A5084222883- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Polar Research and Ecology
- Child Nutrition and Water Access
- Birth, Development, and Health
- Bacteriophages and microbial interactions
- Obesity, Physical Activity, Diet
- RNA modifications and cancer
- Infant Nutrition and Health
- Respiratory viral infections research
- Bioinformatics and Genomic Networks
- Gestational Diabetes Research and Management
- Fecal contamination and water quality
- Metabolomics and Mass Spectrometry Studies
- Human-Animal Interaction Studies
- Genetic Mapping and Diversity in Plants and Animals
- Inflammatory Bowel Disease
- Probiotics and Fermented Foods
- Bat Biology and Ecology Studies
- Diabetes Management and Education
- Clostridium difficile and Clostridium perfringens research
- Parasitic Infections and Diagnostics
- Enterobacteriaceae and Cronobacter Research
- Plant-Microbe Interactions and Immunity
Max Planck Institute for Biology
2022-2024
Max Planck Institute for Developmental Biology
2017-2023
Institute of Developmental Physiology
2023
Stanford University
2023
University of Colorado Boulder
2010-2014
Institut thématique Génétique, génomique et bioinformatique
2010-2014
The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups investigators map microbial component biosphere. In particular, coevolution new platforms and software tools allows data acquisition analysis on an unprecedented scale. Here we report next stage this coevolutionary arms race, using Illumina GAIIx platform sequence a diverse array 25 environmental samples three known “mock communities” at depth averaging 3.1 million reads per sample. We...
The role of specific gut microbes in shaping body composition remains unclear. We transplanted fecal microbiota from adult female twin pairs discordant for obesity into germ-free mice fed low-fat mouse chow, as well diets representing different levels saturated fat and fruit vegetable consumption typical the U.S. diet. Increased total mass, obesity-associated metabolic phenotypes, were transmissible with uncultured communities their corresponding bacterial culture collections. Cohousing...
Significance In this very large-scale longitudinal field study of the maize rhizosphere microbiome, we identify heritable taxa. These taxa display variance in their relative abundances that can be partially explained by genetic differences between lines, above and beyond strong influences field, plant age, weather on diversity microbiome. If these are associated with beneficial traits, they may serve as phenotypes future breeding endeavors.
Abstract Protists are ubiquitous members of soil microbial communities, but the structure these and factors that influence their diversity, poorly understood. We used barcoded pyrosequencing to survey comprehensively diversity protists from 40 sites across a broad geographic range represent variety biome types, tropical forests deserts. In addition taxa known be dominant in soil, including Cercozoa Ciliophora, we found high relative abundances groups such as Apicomplexa Dinophyceae have not...
ABSTRACT Quantitative real-time PCR (qPCR) assays that target the human-associated HF183 bacterial cluster within members of genus Bacteroides are among most widely used methods for characterization human fecal pollution in ambient surface waters. In this study, we show a current TaqMan qPCR assay (HF183/BFDrev) routinely forms nonspecific amplification products and introduce modified (HF183/BacR287) alleviates problem. The performance each was compared head-to-head experiments investigating...
Objective Gestational diabetes mellitus (GDM) is a condition in which women without are diagnosed with glucose intolerance during pregnancy, typically the second or third trimester. Early diagnosis, along better understanding of its pathophysiology first trimester may be effective reducing incidence and associated short-term long-term morbidities. Design We comprehensively profiled gut microbiome, metabolome, inflammatory cytokines, nutrition clinical records 394 before GDM diagnosis. then...
High throughput sequencing technology has opened a window into the vast communities of bacteria that live on and in humans, demonstrating tremendous variability, they play large role health disease. The eukaryotic component human gut microbiome remains relatively unexplored with these methods, but turning tools toward microbial eukaryotes will likely yield myriad insights disease as well ecological evolutionary principles govern microbiota. Microbial are common inhabitants worldwide...
Many hibernating mammals suspend food intake during winter, relying solely on stored lipids to fuel metabolism. Winter fasting in these species eliminates a major source of degradable substrates support growth gut microbes, which may affect microbial community structure and host-microbial interactions. We explored the effect annual hibernation cycle microbiotas using deep sequencing 16S rRNA genes from ground squirrel cecal contents. Squirrel were dominated by members phyla Bacteroidetes,...
Variation in the composition of human oral microbiome health and disease has been observed. We have characterized inter- intra-individual variation microbial communities 107 individuals one largest cohorts to date (264 saliva samples), using culture-independent 16S rRNA pyrosequencing. examined salivary up three time-points during 10 yr spanning adolescence, determined influence genotype, gender, age, weight class. Participants, including 27 monozygotic 18 dizygotic twin pairs, were sampled...
Bisphenol A (BPA) accumulates in the maturing gut and liver utero is known to alter bacterial profiles offspring. Gut dysbiosis may contribute chronic colonic systemic inflammation. We hypothesized that perinatal BPA exposure-induced intestinal (and liver) inflammation offspring due alterations microbiome metabolome. The 16S rRNA amplicon sequencing analysis revealed differences beta diversity with a significant reduction relative abundances of short-chain fatty acid (SCFA) producers such as...
The human gut virome and its early life development are poorly understood. Prior studies have captured single-point assessments with the evolution of infant remaining largely unexplored. We performed viral metagenomic sequencing on stool samples collected longitudinally from a cohort 53 infants age 2 weeks to 3 years (80.7 billion reads), their mothers (9.8 reads) examine compare viromes. asymptomatic consisted bacteriophages, nonhuman dietary/environmental viruses, human-host predominantly...
The human body is inhabited by billions of microbial cells and these symbionts play critical roles in health. Human-associated communities are diverse, the structure variable across habitats, through time, between individuals. We can apply concepts developed plant animal ecologists to better understand predict spatial temporal patterns communities. Due methodological limitations largely unknown natural history most taxa, this integration ecology into research on microbiome still its infancy....
Background & AimsFiber-rich foods promote health, but mechanisms by which they do so remain poorly defined. Screening fiber types, in mice, revealed psyllium had unique ability to ameliorate 2 chronic inflammatory states, namely, metabolic syndrome and colitis. We sought determine the mechanism of action latter.MethodsMice were fed grain-based chow, is naturally rich or compositionally defined diets enriched with semi-purified fibers. Mice studied basally models chemical-induced T-cell...
Abstract Background Standard pediatric growth curves cannot be used to impute missing height or weight measurements in individual children. The Michaelis–Menten equation, for characterizing substrate-enzyme saturation curves, has been shown model many organisms including nonhuman vertebrates. We investigated whether this equation could interpolate data children the first three years of life and compared interpolation several common methods models. Methods developed a modified expected actual...
Microbial ecology is flourishing, and in the process, making contributions to how biology of large organisms understood. Ongoing advances sequencing technology computational methods have enabled collection analysis vast amounts molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity environments ranging simple marine ecosystems complex soil ecologies, more recent research concerned with community functions their dynamics over...
Abstract Gestational diabetes mellitus (GDM) is a condition in which non-diabetic women are diagnosed with glucose intolerance during pregnancy, typically the second trimester. GDM can lead to wide range of obstetrical and metabolic complications for both mother neonate 1 . Early identification risk, along better understanding its pathophysiology first trimester may be effective reducing incidence, as well associated short long term morbidities 2 Here, we comprehensively profiled gut...
Abstract Toll-like receptor (TLR) 5-deficient mice display aberrantly low levels of flagellin-specific antibodies (Flic-IgA) secreted into the gut, combined with excess bacterial flagellin in and together these attributes define microbiome dysbiosis (T5-dysbiosis). How TLR5 signaling deficiency results T5-dysbiosis is unclear. Here, we address role B cells T-dysbiosis. We observed that do not express TLR5, cell transplantation from −/− mouse donors B-cell deficient resulted a slight...
Abstract Mathematical models that accurately describe growth in human infants are lacking. We used the Michaelis-Menten equation, initially derived to relate substrate concentration reaction rate, and subsequently modified applied nonhuman vertebrate growth, model humans from birth 36 months. compared results actual values two pediatric cohorts. The equation showed excellent fit for both infant weight (median RMSE: boys: 0.22kg [IQR:0.19; 90%<0.43]; girls: 0.20kg [IQR:0.32; 90%<0.39])...
Abstract Background and Objectives : Standard pediatric growth curves cannot be used to impute missing height or weight measurements in individual children. The Michaelis-Menten equation, for characterizing substrate-enzyme saturation curves, has been shown model many organisms including nonhuman vertebrates. We investigated this equation could interpolate data children the first three years of life. Methods developed a modified compared expected actual growth, local birth cohort (N=97) then...