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Emerging Trends for Microbiome Analysis： From Single-Cell Functional Imaging to Microbiome Big Data

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Engineering 2017年第1期3卷 66-70页

作者： Jian xu Bo Ma Xiaoquan Su Shi Huang Xin Xu Xuedong Zhou Wei Huang rob knight Single-Cell Center CAS Key Laboratory of Biofuels Shandong Key Laboratory of Energy Genetics Qingdao Institute of BioEnergy and Bioprocess Technology Chinese Academy of Sciences Qingdao Shandong 266101 China Center for Microbiome Innovation Department of Pediatrics Department of Computer Science and Engineering University of California San Diego CA 92093 USA Department of Engineering Science University of Oxford Oxford OX1 3PJ UK State Key Laboratory of Oral Diseases West China Hospital ofStomatology Sichuan University Chengdu 610041 China University of Chinese Academy of Sciences Beijing 100049 China

Method development has always been and will continue to be a core driving force of microbiome science, In this perspective, we argue that in the next decade, method development in microbiome analysis will be driven by three key changes in both ways of thinking and technological platforms： ① a shift from dissecting microbiota structure by sequencing to tracking microbiota state, function, and intercellular interaction via imaging; ② a shift from interrogating a consortium or population of cells to probing individual cells; and ③a shift from microbiome data analysis to microbiome data science. Some of the recent methoddevelopment efforts by Chinese microbiome scientists and their international collaborators that underlie these technological trends are highlighted here. It is our belief that the China Microbiome Initiative has the opportunity to deliver outstanding ＂Made-in-China＂ tools to the international research community, by building an ambitious, competitive, and collaborative program at the forefront of method development for microbiome science.

关键词： Microbiome Method development Single-cell analysis Big data China Microbiome Initiative

宿主微生物组内的基因组突变——适应性进化或纯化选择（英文）

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Engineering 2023年第1期 96-102页

作者：张家超 rob knight School of Food Science and Engineering Hainan University Department of Pediatrics University of California San Diego Center for Microbiome Innovation Jacobs School of Engineering University of California San Diego Department of Bioengineering University of California San Diego Department of Computer Science and Engineering University of California San Diego

下一代测序技术改变了我们评估宿主相关微生物群和微生物组的分类组成功能的能力。更多的人类微生物组研究项目，特别是那些探索微生物组内基因组突变的项目，将在未来十年内启动。本综述侧重于微生物组内微生物的共同进化，这塑造了宿...

下一代测序技术改变了我们评估宿主相关微生物群和微生物组的分类组成功能的能力。更多的人类微生物组研究项目，特别是那些探索微生物组内基因组突变的项目，将在未来十年内启动。本综述侧重于微生物组内微生物的共同进化，这塑造了宿主物种内部和之间的菌株水平多样性。我们还探讨了微生物基因组突变与常见代谢疾病之间的相关性，以及病原体和益生菌在入侵和定植过程中的适应性进化。最后，我们讨论了注释和分析微生物基因组突变的方法和算法的进展。

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Soil bacterial diversity in the Arctic is not fundamentally different from that found in other biomes

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Soil bacterial diversity in the Arctic is not fundamentally ...

微生物组分析技术的发展趋势:从单细胞功能成像到菌群大数据

第十一届全国土壤微生物学术讨论会暨第六次全国土壤生物与生物化学学术研讨会第四届全国微生物肥料生产技术研讨会

作者：褚海燕 Noah Fierer Christian L.Lauber J.Gregory Caporaso rob knight Paul Grogan Institute of Soil Science Chinese Academy of Sciences Department of Biology Queen's UniversityKingston University of Colorado

Soil microbes are diverse,ubiquitous and abundant,yet our understanding of their biogeographical patterns is extraordinarily *** heterogeneity and dispersal limitation are clearly both key determinants of biogeographical patterns in animals and plant *** limitation is considered to be less important for microorganisms,resulting in biogeographical patterns that primarily reflect selection by contemporary environmental *** the influence of dispersal limitation in determining microbial biogeographical patterns at the regional and global scales has not yet been fully evaluated because of the lack spatially explicit studies at these *** soils provide an ideal testbed for understanding the patterns and controls on microbial biogeography because they are subject to particularly severe environmental stresses that may have produced unique and distinct bacterial communities compared to those found in lower *** we show that arctic soil bacterial community composition and diversity are structured according to local variation in soil pH rather than geographical proximity to neighboring sites,suggesting that local environmental heterogeneity is far more important than dispersal limitation in determining communitylevel ***,bacterial community composition varied as much within arctic soils as across soils from a wide range of lower latitude biomes,and diversity levels were also similar,indicating global similarities in the structure of soil bacterial *** results contrast with the well-established latitudinal gradients in animal and plant diversity,suggesting that the controls on bacterial community distributions are fundamentally different from those observed for macro-organisms and that our biome definitions are not useful for predicting variability in soil bacterial communities across the globe.

关键词： Arctic soils Bacterial community Biomes Microbial biogeography Soil pH

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Engineering 2017年第1期3卷 143-153页

作者：徐健马波苏晓泉黄适徐欣周学东黄巍 rob knight Single-Cell Center CAS Key Laboratory of Biofuels Shandong Key Laboratory of Energy Genetics Qingdao Institute of Bio Energy and Bioprocess TechnologyChinese Academy of Sciences University of Chinese Academy of Sciences State Key Laboratory of Oral Diseases West China Hospital of Stomatology Sichuan University Department of Engineering Science University of Oxford Center for Microbiome Innovation Department of Pediatrics Department of Computer Science and Engineering University of California

方法学创新一直是微生物组学研究的核心驱动力。我们认为在未来五到十年,微生物组的方法学体系在研究理念与技术平台方面将发生三大变革:(1)从监测菌群"结构"变化向监测菌群"功能/状态"变化的变革;(2)从细胞"群体"分析精度向细胞"个体"... 详细信息

方法学创新一直是微生物组学研究的核心驱动力。我们认为在未来五到十年,微生物组的方法学体系在研究理念与技术平台方面将发生三大变革:(1)从监测菌群"结构"变化向监测菌群"功能/状态"变化的变革;(2)从细胞"群体"分析精度向细胞"个体"分析精度的转变;(3)从"数据分析"向"数据科学"的跨越。在这里我们针对实现上述三大方法学变革需要克服的关键科学或技术挑战,重点介绍了部分中国微生物组分析方法学研究团队及其国际合作伙伴的最新工作进展。我们相信中国微生物组计划应把握住当前这一重要机遇,通过在微生物组分析方法学前沿开展富有雄心、远见、创意与竞争力的交叉合作研究,为国际微生物组计划贡献一系列"中国制造"的新方法、新工具和新仪器。

关键词：微生物组方法学创新单细胞分析大数据中国微生物组计划

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为什么有的人特别招蚊子？

作者： (美)罗布·奈特(rob knight) (美)布伦丹·布勒(Brendan Buhler)

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运用口腔菌群的时空变化来预测儿童龋病

科学新闻 2016年第1期 93-93页

作者： Fei Teng Fang Yang Shi Huang Cunpei Bo Zhenjiang Zech Xu Amnon Amir rob knight 凌均棨徐健中山大学中山大学口腔医学研究所中华口腔医学会牙体牙髓病学专业委员会中科院青岛生物能源与过程所中科院单细胞研究中心

文章简介基于人体共生菌群的慢性疾病预测具有巨大前景,但其可行性尚需证明。婴幼儿龋(ECC)是儿童中最常见的感染性疾病。研究人员同时跟踪了50位四岁儿童的牙菌斑和唾液中的细菌菌群在两年内的发展过程。在此过程中,这些儿童要么保持健... 详细信息

文章简介基于人体共生菌群的慢性疾病预测具有巨大前景,但其可行性尚需证明。婴幼儿龋(ECC)是儿童中最常见的感染性疾病。研究人员同时跟踪了50位四岁儿童的牙菌斑和唾液中的细菌菌群在两年内的发展过程。在此过程中,这些儿童要么保持健康,要么从健康过渡到新发性龋病,要么经历了龋病的继续发展。本研究发现,相对健康儿童而言,儿童患龋会延迟正常口腔菌群的发育。牙菌斑和唾液菌群在龋病发生阶段与

关键词：口腔菌群儿童龋病牙菌斑

Poverty reduction through the development of inclusive food value chains

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Journal of Integrative Agriculture 2021年第4期20卷 964-978页

作者： rob VOS Andrea CATTANEO International Food Policy Research Institute(IFPRI) WashingtonD.C.20007USA Food and Agriculture Organization of the United Nations(FAO) Rome 00153Italy

Propelled by urbanization,rising incomes,and changing diets,food markets have been expanding in Africa and South Asia,creating the vast potential for job and income opportunities along food supply chains and,hence,for poverty *** novel coronavirus(COVID-19)that spread to a pandemic in early 2020 provokes enormous setbacks to this ***,however,should provide lessons regarding the importance of resilient and inclusive food *** responses to COVID-19 should consider interventions towards that end and leverage the opportunities provided by food markets growth as economies recover from the present economic *** paper assesses options of how this could be done by facilitating the better functioning and interconnectedness of the many small and medium-sized enterprises that are proliferating along the"hidden middle"of food value chains in storage,logistics,transportation,and wholesale and retail *** also explores how policies can help smallholder farmers connect to this"hidden middle"in more gainful ways and help them climb out of poverty as well.

关键词： poverty food security and hunger food supply chains South Asia sub-Saharan Africa

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Ecological networks and greenways in Europe: reasoning and concepts

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Journal of Environmental Sciences 2003年第2期15卷 173-181页

作者： rob H.G. Jongman Wageningen UR Expertise Group on Environmental Sciences

The paper gives an overview of approaches towards ecological networks throughout Europe. It does not intend to present a complete picture, but to highlight common developments within countries and regions and show common principles and differences between countries and regions that have to be taken into account when developing a joint European initiative. Countries or regions that have not been included can be active in the same way, but information was not accessible to the authors for different reasons. This overview shows the comparable trends in decline of landscapes and the diversity in approaches to biodiversity conservation and nature conservation planning. Understanding the differences and common issues are of utmost importance to generalise common principles and to understand the way neighbours and other European partners approach problems.

关键词： ecological networks greenways biodiversity land use change homogenisation fragmentation

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Oxygen and Iron-and Steelmaking:Best Friends and Arch-Enemies

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Journal of Iron and Steel Research International 2011年第S2期18卷 16-27页

作者： BOOM rob Materials innovation institute M2i Department of Materials Science and EngineeringDelft University of TechnologyDelftThe Netherlands

Ironmaking is the art of removal the arch-enemy oxygen from iron ore by means of carbon reduction and thus producing hot *** is the art of removing carbon from liquid hot metal by means of best friend pure oxygen,followed by alloying and deoxidation-where oxygen returns to be the ***-metallic particles in steel such as oxides can have a detrimental effect on the steel product properties in terms of formability,strength and surface *** overview of the battle for clean steel production is given based on the experience of the author in industry as well as university research.

关键词： ironmaking carbon-oxygen equilibrium steelmaking deoxidation tundish metallurgy casting clean steel

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