口腔微生物多样性研究进展

口腔微生物多样性的改变是口腔常见感染性疾病的发病机制之一,随着分子生物学技术的普遍应用,研究者能够不通过纯培养技术即可对人类口腔不同生态系的微生物组成及变化进行研究。本文综述了当前口腔微生物多样性研究的常用方法及各自的特点,从而为口腔微生物生态方面的进一步深入研究提供参考。     

基于16S rDNA高通量测序的短尾猴口腔微生物多样性

口腔微生物群落结构是维持机体健康的重要因素,了解动物口腔微生物多样性有助于认识和理解动物的生态学适应。本研究以栖息于安徽黄山的短尾猴为研究对象,采用非损伤性取样法收集了鱼鳞坑YA1群体中19个短尾猴口腔样本,采用改进高盐提取法提取微生物DNA,利用Illumina Miseq测序平台对微生物16S rDNA V3-V4区扩增产物进行双端测序,分析微生物群落结构多样性。研究共获得206 533条优质序列,发现4 685个OTU,归属20个门、310个属。结果表明：短尾猴口腔微生物物种丰富,以变形菌门(Proteobacteria,占总条带44.58%)、厚壁菌门(Firmicutes, 30.28%)、拟杆菌门(Bacteroidetes, 12.27%)、梭杆菌门(Fusobacteria, 7.72%) 和放线菌门(Actinobacteria,3.70%)为主;24个微生物属在所有样本中均有分布,为其核心微生物属;短尾猴口腔中存在大量与口腔疾病相关的微生物和多种低丰富度的潜在病原菌。本研究为进一步研究短尾猴口腔微生物群落结构形成与适应性提供了基础资料,也提示在保护和管理野生猴群中需要应对人畜共患病传播的潜在风险。     

浅谈微生物与人类生态系统的相互影响

概括介绍了微生物、人类生态系统的基本知识以及二者之间的相互影响。提出：人类首先应该处理好微生物和人类生态系统之间的相互关系,使其协调发展,进而使生物多样性得以维持和发展。在这个基础上再尽量减少或消除微生物对人类生态系统的消极影响,充分发挥微生物的积极作用,达到利用微生物为人类服务的最终目的。     

人类微生物组测序与比较研究

人体微生物群系影响人类的健康,与人类的各种疾病,如肥胖、糖尿病、冠心病、结肠癌等的发生具有密切的关系.近年来,人类微生物组研究日益受到重视.综述人类微生物组的测序和比较研究进展.     

原核微生物的多样性

微生物是一群以分解代谢为主的重要生物类群,其生物学多样性十分丰富。但由于它们的微观性,尤其原核微生物简单的单细胞结构、以无性方式进行快速地繁殖而造成的无准确的基线难以对其进行种群数目和数量的统计,因而对微生物的多样性研究远没有宏观生物那样深入和受到重视。本文根据原核微生物的特性,从其物种、所代表的进化分支、生理代谢类群及遗传背景几个方面简述了它们的多样性及重要意义,意在引起科学界和全社会对这类生物资源的认识和保护的重视。     

微生物多样性的全球影响

微生物多样性的全球影响张树政（中国科学院微生物研究所北京１０００８０）张树政研究员,中国科学院院士。１９４５年毕业于北京大学化学系。１９４５年至今从事微生物生理生化、代谢及酶等基础及应用研究。５０年代即开始曲霉淀粉酶的研究,证明了黑曲霉糖化酶的优越性...     

人类口腔微生物组学研究:现状、挑战及机遇

全球超过一半的人口患有口腔疾病,其医护费用与全球十大常见死亡病因的花费相当,而且口腔感染与早产、动脉粥样硬化、肝硬化、糖尿病、阿尔茨海默病等全身性或慢性疾病显著相关,因此,口腔微生物组一直是人类微生物组计划的主要研究对象之一。与人体其他部位比较,口腔微生物组研究具有取样快捷、宿主反应表征方便、干预手段直接有效等特点;同时,超过65%的口腔细菌类群已可培养,诸多代表性菌株的全基因组信息已破译。因此口腔微生物组在菌群内部调控网络及其与宿主互作机制、局部感染对远隔器官的影响机制、以及基于菌群的慢病早期预警等微生物组研究核心科学问题上具备作为模式研究体系与技术示范对象的重要优势。本文在分析口腔微生物组学国际、国内研究现状的基础上,建议尽快启动中国人口腔微生物组计划(China human oral microbiome project,CHOMP),通过产学研协同攻关,开拓基于口腔菌群的口腔及全身系统性疾病的个体化预防、诊断及治疗策略。     

益生菌对口腔微生物的影响

益生菌(Probiotic)是添加入食物的能够增加营养摄入并改善人体肠道菌群平衡的活菌。大量研究认为益生菌有促进人体健康的作用,目前研究主要集中在益生菌促进人体肠道菌群平衡的作用。口腔是消化道的起始端,最先接触到益生菌并且也有其特有的微生态系统,近年来越来越多的研究关注益生菌对口腔微生物的作用。本文主要从益生菌在口腔的定植,益生菌对口腔微生物群落的影响,益生菌对口腔细菌作用机制三个方面对近年来益生菌对口腔微生物的影响进行综述。     

青藏高原微生物多样性研究

正青藏高原被誉为世界屋脊,其内部除平原外还有许多山峰、冰川、高山湖泊和高山沼泽,是生态环境最为奇特、生物资源最为丰富的自然资源宝库之一。同时,青藏高原的微生物群落结构及其多样性与其他区域存在巨大差异,因而具有极高的科学研究价值,并逐渐被人们所关注。研究发现气候变化对青藏高原高寒草地生态系统草丛-地境界面微生物会产生重要的影响[1]。冰川雪藻的研究主要在南部的Yala冰川开展,     

深海微生物多样性

海洋面积约占地球总面积的70％,平均深度3,800 m,海底平均压力38 MPa,海水以下更是包含有物理化学性质迥异的多种地质结构,例如海洋沉积物、洋壳、热液口以及冷泉等.这些性质迥异的地质结构环境造就了丰富的生物多样性,构成了地球上最大的微生物生态系统.深海海水中最主要的微生物类群是α-,γ-变形菌(Alpha-&Gammaproteobacteria),以及海洋古菌群I(Marine Group I).深海沉积物中微生物含量与有机物含量和距离大陆板块的距离相关,以异养微生物为主.深海冷泉区富集了厌氧甲烷氧化古菌ANME和硫酸盐还原菌(Deltaproteobacteria);深海热液区由于具有化学物质的多样性和快速的动态变化而导致形成微生物的高度多样性.洋壳主要由基性、超基性岩构成,含有丰富的矿物,其中不乏参与铁、锰、硫等关键代谢反应的化能自养微生物.同时,由于环境中99％以上的微生物没有已培养的亲缘种,因此对深海微生物的多样性、生理功能特性以及生物地球化学作用的理解和研究仍然存在巨大的挑战.本文将尝试从不同的深海环境分区来综述深海海水、沉积物、洋壳,以及冷泉区和热液口等特殊生态环境中微生物的分布和多样性.     

Microorganisms, Australia and the Convention on Biological Diversity

The Convention on Biological Diversity arose as an international agreement for the conservation and continued exploitation of Earth's biological diversity (biodiversity). It directly affects those involved in conservation, exploitation and investigation of biodiversity in all its forms, as well as affecting the viability of all life. Australia is one of more than 170 countries that have ratified the Convention. Its involvement in this Convention will be considered in terms of the National Strategy for the Conservation of Biological Diversity with a focus on the coverage of microorganisms within this strategy. Microorganisms represent a major part of the biodiversity on Earth but, as yet, remain relatively unknown. Among those microorganisms that have been described, many, originating from a range of countries, have been deposited in culture collections worldwide. The Convention contains articles that impact on ex situ collections, although precise protocols are not set out therein. An international code of conduct is now being formulated to ensure ongoing access to and exchange of microorganisms in the interests of sustainable development in industrialised and developing nations.     

Diversity and habitat association of small mammals in Aridtsy forest,Awi Zone,Ethiopia

Here, we conducted a survey to examine the diversity, distribution and habitat association of small mammals from August 2011 to February 2012 incorporating both wet and dry seasons in Aridtsy forest, Awi Zone, Ethiopia. Using Sherman live traps and snap traps in four randomly selected trapping grids, namely, natural forest, bushland, grassland and farmland, a total of 468 individuals comprising eight species of small mammals(live traps) and 89 rodents of six species(snap traps) were trapped in 2352 and 1200 trap nights, respectively. The trapped small mammals included seven rodents and one insectivore: Lophuromys flavopuntatus(30.6%), Arvicanthis dembeensis(25.8%), Stenocephalemys albipes(20%), Mastomys natalensis(11.6%), Pelomys harringtoni(6.4%), Acomys cahirinus(4.3%), Lemniscomys zebra(0.2%) and the greater red musk shrew(Crocidura flavescens, 1.1%). Analysis showed statistically significant variations in the abundance and habitat preferences of small mammals between habitats during wet and dry seasons.     

Patterns of habitat utilization of small rodents in an area of Araucaria forest in Southern Brazil

Abstract We investigated patterns of spatial distribution and microhabitat selection of rodents in a patch (26 ha) of mixed ombrophilous forest (or Araucaria forest), dominated by the Araucaria ‘pine’Araucaria angustifolia, in the National Park of Aparados da Serra, RS, in southern Brazil. We conducted monthly trapping sessions lasting 6 days (from June 2000 to June 2001) using a square grid of 121 trap stations, separated by 15 m (2.25 ha). We measured 10 microhabitat variables that could influence species distribution. These variables were related to the occurrence of mammals by using canonical correspondence analysis (CCA) and stepwise multiple regression. The distribution patterns of the three most common rodents differed significantly (χ² = 38.6; P < 0.002), with Delomys dorsalis being more clumped than the other two species. Both CCA and multiple regression analysis showed a significant effect of microhabitat variables on species occurrence. The multiple regression parameters for Oligoryzomys nigripes were R² = 0.142, P < 0.05, for Akodon montensis were R² = 0.222, P < 0.01, and for D. dorsalis R² = 0.323, P < 0.001. Variables that significantly influenced species distribution were vegetation density at 1 m height and length of fallen logs for O. nigripes, canopy cover for A. montensis, and vegetation density at 2 m height, quantity of leaves of Araucaria trees (negative relationship), tree density (except Araucaria trees), and number of potential shelters, for D. dorsalis. The results indicated that D. dorsalis is the most habitat specialist among the rodent species and that there are no apparent competitive interactions.     

Cloning,Expression and Characterization of a Lipase Encoding Gene from Human Oral Metagenome

The human oral metagenomic DNA cloned into plasmid pUC19 was used to construct a DNA library in Escherichia coli. Functional screening of 40,000 metagenomic clones led to identification of a clone LIP2 that exhibited halo on tributyrin agar plate. Sequence analysis of LIP2 insert DNA revealed a 939 bp ORF (omlip1) which showed homology to lipase 1 of Acinetobacter junii SH205. The omlip1 ORF was cloned and expressed in E. coli BL21 (DE3) using pET expression system. The recombinant enzyme was purified to homogeneity and the biochemical properties were studied. The purified OMLip1 hydrolyzed p-nitrophenyl esters and triacylglycerol esters of medium and long chain fatty acids, indicating the enzyme is a true lipase. The purified protein exhibited a pH and temperature optima of 7 and 37 °C respectively. The lipase was found to be stable at pH range of 6–7 and at temperatures lower than 40 °C. Importantly, the enzyme activity was unaltered, by the presence or absence of many divalent cations. The metal ion insensitivity of OMLip1offers its potential use in industrial processes.     

Movement trajectories and habitat partitioning of small mammals in logged and unlogged rain forests on Borneo

1. Non-volant animals in tropical rain forests differ in their ability to exploit the habitat above the forest floor and also in their response to habitat variability. It is predicted that specific movement trajectories are determined both by intrinsic factors such as ecological specialization, morphology and body size and by structural features of the surrounding habitat such as undergrowth and availability of supportive structures. 2. We applied spool-and-line tracking in order to describe movement trajectories and habitat segregation of eight species of small mammals from an assemblage of Muridae, Tupaiidae and Sciuridae in the rain forest of Borneo where we followed a total of 13,525 m path. We also analysed specific changes in the movement patterns of the small mammals in relation to habitat stratification between logged and unlogged forests. Variables related to climbing activity of the tracked species as well as the supportive structures of the vegetation and undergrowth density were measured along their tracks. 3. Movement patterns of the small mammals differed significantly between species. Most similarities were found in congeneric species that converged strongly in body size and morphology. All species were affected in their movement patterns by the altered forest structure in logged forests with most differences found in Leopoldamys sabanus. However, the large proportions of short step lengths found in all species for both forest types and similar path tortuosity suggest that the main movement strategies of the small mammals were not influenced by logging but comprised generally a response to the heterogeneous habitat as opposed to random movement strategies predicted for homogeneous environments. 4. Overall shifts in microhabitat use showed no coherent trend among species. Multivariate (principal component) analysis revealed contrasting trends for convergent species, in particular for Maxomys rajah and M. surifer as well as for Tupaia longipes and T. tana, suggesting that each species was uniquely affected in its movement trajectories by a multiple set of environmental and intrinsic features.     

小兴安岭林区不同生境梯度中小型哺乳动物生物多样性

利用铗日法和陷阱法,于2000年7～8月,对小兴安岭林区7个不同生境梯度中小型哺乳动物群落的多样性变化进行了初步研究。结果表明：(1)铗日法所捕获的物种数和个体数明显大于陷阱法．但后者更适合捕获小体型动物;(2)共捕获小型哺乳动物9种．其中啮齿目(Rodentia)松鼠科(Sciuridae)1种．田鼠亚科(Microtine)3种．鼠科(Muridae)4种．食虫目(Insectivora)鼩鲭科(Soricidae)1种．所捕获的物种中．棕背解(Clethrionomys rufocanus)为优势种．占总数的48．77％．与黑线姬鼠(Apodemus agrarius )、大林姬鼠(A．speciosus)和红背Ping(C．rutilus)一起构成本地区的常见种;(3)物种在不同的生境类型中呈明显的不均匀分布．以中度干扰的灌丛生境内小型哺乳动物从物种丰富度和多样性指数最高．次生林1和农田生境均有较高的物种丰富度和多样性指数,无干扰的原生林1、2中物种丰富度最低,而轻微干扰的原生林3中物种多样性指数最低．受严重干扰的农田生境中小型哺乳动物均匀度最高．其次是次生林1和灌丛,原生林3和干扰较重的次生林2中小型哺乳动物群落均匀度最小;(4)从物种多样性与林地郁闭度和地表草本植物覆盖度的相关分析看出：物种多样性与郁闭度相关性不显著．而与覆盖度呈显著的正相关关系．反映了这些物种对草本植物选择倾向;(5)根据不同生境内群落相似性指数进行系统聚类,将所有的生境聚类为3组．即原生林组(原生林1、原生林2和原生林3)、次生林组(次生林1和次生林2)和农田组(灌丛和农田)．表明组内各生境间小型哺乳动物成分的相似性和组间的明显差异。研究表明．小型哺乳动物多样性受生境内植被演替阶段、食物和隐蔽条件等环境因素影响．而人类干扰也是主要因素之一。     

Human disturbance and natural habitat: a biome level analysis of a global data set

This paper presents an analysis of conversion of natural habitat to human use on a global scale. Human disturbance of natural systems is classified in a three-category system and ranked using a Habitat Index based on remaining undisturbed and partially disturbed land. Data is analysed by biome and biogeographic province, allowing identification of the biomes and provinces which have been the most impacted by human activity. Temperate biomes are found to be generally more disturbed than tropical biomes. Four of the top five most disturbed biomes are temperate. Certain biomes and geographic areas stand out as conservation priorities, notably the islands of Southeast Asia, Mediterranean vegetation types, Temperate Broadleaf Forests and Tropical Dry Forests. Areas for which data deficiencies exist are identified.     

Nest box revealed habitat preferences of arboreal mammals in box‐ironbark forest

Habitat preferences need to be understood if species are to be adequately managed or conserved. Habitat preferences are presumed to reflect requirements for food, shelter and breeding, as well as interactions with predators and competitors. However, one or more of these requirements may dominate. Tree‐cavity‐dependent wildlife species are one example where shelter or breeding site requirements may dominate. We installed 120 nest boxes across 40 sites to target the vulnerable Brush‐tailed Phascogale (Phascogale tapoatafa) and the non‐threatened Sugar Glider (Petaurus breviceps). The provision of shelter sites where few of quality are available may enable better resolution of habitat preferences. Over three years, we observed the Brush‐tailed Phascogale at 17 sites, whereas the Sugar Glider was observed at 39 sites. We tested four broad hypotheses (H1–H4) relating to habitat that may influence occupancy by these species. There was no influence of hollow (cavity) abundance (H1) on either species suggesting our nest boxes had satisfied their shelter requirements. There was no influence of habitat structure (canopy and tree proximity) (H2) immediately around the nest box trees. We found no influence of distance to the forest edge (H3). Variables at and away from the nest box site that appear to reflect foraging substrates (H4) were influential on the Brush‐tailed Phascogale. Sugar Glider occupancy was only influenced by a single variable at the nest box site. The lack of influence of any other variables is consistent with the very high occupancy observed, suggesting most of the forest habitat is suitable when shelter sites are available. We found no evidence that the Sugar Glider reduced site use by the Brush‐tailed Phascogale.     

Ranging patterns and habitat use of Sulawesi Tonkean macaques (Macaca tonkeana) in a human-modified habitat

The goal of this study was to investigate the ecological flexibility of Tonkean macaques (Macaca tonkeana) by examining how they respond to human-induced habitat alteration. To do so, I observed movement patterns, forest strata use, microhabitat use, and home range use in two groups that occupied habitats with different levels of human alteration and habitat quality in Lore Lindu National Park, Sulawesi, Indonesia. The group occupying the heavily altered habitat (Anca) spent a significantly greater proportion of time traveling on the ground than the group in minimally altered habitat (CH), and significantly more time than expected in microhabitats within their range that were characterized by greater alteration (e.g., agroforestry areas). There was no significant difference between the two groups in daily path length, despite differences in group size. The Anca group exhibited a greater home range area per individual than the CH group, and utilized a more limited area within their home range with greater intensity, relative to the CH group. Tonkean macaques therefore show considerable flexibility in response to anthropogenic disturbance by adjusting their use of forest strata to facilitate travel and increase foraging opportunities and by intensively using particular areas within their home range where known resources are present and predictably available.     

海南岛4市县人群口腔假丝酵母菌分布情况的初步调查

目的：调查海南岛海口、三亚市、五指山市和保亭县四市县人群口腔假丝酵母菌的分布情况,为口腔假丝酵母菌分子生物学和遗传学特点研究提供基础资料。方法：分离出的假丝酵母菌经过菌落特征、制片乳酸酚棉蓝染色、芽管形成试验、厚膜孢子形成试验等初步鉴定,并用科玛嘉显色培养基培养确定。结果：海口、三亚市、五指山市和保亭县人群口腔假丝酵母菌总分离率为25．23％．其中白假丝酵母菌占54．48％,光滑假丝酵母菌占14．04％,热带假丝酵母菌占11．06％,克柔假丝酵母菌占9．36％。住院病人和健康人口腔假丝酵母菌的分离率分别为39．95％和11．61％,差异有统计学意义（P〈0．01）,结论：海南地区人群口腔假丝酵母菌的总分离率高于国内其它省份,分离出的假丝酵母菌以白假丝酵母菌为首位,病人口腔假丝酵母菌分离率明显高于健康人。