About

Rob Knight is the founding Director of the Center for Microbiome Innovation and a Professor of Pediatrics, Bioengineering, Computer Science & Engineering, and Data Science at the University of California San Diego. He holds the Wolfe Family Endowed Chair in Microbiome Research at Rady Children's Hospital and is a Visiting Fellow at the Hong Kong Jockey Club Institute of Advanced Science at the Hong Kong University of Science and Technology. Knight was elected to the National Academy of Engineering in 2024 and is a Fellow of the American Association for the Advancement of Science, the American Academy of Microbiology, and the American Institute for Medical and Biological Engineering. He has received prestigious awards including the 2019 NIH Director’s Pioneer Award and the 2017 Massry Prize. Knight is the author of the book "Follow Your Gut: The Enormous Impact of Tiny Microbes" and coauthor of "Dirt is Good: The Advantage of Germs for Your Child’s Developing Immune System," and has coauthored over 1000 scientific articles. His 2014 TED talk has been viewed over 2 million times. Knight's laboratory has developed many of the software tools and laboratory techniques that have enabled high-throughput microbiome science, including QIIME and UniFrac. His work has been cited over half a million times. He is a co-founder of the Earth Microbiome Project, the American Gut Project, and the companies Biota, Inc., and Micronoma, Inc. Additionally, he serves as Vice President of the Microbiota Vault. His research has linked microbes to a wide range of health conditions, from obesity to Alzheimer’s disease, and has expanded understanding of microbial communities in diverse environments such as oceans and deserts. Knight's efforts have made high-throughput sequencing techniques accessible to thousands of researchers worldwide.

Research topics

• Biology
• Computer Science
• Bioinformatics
• Computational biology
• Genetics
• Medicine
• Artificial Intelligence
• Internal medicine
• Biochemistry
• Microbiology
• Endocrinology
• Evolutionary biology
• Immunology
• Chemistry
• Physiology
• Data Mining
• Data science
• Ecology
• Chromatography
• Cell biology
• Virology
• Political Science
• Psychiatry
• Database

Selected publications

• Antibiotic resistant Achromobacter xylosoxidans are highly susceptible to bacteriophages and often are killed synergistically by phage/antibiotic combinations

  Research Square · 2026-04-30

  preprintOpen access
  PublisherDOI

• 511 LARGE-SCALE EVIDENCE FOR DIURNAL AND SEASONAL OSCILLATIONS IN THE HUMAN GUT MICROBIOME

  Gastrointestinal Endoscopy · 2026-05-01

  article
  PublisherDOI

• 511 LARGE-SCALE EVIDENCE FOR DIURNAL AND SEASONAL OSCILLATIONS IN THE HUMAN GUT MICROBIOME

  Gastroenterology · 2026-05-01

  article
  PublisherDOI

• Insects shape the cadaver decomposition microbiome and postmortem interval estimation accuracy

  mSystems · 2026-04-27

  articleOpen access

  The breakdown and recycling of carrion is a crucial ecological process that largely relies on a community of necrophagous insects and microbes. Recent work has shown that a specialized microbial network, likely dispersed throughout the environment by insects, assembles during cadaver decomposition to break down flesh regardless of climate and geography. Because of their broad distribution and successional nature, decomposer microbes have been used in machine learning models to predict the postmortem interval (PMI) of human remains, an important contribution to the field of forensics. How factors such as an indoor environment, which alters insect activity, impact the composition of microbial communities decomposing human remains is unclear. Here, we investigate the effects of enclosed shelter on microbial community assembly and successional patterns during human decomposition and provide important considerations for PMI modeling. Compared to outdoor cadavers, we show that indoor cadavers experienced delayed colonization of key decomposer microbes over the course of decomposition due to restricted insect access. Consequently, machine learning models trained on outdoor cadavers frequently underestimated the PMI of cadavers decomposing indoors. Delayed colonization by blow fly maggots (Diptera: Calliphoridae) was correlated with higher PMI prediction errors, suggesting that insects are an important source of microbial decomposers that drive PMI model predictions. Incorporating microbial data from indoor cadavers and insect activity into PMI models significantly improved prediction capabilities for both indoor and outdoor decomposition environments. Ultimately, we demonstrate the important role insects play in the maintenance and distribution of microbes that help to recycle vertebrate remains.IMPORTANCEMicrobes are critical for the decomposition and recycling of organic matter. Recently, microbiome-based models have shown promising performance in estimating the postmortem interval (PMI). However, many deaths occur indoors, yet no studies have investigated the impact of enclosed shelter on the cadaver microbiome in a controlled setting. Here, cadavers were decomposed indoors, and we found that blow fly maggots serve as an important source of decomposer taxa that significantly alter the cadaver microbiome following infestation. Notably, PMI estimation models trained on outdoor data sets failed to accurately predict the PMI when insect colonization was delayed. We show that incorporating 16S rRNA amplicon data from cadavers decomposing indoors, along with environmental variables, significantly improves PMI estimates, suggesting a microbiome-based forensic tool may be feasible across decomposition environments. Importantly, this research demonstrates the critical ecological role insects play in the dispersal of specialized microbes that are involved in the breakdown and recycling of vertebrate remains.

  PublisherDOI

• Data from Stability of the Fecal and Oral Microbiome over 2 Years at −80°C for Multiple Collection Methods

  2025-11-26

  articleOpen access

  <div>AbstractBackground:<p>In prospective cohorts, biological samples are generally stored over long periods before an adequate number of cases have accrued. We investigated the impact of sample storage at −80°C for 2 years on the stability of the V4 region of the 16S rRNA gene across seven different collection methods (i.e., no additive, 95% ethanol, RNAlater stabilization solution, fecal occult blood test cards, and fecal immunochemical test tubes for feces; OMNIgene ORAL tubes and Scope mouthwash for saliva) among 51 healthy volunteers.</p>Methods:<p>Intraclass correlation coefficients (ICC) were calculated for the relative abundance of the top three phyla, the 20 most abundant genera, three alpha-diversity metrics, and the first principal coordinates of three beta-diversity matrices.</p>Results:<p>The subject variability was much higher than the variability introduced by the sample collection type, and storage time. For fecal samples, microbial stability over 2 years was high across collection methods (range, ICCs = 0.70–0.99), except for the samples collected with no additive (range, ICCs = 0.23–0.83). For oral samples, most microbiome diversity measures were stable over time with ICCs above 0.74; however, ICCs for the samples collected with Scope mouthwash were lower for two alpha-diversity measures, Faith's phylogenetic diversity (0.23) and the observed number of operational taxonomic units (0.23).</p>Conclusions:<p>Fecal and oral samples in most used collection methods are stable for microbiome analyses after 2 years at −80°C, except for fecal samples with no additive.</p>Impact:<p>This study provides evidence that samples stored for an extended period from prospective studies are useful for microbiome analyses.</p></div>

  PublisherDOI

• Supplementary Table 8 from Stability of the Fecal and Oral Microbiome over 2 Years at −80°C for Multiple Collection Methods

  2025-11-26

  articleOpen access

  <p>Differential abundance analysis using the Wilcoxon signed-rank test to identify bacterial taxa at the phylum, family, and genus level which were differentially abundant (FDR < 0.05) among baseline, year 1, and year 2 for each collection method.</p>

  PublisherDOI

• Antimicrobial resistance is widespread among intestinal and extra-intestinal <i>Bacteroides fragilis</i> strains

  Infection and Immunity · 2025-11-24

  articleOpen access

  ABSTRACT Bacteroides fragilis is an important member of the human gut microbiota, where it contributes to immune modulation, intestinal barrier integrity, and colonization resistance. Despite its beneficial roles as a symbiont in the gut, B. fragilis is also the most commonly isolated anaerobe in clinical infections, implicated in intra-abdominal abscesses, bloodstream infections, and soft tissue infections. Antimicrobial resistance (AMR) is increasingly recognized as a major factor in its transition from symbiont to opportunist; however, the relationship between resistance and anatomical site of isolation remains poorly defined. Here, we compared AMR phenotypes and genotypes between intestinal and extra-intestinal B. fragilis isolates to assess whether clinical strains are enriched for resistance determinants. Surprisingly, we found comparable susceptibility profiles and AMR gene content between the two groups. Minimal inhibitory concentrations (MICs) were broadly similar, and β-lactamase activity was detected in ~70% of the isolates regardless of the isolation site. We found that resistance genes were similarly distributed across both intestinal and clinical strains. A microbial genome-wide association study (mGWAS) confirmed the known resistance markers, such as ermF , aadS , and tetQ, and identified novel associations with conjugative transposons, efflux transporters, regulatory genes, and previously uncharacterized loci. These findings suggest that intestinal strains serve as a reservoir of clinically relevant resistance determinants that may be mobilized under selective pressure. Although prior work has largely focused on clinical isolates, our findings highlight the need to surveil AMR within the gut microbiota, where widespread resistance in commensal bacteria has the potential to complicate treatment of extra-intestinal infections.

  PublisherDOI

• Personalised whole-body modelling links gut microbiota to metabolic perturbations in Alzheimer’s disease

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-29

  preprintOpen access

  Abstract The human gut microbiome has been linked to metabolic disturbances in Alzheimer’s disease (AD). However, the mechanisms by which gut microbes might influence metabolic dysfunction in AD remain poorly understood. Previously, we used constraint-based metabolic modelling to associate an increased risk of AD with altered production of microbiome-derived metabolites. In this study, we investigated whether these previous results can also be identified in AD patients. Therefore, we created personalised whole-body metabolic models from gut metagenomics samples from 34 AD dementia patients, 51 individuals with mild cognitive impairments, and 298 healthy controls. These in silico models were profiled to predict the metabolic influences of gut microbiomes on blood metabolites with previously reported alterations in AD. We found an increased capacity of AD host-microbiome co-metabolism to produce S-adenosyl-L-methionine, L-arginine, creatine, taurine, and formate in the blood of AD dementia patients and patients with mild cognitive impairments. The metabolic predictions were then mechanistically linked to gut microbial changes in AD. This analysis identified that increased relative abundances of Bacteroides uniformis and Bacteroides thetaiotamicron were key factors driving the predicted metabolic changes. Furthermore, the predicted altered microbial influences on blood metabolites were also associated with allelic variations in the APOE risk gene in healthy individuals, which confirmed our previous findings. In conclusion, we identified blood metabolites whose perturbations in AD may be influenced by gut microbiota and predicted the key microbial drivers for these metabolic influences. These findings may facilitate the development of microbiome-informed treatments of AD.

  PublisherOA PDFDOI

• Supplementary Table 1 from Stability of the Fecal and Oral Microbiome over 2 Years at −80°C for Multiple Collection Methods

  2025-11-26

  articleOpen access

  &lt;p&gt;ICCs based on the relative abundances of the three most dominant phyla, three alpha diversity metrics (observed OTUs, Shannon Diversity, and Faith’s Phylogenetic Diversity) and three beta diversity metrics (Bray-Curtis, unweighted UniFrac, weighted UniFrac), for microbiome stability comparing fecal samples extracted after 4 days at room temperature (baseline), after 4 days at room temperature and stored for a year at -80°C (year 1), and after 4 days at room temperature and stored two years at -80°C (year 2) for five fecal sample collection methods.&lt;/p&gt;

  PublisherDOI

• Environmental and maternal imprints on infant gut metabolic development

  Cell Host & Microbe · 2025-11-26 · 4 citations

  articleOpen accessSenior author

  Early life is a critical period for immune and metabolic development, but these patterns remain underexplored in populations from low- and middle-income countries. Here, we profile the microbiome and metabolome of 55 Bangladeshi mother-infant dyads over the first 6 months of life. Importantly, we observe an increase in microbially derived bile amidates and N-acyl lipids with age in conjunction with reads matching the bile salt hydrolase/transferase (bsh) gene. Although microbial source tracking confirms maternal fecal seeding, a substantial environmental contribution is also highlighted. Differences in infant fecal metabolic profiles are associated with delivery mode, maternal milk composition, household assets, and household-level water treatment. Cesarean section (C-section) delivery and untreated drinking water are linked to transient metabolic differences, including increases in bile amidates, N-acyl lipids, and other host-microbe co-metabolic products, including acylcarnitines. Multi-omics analysis reveals specific microbial-metabolite relationships, highlighting how early environmental and maternal living circumstances influence gut metabolic development through the microbiome.

  PublisherDOI

Recent grants

• NIH Grant R01HG004872

  NIH · $1.8M · 2013

• NIH Grant P01DK078669

  NIH · $31.3M · 2021

• Alzheimer's Gut Microbiome Project

  NIH · $28.4M · 2019–2026

• Epidemiology of the gut microbiome, prediabetes and diabetes in Latinos

  NIH · $3.5M · 2016–2024

• Epidemiology of the gut microbiome, prediabetes and diabetes in Latinos

  NIH · $829k · 2016–2021

Frequent coauthors

• Pieter C. Dorrestein

  University of California, San Diego

  352 shared

• Daniel McDonald

  University of California, San Diego

  342 shared

• J. Gregory Caporaso

  Translational Genomics Research Institute

  276 shared

• Jack A. Gilbert

  University of California, San Diego

  219 shared

• Yoshiki Vázquez‐Baeza

  Jacobs (United States)

  210 shared

• Noah Fierer

  200 shared

• Pedro Belda‐Ferre

  University of California, San Diego

  161 shared

• Se Jin Song

  University of California, San Diego

  159 shared

Labs

• Knight LabPI

Awards & honors

• 2019 NIH Director’s Pioneer Award
• 2017 Massry Prize
• 2015 Vilceck Prize in Creative Promise for the Life Sciences
• Fellow of the American Association for the Advancement of Sc…
• Fellow of the American Academy of Microbiology