Rob D. Knight

OpenAlex profile · ORCID

Selected research works

Up to 100 selected research works. Source updated 2026-10-28T19:34:56+00:00.

1. QIIME allows analysis of high-throughput community sequencing data · 2010 · 34,887 citations
2. Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 · 2019 · 23,702 citations
3. UCHIME improves sensitivity and speed of chimera detection · 2011 · 15,108 citations
4. Structure, function and diversity of the healthy human microbiome · 2012 · 11,721 citations
5. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample · 2010 · 9,738 citations
6. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences · 2013 · 9,116 citations
7. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms · 2012 · 8,835 citations
8. UniFrac: a New Phylogenetic Method for Comparing Microbial Communities · 2005 · 8,225 citations
9. Human gut microbiome viewed across age and geography · 2012 · 7,816 citations
10. A core gut microbiome in obese and lean twins · 2008 · 7,810 citations
11. Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes · 2011 · 6,514 citations
12. Obesity alters gut microbial ecology · 2005 · 6,179 citations
13. The Human Microbiome Project · 2007 · 6,084 citations
14. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin · 2018 · 5,916 citations
15. Diversity, stability and resilience of the human gut microbiota · 2012 · 5,531 citations
16. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea · 2011 · 5,072 citations
17. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns · 2010 · 4,767 citations
18. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking · 2016 · 4,622 citations
19. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing · 2012 · 4,417 citations
20. Soil bacterial and fungal communities across a pH gradient in an arable soil · 2010 · 4,235 citations
21. Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale · 2009 · 4,062 citations
22. Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice · 2013 · 3,786 citations
23. Evolution of Mammals and Their Gut Microbes · 2008 · 3,748 citations
24. The Impact of the Gut Microbiota on Human Health: An Integrative View · 2012 · 3,706 citations
25. Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease · 2016 · 3,621 citations
26. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons · 2011 · 3,479 citations
27. PyNAST: a flexible tool for aligning sequences to a template alignment · 2009 · 3,398 citations
28. Bacterial Community Variation in Human Body Habitats Across Space and Time · 2009 · 3,229 citations
29. The Treatment-Naive Microbiome in New-Onset Crohn’s Disease · 2014 · 3,220 citations
30. Human Genetics Shape the Gut Microbiome · 2014 · 3,158 citations
31. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases · 2019 · 3,138 citations
32. The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice · 2009 · 3,053 citations
33. UniFrac: an effective distance metric for microbial community comparison · 2010 · 2,823 citations
34. Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities · 2007 · 2,717 citations
35. A communal catalogue reveals Earth’s multiscale microbial diversity · 2017 · 2,679 citations
36. A framework for human microbiome research · 2012 · 2,651 citations
37. Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea · 2017 · 2,622 citations
38. Current understanding of the human microbiome · 2018 · 2,601 citations
39. Succession of microbial consortia in the developing infant gut microbiome · 2010 · 2,540 citations
40. Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys · 2015 · 2,200 citations
41. Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy · 2012 · 2,166 citations
42. Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5 · 2010 · 2,070 citations
43. Normalization and microbial differential abundance strategies depend upon data characteristics · 2017 · 2,064 citations
44. The Long-Term Stability of the Human Gut Microbiota · 2013 · 2,056 citations
45. Best practices for analysing microbiomes · 2018 · 2,005 citations
46. Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans · 2011 · 1,989 citations
47. Analysis of composition of microbiomes: a novel method for studying microbial composition · 2015 · 1,941 citations
48. Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns · 2017 · 1,880 citations
49. Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients · 2011 · 1,869 citations
50. Bayesian community-wide culture-independent microbial source tracking · 2011 · 1,864 citations
51. Global patterns in bacterial diversity · 2007 · 1,830 citations
52. Large-scale association analyses identify host factors influencing human gut microbiome composition · 2021 · 1,784 citations
53. Species-level functional profiling of metagenomes and metatranscriptomes · 2018 · 1,690 citations
54. Worlds within worlds: evolution of the vertebrate gut microbiota · 2008 · 1,672 citations
55. High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity · 2009 · 1,576 citations
56. The gut–liver axis and the intersection with the microbiome · 2018 · 1,477 citations
57. UniFrac – An online tool for comparing microbial community diversity in a phylogenetic context · 2006 · 1,454 citations
58. Examining the global distribution of dominant archaeal populations in soil · 2010 · 1,325 citations
59. The microbiome and human cancer · 2021 · 1,315 citations
60. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex · 2008 · 1,311 citations
61. Bacterial phylogeny structures soil resistomes across habitats · 2014 · 1,290 citations
62. EMPeror: a tool for visualizing high-throughput microbial community data · 2013 · 1,272 citations
63. Strains, functions and dynamics in the expanded Human Microbiome Project · 2017 · 1,266 citations
64. Defining the human microbiome · 2012 · 1,254 citations
65. A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses · 2009 · 1,230 citations
66. Dynamics of the human gut microbiome in inflammatory bowel disease · 2017 · 1,204 citations
67. Human oral, gut, and plaque microbiota in patients with atherosclerosis · 2010 · 1,194 citations
68. Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice · 2019 · 1,181 citations
69. Gut Microbiomes of Malawian Twin Pairs Discordant for Kwashiorkor · 2013 · 1,172 citations
70. GABA-modulating bacteria of the human gut microbiota · 2018 · 1,169 citations
71. Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations · 2018 · 1,144 citations
72. Moving pictures of the human microbiome · 2011 · 1,139 citations
73. Enterotypes in the landscape of gut microbial community composition · 2017 · 1,137 citations
74. The influence of sex, handedness, and washing on the diversity of hand surface bacteria · 2008 · 1,108 citations
75. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data · 2009 · 1,100 citations
76. Cohabiting family members share microbiota with one another and with their dogs · 2013 · 1,084 citations
77. Environmental and ecological factors that shape the gut bacterial communities of fish: a meta‐analysis · 2012 · 1,076 citations
78. Genetic Determinants of the Gut Microbiome in UK Twins · 2016 · 1,048 citations
79. Defining seasonal marine microbial community dynamics · 2011 · 1,044 citations
80. Gut bacteria from multiple sclerosis patients modulate human T cells and exacerbate symptoms in mouse models · 2017 · 1,041 citations
81. Gut Microbes and the Brain: Paradigm Shift in Neuroscience · 2014 · 1,033 citations
82. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer · 2016 · 1,010 citations
83. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges · 2009 · 1,002 citations
84. RETRACTED ARTICLE: Microbiome analyses of blood and tissues suggest cancer diagnostic approach · 2020 · 987 citations
85. Longitudinal analysis of microbial interaction between humans and the indoor environment · 2014 · 920 citations
86. Structure-based protein function prediction using graph convolutional networks · 2021 · 911 citations
87. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome · 2012 · 899 citations
88. Microbiota Regulate Intestinal Absorption and Metabolism of Fatty Acids in the Zebrafish · 2012 · 896 citations
89. Regional variation limits applications of healthy gut microbiome reference ranges and disease models · 2018 · 894 citations
90. Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania · 2017 · 885 citations
91. American Gut: an Open Platform for Citizen Science Microbiome Research · 2018 · 878 citations
92. The Earth Microbiome project: successes and aspirations · 2014 · 878 citations
93. Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome · 2017 · 874 citations
94. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 · 2020 · 867 citations
95. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision · 2016 · 867 citations
96. The microbiome of uncontacted Amerindians · 2015 · 851 citations
97. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science · 2018 · 838 citations
98. Meta‐analyses of human gut microbes associated with obesity and IBD · 2014 · 836 citations
99. Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 · 2019 · 835 citations
100. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications · 2011 · 802 citations