Rob Knight

Research topics

• Gut microbiota and health · 8 papers
• Genomics and Phylogenetic Studies · 4 papers
• Microbial Community Ecology and Physiology · 4 papers
• Urinary Tract Infections Management · 2 papers
• Diet and metabolism studies · 2 papers
• Nutritional Studies and Diet · 2 papers

Frequent co-authors

• Catherine Lozupone · 4 papers
• Noah Fierer · 4 papers
• J. Gregory Caporaso · 3 papers
• Christian L. Lauber · 3 papers
• William Anton Walters · 2 papers
• Curtis Huttenhower · 1 paper
• J. Fah Sathirapongsasuti · 1 paper
• Nicola Segata · 1 paper

Papers

1. Structure, function and diversity of the healthy human microbiomeNature · 2012 · 12,251 citations

   Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial…

2. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platformsThe ISME Journal · 2012 · 9,303 citations

   DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina…

3. UniFrac: a New Phylogenetic Method for Comparing Microbial CommunitiesApplied and Environmental Microbiology · 2005 · 8,702 citations

   We introduce here a new method for computing differences between microbial communities based on phylogenetic information. This method, UniFrac, measures the phylogenetic distance between sets of taxa in a phylogenetic tree as the fraction of the branch length of the…

4. Linking Long-Term Dietary Patterns with Gut Microbial EnterotypesScience · 2011 · 6,727 citations

   Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily by levels of Bacteroides and Prevotella. Enterotypes…

5. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier pluginMicrobiome · 2018 · 6,287 citations

   BACKGROUND: Taxonomic classification of marker-gene sequences is an important step in microbiome analysis. RESULTS: We present q2-feature-classifier ( https://github.com/qiime2/q2-feature-classifier ), a QIIME 2 plugin containing several novel machine-learning and alignment-based methods for taxonomy classification. We evaluated and optimized several commonly…

6. Obesity alters gut microbial ecologyProceedings of the National Academy of Sciences · 2005 · 6,271 citations

   We have analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal (cecal) microbiota of genetically obese ob/ob mice, lean ob/+ and wild-type siblings, and their ob/+ mothers, all fed the same polysaccharide-rich diet. Although the majority of mouse…

7. Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newbornsProceedings of the National Academy of Sciences · 2010 · 4,856 citations

   Upon delivery, the neonate is exposed for the first time to a wide array of microbes from a variety of sources, including maternal bacteria. Although prior studies have suggested that delivery mode shapes the microbiota's establishment and, subsequently, its role…

8. Soil bacterial and fungal communities across a pH gradient in an arable soilThe ISME Journal · 2010 · 4,320 citations

   Soils collected across a long-term liming experiment (pH 4.0-8.3), in which variation in factors other than pH have been minimized, were used to investigate the direct influence of pH on the abundance and composition of the two major soil microbial…

9. Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental ScaleApplied and Environmental Microbiology · 2009 · 4,145 citations

   Soils harbor enormously diverse bacterial populations, and soil bacterial communities can vary greatly in composition across space. However, our understanding of the specific changes in soil bacterial community structure that occur across larger spatial scales is limited because most previous…