Rob Knight

Research interests

Publications

• Greengenes2 unifies microbial data in a single reference tree

  Nature Biotechnology · 2023 · https://doi.org/10.1038/s41587-023-01845-1

• Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

  Nature Genetics · 2022 · https://doi.org/10.1038/s41588-021-00991-z

• The microbiome and human cancer

  Science · 2021 · https://doi.org/10.1126/science.abc4552

• Structure-based protein function prediction using graph convolutional networks

  Nature Communications · 2021 · https://doi.org/10.1038/s41467-021-23303-9

• Large-scale association analyses identify host factors influencing human gut microbiome composition

  Nature Genetics · 2021 · https://doi.org/10.1038/s41588-020-00763-1

• Role of the microbiome in human development

  Gut · 2019 · 10.1136/gutjnl-2018-317503

• Current understanding of the human microbiome

  Nature Medicine · 2018 · 10.1038/nm.4517

• Regional variation limits applications of healthy gut microbiome reference ranges and disease models

  Nature Medicine · 2018 · 10.1038/s41591-018-0164-x

• American Gut: an Open Platform for Citizen Science Microbiome Research

  mSystems · 2018 · 10.1128/msystems.00031-18

• Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

  Microbiome · 2018 · 10.1186/s40168-018-0470-z

• Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

  Nature Biotechnology · 2017 · 10.1038/nbt.3893

• Enterotypes in the landscape of gut microbial community composition

  Nature Microbiology · 2017 · 10.1038/s41564-017-0072-8

• A communal catalogue reveals Earth’s multiscale microbial diversity

  Nature · 2017 · 10.1038/nature24621

• Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

  The ISME Journal · 2016 · 10.1038/ismej.2015.235

• Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease

  Cell · 2016 · 10.1016/j.cell.2016.11.018

• Genetic Determinants of the Gut Microbiome in UK Twins

  Cell Host & Microbe · 2016 · 10.1016/j.chom.2016.04.017

• The microbiome of uncontacted Amerindians

  Science Advances · 2015 · 10.1126/sciadv.1500183

• Human Genetics Shape the Gut Microbiome

  Cell · 2014 · 10.1016/j.cell.2014.09.053

• The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

  Cell Host & Microbe · 2014 · 10.1016/j.chom.2014.02.005

• Gut Microbes and the Brain: Paradigm Shift in Neuroscience

  Journal of Neuroscience · 2014 · 10.1523/jneurosci.3299-14.2014

• Bacterial phylogeny structures soil resistomes across habitats

  Nature · 2014 · 10.1038/nature13377

• The Long-Term Stability of the Human Gut Microbiota

  Science · 2013 · 10.1126/science.1237439

• Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor

  Science · 2013 · 10.1126/science.1229000

• Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

  Science · 2013 · 10.1126/science.1241214

• Cohabiting family members share microbiota with one another and with their dogs

  eLife · 2013 · 10.7554/elife.00458

• Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

  Nature Biotechnology · 2013 · https://doi.org/10.1038/nbt.2676

• Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy

  Cell · 2012 · 10.1016/j.cell.2012.07.008

• Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

  Nature Methods · 2012 · 10.1038/nmeth.2276

• Diversity, stability and resilience of the human gut microbiota

  Nature · 2012 · 10.1038/nature11550

• The Impact of the Gut Microbiota on Human Health: An Integrative View

  Cell · 2012 · 10.1016/j.cell.2012.01.035

• Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

  The ISME Journal · 2012 · 10.1038/ismej.2012.8

• Human gut microbiome viewed across age and geography

  Nature · 2012 · 10.1038/nature11053

• Structure, function and diversity of the healthy human microbiome

  Nature · 2012 · https://doi.org/10.1038/nature11234

• An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

  The ISME Journal · 2011 · 10.1038/ismej.2011.139

• Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

  Science · 2011 · 10.1126/science.1208344

• Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

  Genome Research · 2011 · 10.1101/gr.112730.110

• Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

  Science · 2011 · 10.1126/science.1198719

• UCHIME improves sensitivity and speed of chimera detection

  Bioinformatics · 2011 · https://doi.org/10.1093/bioinformatics/btr381

• Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients

  The ISME Journal · 2011 · 10.1038/ismej.2011.159

• Moving pictures of the human microbiome

  Genome biology · 2011 · 10.1186/gb-2011-12-5-r50

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

  Nature Biotechnology · 2011 · 10.1038/nbt.1823

• Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5

  Science · 2010 · 10.1126/science.1179721

• Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

  Proceedings of the National Academy of Sciences · 2010 · https://doi.org/10.1073/pnas.1000080107

• Human oral, gut, and plaque microbiota in patients with atherosclerosis

  Proceedings of the National Academy of Sciences · 2010 · 10.1073/pnas.1011383107

• Examining the global distribution of dominant archaeal populations in soil

  The ISME Journal · 2010 · 10.1038/ismej.2010.171

• Soil bacterial and fungal communities across a pH gradient in an arable soil

  The ISME Journal · 2010 · 10.1038/ismej.2010.58

• QIIME allows analysis of high-throughput community sequencing data

  Nature Methods · 2010 · https://doi.org/10.1038/nmeth.f.303

• Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

  Proceedings of the National Academy of Sciences · 2010 · 10.1073/pnas.1002601107

• Succession of microbial consortia in the developing infant gut microbiome

  Proceedings of the National Academy of Sciences · 2010 · 10.1073/pnas.1000081107

• Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

  Applied and Environmental Microbiology · 2009 · 10.1128/aem.00335-09

• The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

  Science Translational Medicine · 2009 · 10.1126/scitranslmed.3000322

• Bacterial Community Variation in Human Body Habitats Across Space and Time

  Science · 2009 · 10.1126/science.1177486

• PyNAST: a flexible tool for aligning sequences to a template alignment

  Bioinformatics · 2009 · 10.1093/bioinformatics/btp636

• A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

  The ISME Journal · 2009 · 10.1038/ismej.2008.127

• The influence of sex, handedness, and washing on the diversity of hand surface bacteria

  Proceedings of the National Academy of Sciences · 2008 · 10.1073/pnas.0807920105

• A core gut microbiome in obese and lean twins

  Nature · 2008 · 10.1038/nature07540

• Evolution of Mammals and Their Gut Microbes

  Science · 2008 · 10.1126/science.1155725

• Worlds within worlds: evolution of the vertebrate gut microbiota

  Nature Reviews Microbiology · 2008 · 10.1038/nrmicro1978

• The Human Microbiome Project

  Nature · 2007 · 10.1038/nature06244

• UniFrac: a New Phylogenetic Method for Comparing Microbial Communities

  Applied and Environmental Microbiology · 2005 · 10.1128/aem.71.12.8228-8235.2005

• Obesity alters gut microbial ecology

  Proceedings of the National Academy of Sciences · 2005 · 10.1073/pnas.0504978102

Current projects

No projects listed.