Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats

With the current fast accumulation of microbial community samples and related metagenomic sequencing data, data integration and analysis system is urgently needed for in-depth analysis of large number of metagenomic samples (also referred to as “microbial communities”) of interest. Although several existing databases have collected a large number of metagenomic samples, they mostly serve as data repositories with crude annotations, and offer limited functionality for analysis. Moreover, the few available tools for comparative analysis in the literature could only support the comparison of a few pre-defined set of metagenomic samples. To facilitate comprehensive comparative analysis on large amount of diverse microbial community samples, we have designed a Meta-Mesh system for a variety of analyses including quantitative analysis of similarities among microbial communities and computation of the correlation between the meta-information of these samples. We have used Meta-Mesh for systematically and efficiently analyses on diverse sets of human associate-habitat microbial community samples. Results have shown that Meta-Mesh could serve well as an efficient data analysis platform for discovery of clusters, biomarker and other valuable biological information from a large pool of human microbial samples.     

Efficient molecular cloning of environmental DNA from geothermal sediments

An efficient and simple method for constructing an environmental library using mechanically sheared DNA obtained directly from geothermal sediments is presented. The method is based on blunt-end modification of DNA fragments followed by 3-adenylation using Vent DNA polymerase and Taq DNA polymerase, respectively. The prepared DNA fragments are then ligated into a TA cloning vector and used in the transformation of Escherichia coli. This method has been successfully applied to the cloning of ORFs derived from uncultivated prokaryotes present in geothermal sediment.     

Microbial and viral metagenomes of a subtropical freshwater reservoir subject to climatic disturbances

Extreme climatic activities, such as typhoons, are widely known to disrupt our natural environment. In particular, studies have revealed that typhoon-induced perturbations can result in several long-term effects on various ecosystems. In this study, we have conducted a 2-year metagenomic survey to investigate the microbial and viral community dynamics associated with environmental changes and seasonal variations in an enclosed freshwater reservoir subject to episodic typhoons. We found that the microbial community structure and the associated metagenomes continuously changed, where microbial richness increased after typhoon events and decreased during winter. Among the environmental factors that influenced changes in the microbial community, precipitation was considered to be the most significant. Similarly, the viral community regularly showed higher relative abundances and diversity during summer in comparison to winter, with major variations happening in several viral families including Siphoviridae, Myoviridae, Podoviridae and Microviridae. Interestingly, we also found that the precipitation level was associated with the terrestrial viral abundance in the reservoir. In contrast to the dynamic microbial community (L-divergence 0.73±0.25), we found that microbial metabolic profiles were relatively less divergent (L-divergence 0.24±0.04) at the finest metabolic resolution. This study provides for the first time a glimpse at the microbial and viral community dynamics of a subtropical freshwater ecosystem, adding a comprehensive set of new knowledge to aquatic environments.     

基于皱皮软海绵宏基因组的PKS基因筛选的研究

提取皱皮软海绵及其共附生微生物的宏基因组总DNA,使用聚酮合酶(PKS)基因的酮酰合酶(KS)域引物PCR扩增PKS基因片段获得一条671bp的片段,以pUCm-T vector为载体将该基因片段克隆到大肠杆菌中,从阳性克隆中分离出PKS基因片段,测序推导出氨基酸序列。通过BLAST比对发现此氨基酸序列与红细菌目的Rhodobacterales bacterium PKS基因KS域的氨基酸序列有96%的同源性。通过基于氨基酸序列的系统发育分析,推测此筛选得到的PKS基因属于trans-AT型。本文首次证实了皱皮软海绵中存在细菌来源的PKS基因。     

Meta-Mesh——元基因组数据分析系统

随着元基因组数据的不断增多,建立一个包含高品质的元基因组样本(也称为"微生物群落")数据的集成化的分析平台成为可能,使得微生物群落样本能够被有效分析、比较与搜索,从中发现更加深入的生物学意义。然而,一方面目前大部分元基因组数据库仅仅提供了简单的数据存储,缺乏良好的样本注释或者仅仅提供了很少的分析功能。另一方面,用于计算微生物群落数据相似性的方法所能够接受的样本数据量非常有限。长期以来,科学家们一直在寻找有效的方法计算海量微生物群落之间的相似性,从而研究样本之间的相似度并发现元基因组数据信息的相关性。Meta-Mesh是一个全新的在线元基因组分析系统,它包括元基因组数据库和分析平台,可以对元基因组样本进行系统、有效地分析,并实现样本的群落结构比较和精确搜索。其中,元基因组数据库已经从公共领域和内部实验室收集了超过7 000个高品质、带有有效注释的样本。同时,Meta-Mesh的分析平台提供了多种在线分析工具,可以对元基因组样本进行群落的结构分析与注释,多角度比较,并能通过快速索引策略和群落结构相似性算法在数据库中高效搜索近似的样本。Meta-Mesh通过"人体微生物群落样本的数据库搜索识别"以及"基于相似度矩阵的样本的聚类"等一系列的元基因组研究案例证明了其分析方面的性能。作为一个在线的元基因组数据库和分析系统,Meta-Mesh将服务于元基因组样本的快速分析、识别、比对、搜索等相关领域。     

传粉网络构建的定性定量分子研究: 应用与展望

传粉者是重要的生态功能提供者, 在维持稳定的生态系统和高效的农业生产力中发挥着重要作用。因此, 传粉网络的构建和监测工作对评价生态系统平衡和调控农业生产至关重要。该工作的基础就是通过对传粉者及植物的物种鉴定构建其相关性。传统的形态学物种鉴定对分类学专家的专业知识、时间和经验都提出较高的要求。DNA条形码和高通量测序技术(high-throughput sequencing, HTS)的发展及其在传粉网络研究中的应用, 提供了高效、准确鉴定传粉者与植物的方法, 大大提高了传粉网络构建的效率。本文阐述了传粉网络研究相关的研究方法和技术进展, 并提出利用高通量测序技术结合无PCR扩增(PCR-free)的“超级条形码”技术, 有望实现以更高的灵敏度和分辨率对混合物种样品进行定性及相对定量的监测。该方法的有效性已在其他生物多样性研究中得以验证, 在传粉网络研究中虽处于初始阶段, 但应用前景广阔。     

Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe

Foraging intensity of large herbivores may exert an indirect top‐down ecological force on soil microbial communities via changes in plant litter inputs. We investigated the responses of the soil microbial community to elk (Cervus elaphus) winter range occupancy across a long‐term foraging exclusion experiment in the sagebrush steppe of the North American Rocky Mountains, combining phylogenetic analysis of fungi and bacteria with shotgun metagenomics and extracellular enzyme assays. Winter foraging intensity was associated with reduced bacterial richness and increasingly distinct bacterial communities. Although fungal communities did not respond linearly to foraging intensity, a greater β‐diversity response to winter foraging exclusion was observed. Furthermore, winter foraging exclusion increased soil cellulolytic and hemicellulolytic enzyme potential and higher foraging intensity reduced chitinolytic gene abundance. Thus, future changes in winter range occupancy may shape biogeochemical processes via shifts in microbial communities and subsequent changes to their physiological capacities to cycle soil C and N.     

Evidence for dynamic exchange of qac gene cassettes between class 1 integrons and other integrons in freshwater biofilms

Class 1 integrons carried by pathogens have acquired over 100 different gene cassettes encoding resistance to antimicrobial compounds, helping to generate a crisis in the management of infectious disease. It is presumed that these cassettes originated from environmental bacteria, but exchange of gene cassettes has surprisingly never been demonstrated outside laboratory or clinical contexts. We aimed to identify a natural environment where such exchanges might occur, and determine the phylogenetic range of participating integrons. Here we examine freshwater biofilms and show that families of cassettes conferring resistance to quaternary ammonium compounds ( qac ) are found on class 1 integrons identical to those from clinical contexts, on sequence variants of class 1 integrons only known from natural environments, and on other diverse classes of integrons only known from the chromosomes of soil and freshwater Proteobacteria . We conclude that gene cassettes might be readily shared between different integron classes found in environmental, commensal and pathogenic bacteria. This suggests that class 1 integrons in pathogens have access to a vast pool of gene cassettes, any of which could confer a phenotype of clinical relevance. Exploration of this resource might allow identification of resistance or virulence genes before they become part of multi-drug-resistant human pathogens.     

An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome

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