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  1. Article

    Open Access

    Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition

    Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, im...

    Hao-Wei Chang, Evan M. Lee, Yi Wang, Cyrus Zhou, Kali M. Pruss… in Nature Microbiology (2024)

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  2. No Access

    Article

    The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

  3. The human genome encodes only a small number of digestive glycoside hydrolases for the breakdown of sucrose, lactose and starch. Instead, the large diversity o...

    4. Abdessamad El Kaoutari, Fabrice Armougom, Jeffrey I. Gordon… in Nature Reviews Microbiology (2013)

  4. No Access

    Article

    Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

    A systematic evaluation of parameters that affect short amplicons sequenced on Illumina platforms provides guidelines for how to eliminate erroneous reads and improve data interpretation.

    Nicholas A Bokulich, Sathish Subramanian, Jeremiah J Faith, Dirk Gevers… in Nature Methods (2013)

  5. No Access

    Article

    Going viral: next-generation sequencing applied to phage populations in the human gut

  6. Methods for purifying virus-like particles (VLPs) from microbial communities, procedures for amplifying the small quantities of DNA that are recovered from VLP...

    7. Alejandro Reyes, Nicholas P. Semenkovich, Katrine Whiteson… in Nature Reviews Microbiology (2012)

  7. No Access

    Article

    Unlocking the potential of metagenomics through replicated experimental design

    Metagenomics holds enormous promise for discovering novel enzymes and organisms that are biomarkers or drivers of processes relevant to disease, industry and the environment. In the past two years, we have see...

    Rob Knight, Janet Jansson, Dawn Field, Noah Fierer, Narayan Desai… in Nature Biotechnology (2012)

  8. No Access

    Article

    Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries

    Insertion sequencing (INSeq) is a method for determining the insertion site and relative abundance of large numbers of transposon mutants in a mixed population of isogenic mutants of a sequenced microbial spec...

    Andrew L Goodman, Meng Wu, Jeffrey I Gordon in Nature Protocols (2011)

  9. No Access

    Article

    Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

    Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for...

    Pelin Yilmaz, Renzo Kottmann, Dawn Field, Rob Knight, James R Cole… in Nature Biotechnology (2011)

  10. No Access

    Article

    QIIME allows analysis of high-throughput community sequencing data

    J Gregory Caporaso, Justin Kuczynski, Jesse Stombaugh, Kyle Bittinger… in Nature Methods (2010)

  11. No Access

    Article

    Worlds within worlds: evolution of the vertebrate gut microbiota

  12. Comparative analyses between microbial communities in the human gut versus diverse other environments can help elucidate the environmental and evolutionary par...

    13. Ruth E. Ley, Catherine A. Lozupone, Micah Hamady, Rob Knight… in Nature Reviews Microbiology (2008)

  13. No Access

    Article

    DNA microarrays and beyond: completing the journey from tissue to cell

    For the cell biologist, identifying changes in gene expression using DNA microarrays is just the start of a long journey from tissue to cell. We discuss how chip users can first filter noise (false-positives) ...

    Jason C. Mills, Kevin A. Roth, Ross L. Cagan, Jeffrey I. Gordon in Nature Cell Biology (2001)

  14. No Access

    Article

    Structure of N-myristoyltransferase with bound myristoylCoA and peptide substrate analogs

    N-myristoyltransferase (Nmt) attaches myristate to the N-terminal glycine of many important eukaryotic and viral proteins. It is a target for anti-fungal and anti-viral therapy. We have determined the structur...

    Rajiv S. Bhatnagar, Klaus Fütterer, Thalia A. Farazi… in Nature Structural Biology (1998)