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| 1 | Emerging Trends for Microbiome Analysis: From Single-Cell Functional Imaging to Microbiome Big Data显示文摘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(3) a 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. | Jian xu Bo Ma Xiaoquan Su Shi Huang Xin Xu Xuedong Zhou Wei Huang Rob Knight | 2017 | Engineering2017，3，1： | 9 |
| 2 | The Impact of the Gut Microbiota on Human Health: An Integrative View显示文摘 | Jose C. Clemente Luke K. Ursell Laura Wegener Parfrey Rob Knight | 2012 | Cell2012，，6： | 4 |
| 3 | Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy显示文摘 | Omry Koren Julia K. Goodrich Tyler C. Cullender Aymé Spor Kirsi Laitinen Helene Kling B?ckhed Antonio Gonzalez Jeffrey J. Werner Largus T. Angenent Rob Knight Fredrik B?ckhed Erika Isolauri Seppo Salminen Ruth E. Ley | 2012 | Cell2012，，3： | 2 |
| 4 | Characterizing microbial communities through space and time显示文摘 | Antonio Gonzalez Andrew King Michael S Robeson II Sejin Song Ashley Shade Jessica L. Metcalf Rob Knight | 2011 | Current Opinion in Biotechnology2011，，3： | 1 |
| 5 | The Impact of the Gut Microbiota on Human Health: An Integrative View显示文摘 | Jose C. Clemente Luke K. Ursell Laura Wegener Parfrey Rob Knight | 2012 | Cell2012，，6： | 1 |
| 6 | Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish显示文摘 | Ivana Semova Juliana D. Carten Jesse Stombaugh Lantz C. Mackey Rob Knight Steven A. Farber John F. Rawls | 2012 | Cell Host & Microbe2012，，3： | 1 |
| 7 | Reconstructing the Microbial Diversity and Function of Pre-Agricultural Tallgrass Prairie Soils in the United States显示文摘 | Noah Fierer Joshua Ladau Jose C. Clemente Jonathan W. Leff Sarah M. Owens Katherine S. Pollard Rob Knight Jack A. Gilbert Rebecca L. McCulley | 2013 | 2013 (6158)2013，，6158： | 1 |
| 8 | Meta-analyses of human gut microbes associated with obesity and IBD显示文摘 | William A. Walters Zech Xu Rob Knight | 2014 | FEBS Letters2014，，22： | 1 |
| 9 | The Impact of the Gut Microbiota on Human Health: An Integrative View显示文摘 | Jose C. Clemente Luke K. Ursell Laura Wegener Parfrey Rob Knight | 2012 | Cell2012，，6： | 1 |
| 10 | Fast UniFrac :fa- cilitating high - throughput phylogenetic analyses of microbia| com-munities including analysis of pyrosequencing and PhyloChip data 显示文摘 | Hamady Micah Lozupone Catherine Knight Rob | 2010 | ISME Journal2010，4，1： | 1 |
| 11 | Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota显示文摘 | Purna C. Kashyap Angela Marcobal Luke K. Ursell Samuel A. Smits Erica D. Sonnenburg Elizabeth K. Costello Steven K. Higginbottom Steven E. Domino Susan P. Holmes David A. Relman Rob Knight Jeffrey I. Gordon Justin L. Sonnenburg | 2013 | Proceedings of the National Academy of Sciences2013，，42： | 1 |
| 12 | Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau显示文摘 | Jinbo Xiong Yongqin Liu Xiangui Lin Huayong Zhang Jun Zeng Juzhi Hou Yongping Yang Tandong Yao Rob Knight Haiyan Chu | 2012 | Environmental Microbiology2012，，9： | 1 |
| 13 | High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity显示文摘 | Marie A. Hildebrandt Christian Hoffmann Scott A. Sherrill–Mix Sue A. Keilbaugh Micah Hamady Ying–Yu Chen Rob Knight Rexford S. Ahima Frederic Bushman Gary D. Wu | 2009 | Gastroenterology2009，，5： | 1 |
| 14 | Fast UniFrac:facil- itating high - throughput phylogenetic analyses of microbial communities in- cluding analysis of pyrosequencing and PhyloChip data 显示文摘 | Hamady Micah Lozupone Catherine Knight Rob | 2010 | ISME Jour- nal2010，4，1： | 1 |
| 15 | Development of the Human Gastrointestinal Microbiota and Insights From High-Throughput Sequencing显示文摘 | Maria Gloria Dominguez-Bello Martin J. Blaser Ruth E. Ley Rob Knight | 2011 | Gastroenterology2011，，6： | 1 |
| 16 | Genomic Mutations Within the Host Microbiome: Adaptive Evolution or Purifying Selection显示文摘Next-generation sequencing technology has transformed our ability to assess the taxonomic composition functions of host-associated microbiota and microbiomes. More human microbiome research projects—particularly those that explore genomic mutations within the microbiome—will be launched in the next decade. This review focuses on the coevolution of microbes within a microbiome, which shapes strain-level diversity both within and between host species. We also explore the correlation between microbial genomic mutations and common metabolic diseases, and the adaptive evolution of pathogens and probiotics during invasion and colonization. Finally, we discuss advances in methods and algorithms for annotating and analyzing microbial genomic mutations. | Jiachao Zhang Rob Knight | 2023 | Engineering2023，，1： | 0 |
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