌属（Gemmatimonas）、土壤红杆菌属（Solirubrobacter）、未分类绿弯菌属（unclassified_Chloroflexi）和链霉菌属（Streptomyces）等为主;Gemmatirosa、未分类绿弯菌属（unclassified_Conexibacter）、未分类念珠菌门（unclassified_Candidatus Rokubacteria）、Gaiella和Geminicoccus等5个属分类土壤微生物可作为研究区退耕地碳固定途径标记性微生物种群,coxL.cutL和ACO.acnA等是研究区退耕地土壤微生物碳固定途径主要响应功能基因;腈基降解菌属（Nitriliruptor）、未分类念珠菌门（unclassified_Candidatus Rokubacteria）、Geminicoccus、未分类绿弯菌属（unclassified_Conexibacter）、土壤红杆菌属（Solirubrobacter）、未分类酸杆菌门（unclassified_Acidobacteria）和红色杆菌属（Rubrobacter）等7个属分类土壤微生物可作为研究区退耕地氮代谢途径标记性微生物种群,GDH2和E1.4.7.1是研究区退耕地土壤微生物氮代谢途径主要响应功能基因。该结果对于明确退耕影响下民勤绿洲土壤碳氮循环过程具有重要意义。     

海洋微生物资源及其产生生物活性代谢产物的研究

海洋微生物,尤其海洋细菌以其分类的多样性和规模而言,作为生物活性物质产生菌的潜力是巨大的。海洋微生物研究依据分离菌的生境来源可分为海水、沉积物、共栖、共生和深海菌群。生境的不同,不但影响菌群的分布,而且影响微生物代谢产物的合成。从报道的研究结果看,沉积物细菌、共栖细菌和共生细菌是海洋微生物天然药物筛选的重要来源。目前海洋微生物生物活性代谢产物资源的研究仍主要限制在那些在“标准”条件下易于生长和培养的微生物类群。本文对海洋微生物资源产生的生物活性物质的研究进展进行了综述。     

大港孔店油田水驱油藏微生物群落的分子分析

通过多聚酶链式反应温度梯度凝胶电泳（PCRTGGE）和构建16S rRNA基因克隆文库两种方法对比研究了大港油田孔二北断块注水井和采油井的微生物群落结构。16S rDNA V3区PCR扩增产物的TGGE图谱分析表明,这两个油井的微生物群落结构差异很大。注水井样品的TGGE图谱中有6条主要条带,而采油井样品中只有一个条带占绝对优势。同时,建立了两个样品的16S rRNA基因克隆文库,从中分别挑选了108和50个克隆进行限制性酶切片段长度多样性分析（ARDRA）。注水井样品有33个操作分类单元（OUT）,其中6个OUT是优势类型;而采油井样品只有8个OUT,有1个OUT在文库中占绝对优势。克隆文库和TGGE的研究结果一致,均表明注水井样品的微生物多样性比采油井丰富很多。每个OUT的代表克隆序列分析结果表明,注水井样品中的细菌主要属于α、β、γ变形菌纲和放线菌纲,尤其是红细菌亚纲（47%）。采油井样品的细菌主要属于α、β、γ变形菌纲,尤其是假单胞菌属（62%）。油藏微生物多样性的分子分析可为开展微生物采油技术研究奠定基础。     

孢子发生在真菌菌种鉴定中的作用

孢子发生（conidiogenesis）一词指的是孢子从产孢细胞发生的过程,即产孢细胞产生孢子当时和孢子产生后的发展形态。Hughes于1953年将观察孢子发生方式用于半知菌（fungi imperfecti）的鉴定。半知菌过去指有性阶段不清楚的真菌,现称丝裂孢子真菌（mitosporic fungi）。由于这组真菌的形态变化多样,鉴定存在困难。早期使用的是Saccardo的分类法对其进行分类（见半知菌图解）。该体系将孢子分为七类：单孢（Ameroporae）、双孢（Didynoporae）、多孢（Phragmosporae）、砖格（Dictyosporae）、螺旋（Helicosporae）、线状（Scolicosporae）、星状（Starosporae）。这种方法只是比较机械地对孢子特点进行观察,没有结合其产孢过程和产孢细胞的特点。1979年Cole和Samson应用电镜观察了孢子发生的情况。1983年Minre等用光镜和电镜观察并总结了分生孢子产生全部过程。de Hoog等主编的《Atlas of Clinical Fungi》一书中也介绍了孢子发生在真菌鉴定中的作用。我们在20世纪80～90年代也以暗色真菌为切人点全面观察和研究了孢子发生的全部过程。为了提高医学真菌的实验室鉴定水平,现结合我们的经验将孢子发生在真菌菌种鉴定中的作用介绍如下。     

基于PubMed数据库毛孢子菌病临床研究文献计量学分析

目的分析国际毛孢子菌病文献概貌,了解毛孢子菌病临床相关研究现状,为更好地开展毛孢子菌临床研究提供思路和依据。方法利用汤森路透TDA软件分析PubMed数据库收录的毛孢子菌病临床相关文献的时间、国家、期刊、作者和高频主题词分布,并获得作者合作网络图。结果临床毛孢子菌病相关文献始于1970年,经过1981～1992年的快速增长期后,近年来数量增长不明显。日本在临床毛孢子菌病研究领域具有领先优势,美国、印度、巴西、法国和中国内地发文量也较多。刊载毛孢子菌病临床研究文献最多的期刊是《日本胸部疾病杂志》（Nihon Kyobu Shikkan Gakkai Zasshi,Japa—nese Journal of Thoracic Diseases）和《临床微生物学杂志》（Journal of Clinical Microbiology）。发文量最多的作者分别是熊本大学医学部的Ando M、Araki S和琦玉医科大学的Sakata T。毛孢子菌病的高频主题词涉及毛孢子菌病的诊治、宿主免疫和毛孢子菌致病机制等。结论日本和美国仍是相关领域的研究大国,但近5a来,更多的中国科研团队加入到这一研究领域,提高了我国学者的学术影响力。侵袭性毛孢子菌病的诊治是临床毛孢子菌病研究的主要关注点。     

海洋微生物资源及其产生生物活性代谢产物的研究

海洋微生物,尤其海洋细菌以其分类的多样性和规模而言,作为生物活性物质产生菌的潜力是巨大的。海洋微生物研究依据分离菌的生境来源可分为海水、沉积物、共栖、共生和深海菌群。生境的不同,不但影响菌群的分布,而且影响微生物工谢产物的合成。从报道的研究结果看,沉积物细菌、共栖细菌和共生细菌是海洋微生物天然药物筛选的重要来源。目前海洋微生物生物活笥代谢产物资源的研究仍主要限制在那些在“标准”条件下易于生长和培养     

一株耐热嗜盐菌的分离及16SrRNA基因序列分析

目的利用盐固体分离培养基,从西藏自治区澜沧江边康宁镇一个47℃的盐井样品中分离纯化到一株耐热嗜盐菌菌株YJ0232。方法通过形态观察、生理生化特性和16srRNA基因序列分析,鉴定嗜盐菌菌株YJ0232分类学地位。结果菌株YJ0232初步鉴定为中度嗜盐菌,属于盐单胞菌属（Halomonassp．）菌株。其16SrRNA基因序列已被GenBank数据库收录,序列号为EU029645。结论本研究对澜沧江高盐环境微生物资源进行了初步探索研究。可为今后研究同类极端环境中新的物种资源以及微生物多样性提供参考。     

食品微生物蛋白质组指纹图谱数据解析与应用的研究

作为蛋白质组支柱技术的基质辅助激光解析电离飞行时间质谱可直接将样品点靶,生成微生物的蛋白质指纹图谱与数据库中的相关数据比对匹配后,由相关软件给出鉴定结果。本文围绕样品处理方式、谱图数据处理、谱图格式等,介绍蛋白质指纹图谱数据的解析与应用。通过构建标准化的食品微生物蛋白质指纹图谱数据库,并实现数据库资源及时有效的扩充,能为我国食品微生物快速检测提供良好的技术支撑平台。     

叶酸调控对高尿酸血症大鼠肠道微生物的影响

探究叶酸对高尿酸血症大鼠肠道微生物的影响,为治疗高尿酸血症提供新思路。将SPF 级雄性大鼠分为空白对照组、模型组和叶酸组,采集大鼠的粪便样本,采用16S rRNA高通量测序技术分析肠道微生物的多样性、群落组成以及结构的变化。研究结果显示,Alpha多样性和Beta多样性分析表明,空白对照组、模型组和叶酸组大鼠粪便中微生物多样性和群落组成存在明显差异,其中模型组大鼠粪便微生物具有较高的物种丰度和种群差异性。对门分类水平上的物种丰度分析发现,微生物种群主要由厚壁菌门（Firmicutes）和拟杆菌门（Bacteroidetes）组成;对属分类水平上的物种丰度分析发现,微生物种群由乳杆菌属（Lactobacillus）、Muribaculaceae、拟杆菌属（Bacteroides）、柯林斯菌属（Collinsella）、梭菌属（Clostridium）、罗姆布茨菌（Romboutsia）、劳特氏菌属（Blautia）和毛螺菌科NK4A136群（Lachnospiraceae NK4A136_group）等菌属组成,与空白对照组相比,模型组中Muribaculaceae和柯林斯菌属的丰度显著升高,乳杆菌属、梭菌属、罗姆布茨菌和毛螺菌科的丰度显著下降;叶酸组中Muribaculaceae、拟杆菌属、柯林斯菌属和劳特氏菌属的丰度显著升高,梭菌属、罗姆布茨菌和毛螺菌科的丰度显著下降。研究探索了叶酸干预调控高尿酸血症大鼠肠道微生物的变化,为治疗高尿酸血症提供参考。     

原核微生物之竿菌

140多年前发表的竿菌和杆(小杆)菌同属最早发现和定名的细菌类之一,迄今已有成百上千的菌种得到鉴定、分类和命名。中文微生物学命名和整理滞后,引发了一些不必要的麻烦和困惑,不利于我国微生物学的普及发展和国际交流。本文试图对已经合格发表的近100属1 130多种竿菌进行系统的形态学(含芽孢和/或孢子)、生境、生物化学和细菌属性梳理和分类,理清和制定竿菌种属的中文-拉丁文互译规则,有利于推动中外交流和发展。     

Burden of emerging anaerobes in the MALDI-TOF and 16S rRNA gene sequencing era

The isolation of anaerobes from patients has declined in recent years, whereas their detection by molecular techniques has increased. In the present work, we analyzed the application of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing to routine identification of anaerobes in clinical microbiology laboratory. We identified 544 isolates of 79 species by routine culture from deep samples in our hospital. MALDI-TOF MS allowed identification of 332 isolates (61%). The remaining 212 (39%) were identified by 16S rRNA gene sequencing, allowing identification of 202 at the species level. The most common anaerobes were Propionibacterium spp. (12%), Finegoldia magna (4%), Fusobacterium spp. (6%) and Bacteroides spp. (6%). However, among the 79 identified species, seven were new species or genera, including two Prevotella conceptionensis, a species previously detected by our team by amplification and sequencing, five Anaerococcus sp. and one Prevotella sp. Beyond the identification of these new species, we also identified several uncommon or previously not described associations between species and specific pathologic conditions. MALDI-TOF MS-based identification, which will become more effective with future spectra database improvement, will be likely responsible of a burden of emerging anaerobes in clinical microbiology.     

70 years of permanent plot research in The Netherlands

Abstract. Within the framework of the Dutch ‘Network Ecological Monitoring’, a large set of new permanent plots has been established to monitor selected plant communities throughout The Netherlands for studying the effects of environmental changes on species composition of semi‐natural communities. This national programme will also make use of pre‐existing permanent plots. These plots reflect the long and comprehensive history of research using permanent plots in The Netherlands, where the first permanent plots were established in the early 1930s. To enhance the usefulness of preexisting permanent plots, a comprehensive permanent plot database was compiled. This database was derived from the Dutch National Vegetation Database, that was established for the recent vegetation classification of The Netherlands. This was supplemented with information from various organizations and a number of individual researchers. Currently, the permanent plot database contains ca. 6000 permanent plots. More than 2500 of these plots have been sampled at least 5, and ca. 1500 plots at least 10. Most of the plots are from grasslands, followed by forests and dune systems. This database not only provides insight into vegetation succession, fluctuations within plant communities over time, and the effects of changes of the environment on the vegetation but, indirectly, italso offers the possibility of studying the long‐term behaviour of individual plant species (e.g. establishment, competition, longevity). For the Network Ecological Monitoring a selection of these (historical) plots will be added to the new network of permanent plots in The Netherlands, thus supplying information of past vegetation conditions.     

三江源红外相机社区监测平台概述

三江源红外相机社区监测平台以当地牧民为监测工作的主体, 开展该地区的生物多样性监测、野生动物生态学和行为学研究, 以及基于社区的自然资源管理与保护成效评估。三江源红外相机社区监测平台于2013年10月由北京大学自然保护与社会发展研究中心与山水自然保护中心联合三江源当地社区共同建立与管理。截至2019年6月, 该平台共有有效监测样区9个, 监测覆盖面积7,000多平方公里, 覆盖三江源区域的玉树州全境五县一市和果洛州班玛县, 培养了社区监测队员264名。已处理照片总数252.43万张, 动物独立探测总数12万次, 共识别出30种野生兽类和37种野生鸟类。该平台在调查野生动物多样性本底, 研究雪豹(Panthera uncia)种群密度与动态、雪豹与同域分布的其他食肉动物的关系, 总结社区监测的管理经验等方面取得部分成果。平台未来的工作重点包括总结与发表平台的研究结果、构建云端数据库实现红外相机照片数据的共享与公众参与、打造可互动数据库管理平台和相应监测队员手持客户端以及人工智能辅助下的物种与个体识别。     

GB Non-native Species Information Portal: documenting the arrival of non-native species in Britain

Information on non-native species (NNS) is often scattered among a multitude of sources, such as regional and national databases, peer-reviewed and grey literature, unpublished research projects, institutional datasets and with taxonomic experts. Here we report on the development of a database designed for the collation of information in Britain. The project involved working with volunteer experts to populate a database of NNS (hereafter called “the species register”). Each species occupies a row within the database with information on aspects of the species’ biology such as environment (marine, freshwater, terrestrial etc.), functional type (predator, parasite etc.), habitats occupied in the invaded range (using EUNIS classification), invasion pathways, establishment status in Britain and impacts. The information is delivered through the Great Britain Non-Native Species Information Portal hosted by the Non-Native Species Secretariat. By the end of 2011 there were 1958 established NNS in Britain. There has been a dramatic increase over time in the rate of NNS arriving in Britain and those becoming established. The majority of established NNS are higher plants (1,376 species). Insects are the next most numerous group (344 species) followed by non-insect invertebrates (158 species), vertebrates (50 species), algae (24 species) and lower plants (6 species). Inventories of NNS are seen as an essential tool in the management of biological invasions. The use of such lists is diverse and far-reaching. However, the increasing number of new arrivals highlights both the dynamic nature of invasions and the importance of updating NNS inventories.     

Conservation Genetic Resources for Effective Species Survival (ConGRESS): Bridging the divide between conservation research and practice

Policy makers and managers are increasingly called upon to assess the state of biodiversity, and make decisions regarding potential interventions. Genetic tools are well-recognised in the research community as a powerful approach to evaluate species and population status, reveal ecological and demographic processes, and inform nature conservation decisions. The wealth of genetic data and power of genetic methods are rapidly growing, but the consideration of genetic information and concerns in policy and management is limited by the currently low capacity of decision-makers to access and apply genetic resources. Here we describe a freely available, user-friendly online resource for decision-makers at local and national levels (http://congressgenetics.eu), which increases access to current knowledge, facilitates implementation of studies and interpretation of available data, and fosters collaboration between researchers and practitioners. This resource was created in partnership with conservation practitioners across the European Union, and includes a spectrum of taxa, ecosystems and conservation issues. Our goals here are to (1) introduce the rationale and context, (2) describe the specific tools (knowledge summaries, publications database, decision making tool, project planning tool, forum, community directory), and the challenges they help solve, and (3) summarise lessons learned. This article provides an outlook and model for similar efforts to build policy and management capacity.     

Bacterial spore structures and their protective role in biocide resistance

The structure and chemical composition of bacterial spores differ considerably from those of vegetative cells. These differences largely account for the unique resistance properties of the spore to environmental stresses, including disinfectants and sterilants, resulting in the emergence of spore-forming bacteria such as Clostridium difficile as major hospital pathogens. Although there has been considerable work investigating the mechanisms of action of many sporicidal biocides against Bacillus subtilis spores, there is far less information available for other species and particularly for various Clostridia. This paucity of information represents a major gap in our knowledge given the importance of Clostridia as human pathogens. This review considers the main spore structures, highlighting their relevance to spore resistance properties and detailing their chemical composition, with a particular emphasis on the differences between various spore formers. Such information will be vital for the rational design and development of novel sporicidal chemistries with enhanced activity in the future.     

Plant protein annotation in the UniProt Knowledgebase

The Swiss-Prot, TrEMBL, Protein Information Resource (PIR), and DNA Data Bank of Japan (DDBJ) protein database activities have united to form the Universal Protein Resource (UniProt) Consortium. UniProt presents three database layers: the UniProt Archive, the UniProt Knowledgebase (UniProtKB), and the UniProt Reference Clusters. The UniProtKB consists of two sections: UniProtKB/Swiss-Prot (fully manually curated entries) and UniProtKB/TrEMBL (automated annotation, classification and extensive cross-references). New releases are published fortnightly. A specific Plant Proteome Annotation Program (http://www.expasy.org/sprot/ppap/) was initiated to cope with the increasing amount of data produced by the complete sequencing of plant genomes. Through UniProt, our aim is to provide the scientific community with a single, centralized, authoritative resource for protein sequences and functional information that will allow the plant community to fully explore and utilize the wealth of information available for both plant and non-plant model organisms.