Genomic approaches to studying the human microbiota

The human body is colonized by a vast array of microbes, which form communities of bacteria, viruses and microbial eukaryotes that are specific to each anatomical environment. Every community must be studied as a whole because many organisms have never been cultured independently, and this poses formidable challenges. The advent of next-generation DNA sequencing has allowed more sophisticated analysis and sampling of these complex systems by culture-independent methods. These methods are revealing differences in community structure between anatomical sites, between individuals, and between healthy and diseased states, and are transforming our view of human biology.     

Human gut microbiome viewed across age and geography

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.     

16S rRNA sequences reveal numerous uncultured microorganisms in a natural community.

Microbiologists have been constrained in their efforts to describe the compositions of natural microbial communities using traditional methods. Few microorganisms have sufficiently distinctive morphology to be recognized by microscopy. Culture-dependent methods are biased, as a microorganism can be cultivated only after its physiological niche is perceived and duplicated experimentally. It is therefore widely believed that fewer than 20% of the extant microorganisms have been discovered, and that culture methods are inadequate for studying microbial community composition. In view of the physiological and phylogenetic diversity among microorganisms, speculation that 80% or more of microbes remain undiscovered raises the question of how well we know the Earth's biota and its biochemical potential. We have performed a culture-independent analysis of the composition of a well-studied hot spring microbial community, using a common but distinctive cellular component, 16S ribosomal RNA. Our results confirm speculations about the diversity of uncultured microorganisms it contains.     

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.     

天河机场蜘蛛群落结构研究

在武汉天河机场4种生境中共采集到蜘蛛52种,隶属于12科34属。研究表明：4种生境中的蜘蛛群落相拟性较小,群落结构组成不同,丰富度、多样性指数,均匀度、优势度均不同。这主要与植被类型、密度等生态因子相关,农事活动也是另一个重要影响因素。     

Functional metagenomic profiling of nine biomes

Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.     

土壤微生物多样性与植物多样性

土壤中生活着丰富的微生物类群,是一个重要的地下生物宝库.土壤微生物是土壤中的主要分解者,对环境起着天然的“过滤”和“净化”作用,在自然生态系统的功能发挥和维持能力方面极其重要.植物、土壤和微生物相互作用,构成了一个植物-土壤-微生物的有机整体.土壤微生物多样性代表着微生物群落的稳定性,指生命体在遗传、种类和生态系统层次上的变化.从遗传、分类、生态功能以及系统发育等多方面阐述了当前土壤微生物多样性的研究工作.同时探讨了植物多样性与土壤微生物多样性之间的内在联系,植被的破坏可直接导致土壤微生物多样性的丧失,而土壤微生物对植物物种多样性的维持又具有重要作用.因此,加强土壤微生物多样性研究对植物多样性保护具有重要意义.     

植食性昆虫、植物和共生微生物的功能关联

植食性昆虫和植物均能与微生物形成密切关系，它们各自的生态功能及相互关系也常被共生微生物所影响。近年来，随着分子水平研究方法的进展，植食性昆虫和植物中很多可遗传共生微生物（细菌、真菌等）被发现。共生微生物能够在营养、生殖、防御和解毒等方面给宿主带来显著影响，并与宿主形成竞争、互利或寄生等关系。植食性昆虫体内的含菌胞、肠道、血淋巴、唾液腺等常含有重要功能的共生微生物。新的分子生物学手段和高通量测序技术的应用使得我们能够增加对宿主和共生微生物（即使处于低丰度）之间关系的了解。本文尝试总结了植食性昆虫和植物共生微生物的多样性及其关系、昆虫和植物互作机制、昆虫共生菌解毒植物毒素等方面的近期证据，突出强调了应以系统观思维来理解共生微生物、植食性昆虫和植物间的功能关联，并就将来值得研究的问题提出了建议。     

不同分解程度木麻黄凋落物的养分特征及微生物功能多样性分析

【目的】通过了解木麻黄凋落物分解过程中的养分变化以及微生物碳源的利用特征,明确凋落物微生物多样性与养分之间的关系。【方法】在海南省海口市桂林洋海滨选取10~15年生木麻黄林,按照“S”形五点取样法,分别采集0~5 cm、≥5~10 cm、≥10~15 cm 等3种不同分解程度的凋落物样品,测定其理化性质,并利用Biolog微孔板法测定凋落物外生菌和内生菌的群落功能多样性,对其进行主成分PCA分析和冗余RDA分析。【结果】①凋落物的分解程度越高,其有机碳、全氮、全磷含量越低。②不同分解程度木麻黄凋落物中外生菌和内生菌功能多样性差异显著,外生菌平均颜色变化率(AWCD)随分解程度增加而增大,而内生菌AWCD则降低。③凋落物分解程度越高,外生菌的Shannon、Simpson指数明显升高,McIntosh指数无显著差异;内生菌的Shannon、Simpson指数也随之增加,而McIntosh指数则明显降低。④外生菌和内生菌对6大类碳源利用强度存在差异,优势碳源分别为糖类和多聚物,分解后期胺类和酚类的利用率均有提高。⑤主成分PCA分析表明,不同分解程度的凋落物外生菌和内生菌对31种碳源的利用均有显著差异;RDA分析表明,碳、氮含量与凋落物外生菌微生物功能多样性指数呈最大相关。【结论】木麻黄凋落物分解程度越大,外生菌碳代谢强度和多样性越高,而内生菌碳代谢强度越低,其多样性越高;凋落物的氮、碳含量是影响凋落物微生物功能多样性的主要因素。因此,外生菌和内生菌在木麻黄凋落物的分解中发挥着不同的作用。     

人工构建微生物组对制革废水的氨氮去除及微生物组的对比变化分析

为探究复合人工微生物组对制革废水处理体系中微生物群落的影响,在传统的厌氧/好氧(A/O)污水处理工艺处理制革废水的基础上,投加微生物复合菌形成人工微生物组。利用复合人工微生物组强化废水处理,应用高通量测序技术测定各样品中的细菌16S rRNA V3-V4变异区序列,并对测序数据进行生物信息学分析、Alpha多样性分析以及物种组成分析。结果表明,投加微生物组后,化学需氧量(COD)和氨氮的处理效果得到提升,COD的去除率约为82.60%,氨氮的去除率约为99.47%。高通量测序结果表明,人工投加微生物组使得活性污泥中微生物群落丰度以及多样性提高,污染物降解功能菌占比有所提升,陶厄氏菌属(Thauera)成为其最主要的优势菌属。复合人工微生物组的投加对强化制革废水处理系统有一定潜力。     

中国东北条子河中微生物群落变化与锌砷污染的关系研究

研究目的：通过研究河流微生物与污染物的互作关系,为河流污染治理等相关研究提供新途径。创新要点：研究选择的目标河流是报道较少的辽河二级支流,该研究对于了解支流污染特别是东北地区河流污染有重要的意义。将分子生态学技术应用于分析不同污染程度的河流底泥微生物变化,建立微生物种群变化和污染物的互作关系。研究方法：选取沿条子河的8个代表性区段,分析河水和底泥中重金属和污染物的变化情况。通过变性梯度凝胶电泳（DGGE）技术分析不同河流区段内真核和原核微生物种群变化,解析河流中污染物对底泥微生物的影响,建立微生物种群变化和重金属污染的互作关系。重要结论：重金属污染物的存在能抑制底泥中微生物生长,仅少量具有较强抗性的微生物存活（见图4）;有机污染物的增加使对重金属有较强抗性的Limnodrilus hoffmeisteri 大量繁殖（见图2~4）,从而大量消耗溶解氧,导致好氧微生物死亡和河水自净能力退化,最终引起水质恶化。由此可见,微生物对环境污染物的变化有很敏感的响应,通过对环境中微生物的监测有助于进一步分析环境污染的变化。     

内陆河流域浮床植物根际微生物群落特征与比较

为研究内陆河流域不同浮床植物的根际微生物群落结构、多样性、潜在生态功能及其差异,采集了位于沱江二级支流赤水河生态浮床上的风车草（Cyperus involucratus）、黄菖蒲（Iris pseudacorus）、再力花（Thalia dealbata）、鸢尾（Iris tectorum）、美人蕉（Canna indica）、梭鱼草（Pontederia cordata）6种植物生长旺盛时期的根系样本,通过细菌16sRNA片段高通量测序和生物信息学手段,分析了微生物群落结构组成、生物多样性以及潜在的生态功能。结果表明,变形菌门（Proteobacteria）在6种浮床植物根际细菌中占绝对优势,丰度达47.5% - 72.2%,在植物生长环境较为相似且空间距离较近的情况下,不同浮床植物根际微生物属水平优势种群丰度差异仍较大。微生物群落多样性由大到小依次为鸢尾、美人蕉、黄菖蒲、风车草、再力花、梭鱼草,同科同属的黄菖蒲和鸢尾根际细菌组成相对较为相似。风车草根际硝化/反硝化功能菌群丰度更高,梭鱼草根际芳香族化合物降解功能菌群丰度显著高于另外5种植物。根长、株高和生物量更大的植物根际微生物中芽殖杆菌属丰度显著更高,植物生长指标与部分根际细菌氮转化存在正相关关系。研究结果可为浮床植物根际微生物群落研究和生态浮床的建设优化提供参考。     

山地植物群落数量分类和排序研究进展

在区域至全球尺度上,水热条件是决定植物种、生活型或植被类型分布的主导因素,而在景观及更小的尺度上,区域环境因子则主导着植被的分布格局。数量分类和排序是研究群落生态关系的重要数量方法,它为客观、准确地揭示植被、植物群落及植被与环境之间的生态关系提供了合理、有效的途径。笔者从群落分布格局和物种多样性格局的角度出发,综述了我国山地植物群落数量分类和排序的相关研究,阐述了采用数量分类和排序方法研究山地植被与环境因子关系的必要性,并探讨了我国山地植物群落数量分类和排序研究的发展趋势以及亟待解决的一些问题。     

内蒙古灌木群落物种丰富度与气候的关系

为了验证几种重要的物种多样性地理格局假说(水分能量动态假说、生产力假说、寒冷忍耐假说、生态学代谢假说)在干旱、半干旱地区灌木群落中的适用性, 对内蒙古中西部地区1100 km样线内的灌木群落进行调查, 结合气候数据、植被归一化指数研究不同气候或生产力因子对群落物种丰富度的解释能力。同时研究了不同功能型的植物在物种多样性?气候关系方面的差异, 包括不同的生活型(木本、草本)、水分生态型(旱生、中旱生、中生)。结果表明: 1) 水分能量动态假说能较好地解释本研究区灌木群落多样性的地理格局, 植物能获得的有效水分是影响物种丰富度的主要因素; 2) 研究结果与代谢假说的预测相反, 该假说无法解释干旱、半干旱区的群落多样性格局, 结果不支持寒冷忍耐假说在研究区的适用性, 而生产力也只能解释部分功能型的物种丰富度; 3) 不同功能型的植物对气候、 生产力梯度的响应表现出很大的差异, 物种的生态特性以及种间相互作用对物种丰富度格局有着重要的影响, 深入理解群落的构建机制可能是理解生物多样性的地理格局所必需的。     

基于高通量测序研究锦屏极深岩层微生物多样性

本研究旨在探索中国锦屏地下原始极深环境中极端微生物群落结构及功能。本研究采用高通量测序技术对锦屏极深环境中4个岩石样品和7个水样中存在的微生物群落进行了研究,共获得732 477条高质量序列(Clean tags),可聚类到1 318个有效OTUs,各样品菌群之间存在一定差异,但其优势菌门一致,为变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)和厚壁菌门(Firmicutes)。采用PICRUSt分析了样品菌群对应的基因功能,结果表明涉及碳水化合物代谢、氨基酸代谢、能量代谢、辅助因子和维生素代谢等基因功能的丰度最高。结果表明锦屏地下原始极深环境中微生物群落复杂,但主要菌群相对稳定。     

Coral communities are regionally enriched along an oceanic biodiversity gradient

Ecological communities are influenced by processes operating at multiple scales. Thus, a better understanding of how broad- as well as local-scale processes affect species diversity and richness is increasingly becoming a central focus in modern community ecology. Here, in a study of unprecedented geographical scope, we show significant regional and local variation in the species richness of coral assemblages across an oceanic biodiversity gradient. The gradient that we sampled extends 10,000 km eastwards from the world's richest coral biodiversity hotspot in the central Indo-Pacific. Local richness and the size of regional species pools decline significantly across 15 islands spanning the gradient. In addition, richness declines across three adjacent habitats (reef slopes, crests and flats). In each habitat, a highly consistent linear relationship between local and regional species richness indicates strong regional enrichment. Thus, even on the most diverse coral reefs in the world, local coral assemblages are profoundly affected by regional-scale processes. Understanding these historical and biogeographical influences is essential for the effective management and preservation of these endangered communities.     

微生物相互作用研究进展：从观察到预测?

地球上的微生物有着极高的丰富度和多样性.它们的生命活动和相互作用对维持生态系统稳定性起到关键作用;生存在宿主体内的微生物对其宿主的健康有重要影响.第二代测序技术的发展使得科学家获得了大量的关于微生物群落和功能基因组成的数据;而微生物群落和生态系统生态学的重点,正在从获得观测数据转变到理解微生物相互作用过程,并预测群落结构和功能的动态变化.近年来发展了很多针对第二代测序数据的算法和数学模型,以推测微生物种间相互作用网络,但这种自上而下的研究仍存在局限性.自下而上的实验研究可以对微生物种间作用进行直接验证,并帮助我们理解更高层次上的生态学模式和过程.与此同时,基于数学分析或模拟的理论研究展示了微生物相互作用的动态及其对群落动态和功能的影响.今后的研究应该结合观测数据、实验验证、理论模型多种研究方法,增进我们对微生物种间相互作用的理解并做出预测,以应对全球气候变化、传染病暴发、抗生素抗性进化等诸多挑战.     

稻田生态系统中杂草地捕食性节肢动物群落研究

采用吸虫器法采样，对稻田生态系统中杂草地捕食性节肢动物天敌群落物种多样性、结构动态等进行了系统的研究。在杂草地生境中采集到73种捕食性节肢动物，其中55种为捕食性蜘蛛，18种为捕食性昆虫。在冬春闲期，杂草地生境的捕食性节肢动物物种多样性和单位面积内的个体数量较高。水稻移栽后，杂草地中的捕食性节肢动物种群迁进稻田，为稻田提供天敌移居者，杂草地生境中的捕食性天敌物种数减少，单位面积内的个体数量降低；水稻成熟后、夏闲期始及冬闲期始，杂草地接纳从稻田中迁出的天敌种群，捕食性天敌物种数和单位面积内的个体数量呈上升趋势。杂草地为保护稻田捕食性天敌，提供了一个良好的庇难所。     

Two episodes of microbial change coupled with Permo/Triassic faunal mass extinction

Microbial expansion following faunal mass extinctions in Earth history can be studied by petrographic examination of microbialites (microbial crusts) or well-preserved organic-walled microbes. However, where preservation is poor, quantification of microbial communities can be problematic. We have circumvented this problem by adopting a lipid biomarker-based approach to evaluate microbial community changes across the Permo/Triassic (P/Tr) boundary at Meishan in South China. We present here a biomarker stratigraphic record showing episodic microbial changes coupled with a high-resolution record of invertebrate mass extinction. Variation in the microbial community structure is characterized by the 2-methylhopane (2-MHP) index (a ratio of the abundance of cyanobacterial biomarkers to more general bacterial biomarkers). Two episodes of faunal mass extinction were each preceded by minima in the 2-MHP index, followed by strong maxima, likely reflecting microbial responses to the catastrophic events that caused the extinction and initiated ecosystem changes. Hence, both cyanobacterial biomarker and invertebrate fossil records provide evidence for two episodes of biotic crisis across the P/Tr boundary.