journal article

• Retraction Note: Microbiome analyses of blood and tissues suggest cancer diagnostic approach..  Nature. 694. 2024
• Multiomic Analyses of Nascent Preterm Infant Microbiomes Differentiation Suggest Opportunities for Targeted Intervention.  Advanced Biosystems. 2022
• Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding.  951-+. 2021
• Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome..  mSystems. 2020
• Microbiome analyses of blood and tissues suggest cancer diagnostic approach.  Nature. 567-+. 2020
• Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats.  mBio. 2020
• Learning representations of microbe-metabolite interactions..  Nature Methods. 1306-1314. 2019
• Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2..  Nature Biotechnology. 1091. 2019
• Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2..  Nature Biotechnology. 852-857. 2019
• Is there convergence of gut microbes in blood-feeding vertebrates?.  Philosophical Transactions of the Royal Society B: Biological Sciences. 2019
• Major shifts in gut microbiota during development and its relationship to growth in ostriches.  Molecular Ecology. 2653-2667. 2019
• Engineering the microbiome for animal health and conservation.  Experimental Biology and Medicine. 494-504. 2019
• Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes.  The ISME Journal: multidisciplinary journal of microbial ecology. 576-587. 2019
• American Gut: an Open Platform for Citizen Science Microbiome Research.  mSystems. 2018
• A communal catalogue reveals Earth's multiscale microbial diversity.  Nature. 457-+. 2017
• Evaluating the impact of domestication and captivity on the horse gut microbiome.  Scientific Reports. 2017
• The Effects of Captivity on the Mammalian Gut Microbiome.  Integrative and Comparative Biology. 690-704. 2017
• Balance Trees Reveal Microbial Niche Differentiation.  mSystems. 2017
• Prevalence and genetic diversity of Blastocystis in family units living in the United States.  Infection, Genetics and Evolution. 95-97. 2016
• Tiny microbes, enormous impacts: what matters in gut microbiome studies?.  Genome Biology. 2016
• The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat.  mSystems. 2016
• Using the gut microbiota as a novel tool for examining colobine primate GI health.  Global Ecology and Conservation. 225-237. 2016
• Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies.  mSystems. 2016
• Stress response, gut microbial diversity and sexual signals correlate with social interactions.  Biology Letters. 2016
• From Sample to Multi-Omics Conclusions in under 48 Hours.  mSystems. 2016
• The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.  mBio. 2016
• Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer.  Nature Medicine. 250-253. 2016
• Walls talk: Microbial biogeography of homes spanning urbanization.  Science Advances. 2016
• Microbial community assembly and metabolic function during mammalian corpse decomposition.  Science. 158-162. 2016
• The microbiome of uncontacted Amerindians.  Science Advances. 2015
• The Treatment-Naive Microbiome in New-Onset Crohn's Disease.  Cell Host and Microbe. 382-392. 2014
• Convergence of gut microbiomes in myrmecophagous mammals.  Molecular Ecology. 1301-1317. 2014
• Tracking down the sources of experimental contamination in microbiome studies.  Genome Biology. 2014
• Cohabiting family members share microbiota with one another and with their dogs.  eLife. 2013
• How delivery mode and feeding can shape the bacterial community in the infant gut.  CMAJ. 373-374. 2013
• Advancing Our Understanding of the Human Microbiome Using QIIME.  Methods in Enzymology. 371-444. 2013
• Characterizing microbial communities through space and time.  Current Opinion in Biotechnology. 431-436. 2012
• From superspreaders to disease hotspots: linking transmission across hosts and space.  Frontiers in Ecology and the Environment. 75-82. 2012
• From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome.  Annual Review of Ecology, Evolution and Systematics. 137-155. 2012
• Our microbial selves: what ecology can teach us.  EMBO Reports. 775-784. 2011