Dan Knights
A5082358375- Gut microbiota and health
- Diet and metabolism studies
- Clostridium difficile and Clostridium perfringens research
- Genomics and Phylogenetic Studies
- Nutritional Studies and Diet
- Metabolomics and Mass Spectrometry Studies
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Gastrointestinal motility and disorders
- Dietary Effects on Health
- Inflammatory Bowel Disease
- Microscopic Colitis
- Epigenetics and DNA Methylation
- Infant Nutrition and Health
- Mycobacterium research and diagnosis
- Neutropenia and Cancer Infections
- Bacteriophages and microbial interactions
- Oral microbiology and periodontitis research
- Diabetes and associated disorders
- Scientific Computing and Data Management
- Dermatology and Skin Diseases
- Digestive system and related health
- Salmonella and Campylobacter epidemiology
- Colorectal Cancer Screening and Detection
- Gene expression and cancer classification
University of Minnesota
2016-2025
Biotechnology Institute
2016-2025
University of Minnesota System
2019-2025
Diversitech (United States)
2020-2024
Minneapolis Institute of Arts
2020
Broad Institute
2013-2019
Massachusetts General Hospital
2013-2019
Harvard University
2019
Minot State University
2018
Twin Cities Orthopedics
2018
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 levels of Bacteroides Prevotella. Enterotypes were associated with long-term diets, particularly protein animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study 10 subjects showed that composition changed...
The normal range of physiological and metabolic phenotypes has been shaped by coevolution with microbial symbionts.
Abstract Background Understanding the normal temporal variation in human microbiome is critical to developing treatments for putative microbiome-related afflictions such as obesity, Crohn's disease, inflammatory bowel disease and malnutrition. Sequencing computational technologies, however, have been a limiting factor performing dense time series analysis of microbiome. Here, we present largest microbiota date, covering two individuals at four body sites over 396 timepoints. Results We find...
Kwashiorkor, an enigmatic form of severe acute malnutrition, is the consequence inadequate nutrient intake plus additional environmental insults. To investigate role gut microbiome, we studied 317 Malawian twin pairs during first 3 years life. During this time, half remained well nourished, whereas 43% became discordant, and 7% manifested concordance for malnutrition. Both children in discordant kwashiorkor were treated with a peanut-based, ready-to-use therapeutic food (RUTF). Time-series...
Human-associated microbial communities vary across individuals: possible contributing factors include (genetic) relatedness, diet, and age. However, our surroundings, including individuals with whom we interact, also likely shape communities. To quantify this exchange, surveyed fecal, oral, skin microbiota from 60 families (spousal units children, dogs, both, or neither). Household members, particularly couples, shared more of their than different households, stronger effects co-habitation...
Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging integrate extent of microbial molecular diversity in stool remains unknown. Using standardized protocols Earth Microbiome Project sample contributions over 10,000 citizen-scientists, together with an open research network, we compare specimens primarily United States, Kingdom, Australia one another environmental samples. Our results show...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
Anaerobic digestion is the most successful bioenergy technology worldwide with, at its core, undefined microbial communities that have poorly understood dynamics. Here, we investigated relationships of bacterial community structure (>400,000 16S rRNA gene sequences for 112 samples) with function (i.e., bioreactor performance) and environment operating conditions) in a yearlong monthly time series nine full-scale facilities treating brewery wastewater (>20,000 measurements). Each had...
Diet is a key determinant of human gut microbiome variation. However, the fine-scale relationships between daily food choices and composition remain unexplored. Here, we used multivariate methods to integrate 24-h records fecal shotgun metagenomes from 34 healthy subjects collected over 17 days. Microbiome depended on multiple days dietary history was more strongly associated with than conventional nutrient profiles, microbial responses diet were highly personalized. Data two consuming only...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
Metagenomic analyses of gnotobiotic mice and monozygotic twins reveal the effects eating a popular fermented milk product on their microbiomes.