Author
Rob Knight
Other affiliations: Anschutz Medical Campus, University of Sydney, Veterans Health Administration ...read more
Bio: Rob Knight is an academic researcher from University of California, San Diego. The author has contributed to research in topics: Microbiome & Gut flora. The author has an hindex of 201, co-authored 1061 publications receiving 253207 citations. Previous affiliations of Rob Knight include Anschutz Medical Campus & University of Sydney.
Topics: Microbiome, Gut flora, Medicine, Metagenomics, Biology
Papers published on a yearly basis
Papers
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01 Jan 2014
TL;DR: The human microbiome can be far more personalized, that is more different between individuals than within an individual, than the human genome, which is mostly stable over the authors' lives.
Abstract: SUMMARY ➤ The human microbiome can be far more personalized, that is more different between individuals than within an individual, than the human genome. While the human genome is mostly stable over our lives, our microbiome changes on a daily basis. ➤ Features of the microbiome that differ across individuals include its taxonomic composition and structure, in other words, which taxa are present and at what abundances, and the rate at which the composition and structure change over time. ➤ Our personalized microbiomes reflect our lives. Some features are inherited, with incomplete penetrance, via our genomes; other features develop stochastically due to the timing of our exposure to particular organisms; and still others result from personal choices such as diet or environmental exposures.
4 citations
4 citations
TL;DR: In this article, the authors used Acinetobacter baylyi to detect donor DNA from the genomes of colorectal cancer (CRC) cells and organoids, and achieved 100% discrimination between mice with and without CRC using both delivery methods.
Abstract: Advances in bacterial engineering have catalysed the development of living cell diagnostics and therapeutics, including microbes that respond to diseases such as gut inflammation, intestinal bleeding, pathogens and hypoxic tumors. Bacteria can easily access the entire gastrointestinal tract via oral administration, and they can produce outputs that can be noninvasively measured in stool or urine. Cellular memory, such as bistable switches or genomic rearrangement, has been used to allow bacteria to store information over time. However, living biosensors have not yet been engineered to detect specific DNA sequences or mutations from outside the cell. Here, we engineer naturally competent Acinetobacter baylyi to detect donor DNA from the genomes of colorectal cancer (CRC) cells and organoids. We characterize the functionality of the biosensors in vitro with co-culture assays and then validate in vivo with sensor bacteria delivered orally or rectally into mice injected with orthotopic donor CRC organoids. We observe horizontal gene transfer from the tumor to the sensor bacteria in vivo, allowing their detection in stool. The sensor bacteria achieved 100% discrimination between mice with and without CRC using both delivery methods. Our findings establish a framework for biosensing applications that require the detection of mutations or organisms within environments that are difficult to sample. In addition, the platform can be readily expanded to include in situ production and delivery of therapeutic payloads at the detection site.
4 citations
Max Planck Society1, University of Oxford2, University of Colorado Boulder3, Michigan State University4, Marine Biological Laboratory5, Argonne National Laboratory6, European Bioinformatics Institute7, Yonsei University8, University of Manchester9, Massachusetts Institute of Technology10, New York University11, National Institutes of Health12, Jacobs University Bremen13, Los Alamos National Laboratory14, University of Maryland, Baltimore15, Ghent University16, Lawrence Berkeley National Laboratory17, University of Southern California18, National Ecological Observatory Network19, Human Genome Sequencing Center20, University of New Mexico21, Washington University in St. Louis22, Joint Genome Institute23, Baylor College of Medicine24, Cornell University25, Cooperative Institute for Research in Environmental Sciences26, Technische Universität München27, J. Craig Venter Institute28, University of Waterloo29, Oak Ridge National Laboratory30, National Science Foundation31, Vrije Universiteit Brussel32, Stanford University33
TL;DR: The Genomic Standards Consortium's (GSC) Minimum Information about an ENvironmental Sequence (MIENS) standard for describing marker genes as discussed by the authors has been adopted for gene annotation.
Abstract: We present the Genomic Standards Consortium’s (GSC) “Minimum Information about an ENvironmental Sequence” (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
4 citations
TL;DR: Behavioral, physiological and neuroanatomical correlates of the ability to rapidly allocate attention to different regions of visual space are provided.
Abstract: Muller and colleagues provide behavioral, physiological and neuroanatomical correlates of our ability to rapidly allocate attention to different regions of visual space.
4 citations
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TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Abstract: Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion of QIIME analyses presented in the main text; Sequencing of 16S rRNA gene amplicons; QIIME analysis notes; Expanded Figure 1 legend; Links to raw data and processed output from the runs with and without denoising.
28,911 citations
28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
18,940 citations
TL;DR: The extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
Abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive web resource for up to date, quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. The referred database release 111 (July 2012) contains 3 194 778 small subunit and 288 717 large subunit rRNA gene sequences. Since the initial description of the project, substantial new features have been introduced, including advanced quality control procedures, an improved rRNA gene aligner, online tools for probe and primer evaluation and optimized browsing, searching and downloading on the website. Furthermore, the extensively curated SILVA taxonomy and the new non-redundant SILVA datasets provide an ideal reference for high-throughput classification of data from next-generation sequencing approaches.
18,256 citations
University of Massachusetts Amherst1, University of Michigan2, University of New Mexico3, University of British Columbia4, Texas A&M University5, University of Minnesota6, University of Warwick7, Dalhousie University8, Colorado School of Mines9, University of Ljubljana10, Graz University of Technology11, Louisiana State University12
TL;DR: M mothur is used as a case study to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments.
Abstract: mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the alpha and beta diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.
17,350 citations
TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Abstract: Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification.
Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Availability: Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch
Contact: [email protected]
Supplementary information:Supplementary data are available at Bioinformatics online.
17,301 citations