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Author

Rob Knight

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
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Posted ContentDOI
06 Jun 2021-bioRxiv
TL;DR: In this paper, an integrated omics approach is used to describe the Earth's metabolome, which is a direct survey of metabolites associated with microbial communities spanning diverse environments using untargeted metabolomics coupled with metagenome analysis.
Abstract: Microbes produce an array of secondary metabolites that perform diverse functions from communication to defense1. These metabolites have been used to benefit human health and sustainability2. In their analysis of the Genomes from Earth’s Microbiomes (GEM) catalog3, Nayfach and co-authors observed that, whereas genes coding for certain classes of secondary metabolites are limited or enriched in certain microbial taxa, “specific chemistry is not limited or amplified by the environment, and that most classes of secondary metabolites can be found nearly anywhere”. Although metagenome mining is a powerful way to annotate biosynthetic gene clusters (BCGs), chemical evidence is required to confirm the presence of metabolites and comprehensively address this fundamental hypothesis, as metagenomic data only identify metabolic potential. To describe the Earth’s metabolome, we use an integrated omics approach: the direct survey of metabolites associated with microbial communities spanning diverse environments using untargeted metabolomics coupled with metagenome analysis. We show, in contrast to Nayfach and co-authors, that the presence of certain classes of secondary metabolites can be limited or amplified by the environment. Importantly, our data indicate that considering the relative abundances of secondary metabolites (i.e., rather than only presence/absence) strengthens differences in metabolite profiles across environments, and that their richness and composition in any given sample do not directly reflect those of co-occurring microbial communities, but rather vary with the environment.

7 citations

Journal ArticleDOI
TL;DR: To mark the 15th anniversary of Nature Methods, scientists from across diverse fields of basic biology research were asked for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future.
Abstract: To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future.

7 citations

Patent
27 Feb 2014
TL;DR: The electrode has a partially ring shape, and the ring-shaped electrode had a diameter less than about 3 mm and a length less thanabout 3 mm as discussed by the authors. But this method is limited to a single head.
Abstract: PROBLEM TO BE SOLVED: To provide an electrode for a brain wave capable of effectively receiving a signal, fit for every head shape, and comfortable for a subject, and to provide a system and a method for collecting and analyzing brain wave data.SOLUTION: A headset 100 has a plurality of independently adjustable bands 102, 104, 106, 108, and each band includes a plurality of electrodes for receiving signals from the head of a subject. The electrode has a partially ring shape, and the ring-shaped electrode has a diameter less than about 3 mm and a length less than about 3 mm. Each band has a shape of a spine-like structure 110, 112, 114, 116.

7 citations

Journal ArticleDOI
TL;DR: Data derived from seven independent genetic studies were re-analyzed using statistical methods developed by ecologists for estimating the number of species in a community to reveal that more mutations will continue to be identified as more patients are genotyped.

7 citations

Journal ArticleDOI
TL;DR: Cell Tracking Profiler is developed and used to examine RhoA and myosin II control of muscle stem cell behaviour during zebrafish regeneration and can be used to reveal changes to cell behaviour of muSCs in response to manipulation of the cell cytoskeleton by small-molecule inhibitors.
Abstract: Accurate measurements of cell morphology and behaviour are fundamentally important for understanding how disease, molecules and drugs affect cell function in vivo. Using muscle stem cell (muSC) responses to injury in zebrafish as our biological paradigm we established a ground truth for muSC behaviour. This revealed segmentation and tracking algorithms from commonly used programs are error-prone, leading us to develop a fast semi-automated image analysis pipeline that allows user defined parameters for segmentation and correction of cell tracking. Cell Tracking Profiler (CTP) is a package that runs two existing programs, HK Means and Phagosight within the Icy image analysis suite, to enable user-managed cell tracking from 3D time-lapsed datasets to provide measures of cell shape and movement. We demonstrate how CTP can be used to reveal changes to cell behaviour of muSCs in response to manipulation of the cell cytoskeleton by small molecule inhibitors. CTP and the associated tools we have developed for analysis of outputs thus provide a powerful framework for analysing complex cell behaviour in vivo from 4D datasets that are not amenable to straightforward analysis.

7 citations


Cited by
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Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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

Journal ArticleDOI
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