A5103172153- Gut microbiota and health
- Microbial Community Ecology and Physiology
- Plant-Microbe Interactions and Immunity
- Legume Nitrogen Fixing Symbiosis
- Dietary Effects on Health
- Genomics and Phylogenetic Studies
- Diet and metabolism studies
- Epigenetics and DNA Methylation
- Mycorrhizal Fungi and Plant Interactions
- Genomics and Chromatin Dynamics
- Single-cell and spatial transcriptomics
- Coastal wetland ecosystem dynamics
- GABA and Rice Research
- Food composition and properties
- Plant tissue culture and regeneration
- Wastewater Treatment and Nitrogen Removal
- Probiotics and Fermented Foods
BGI Group (China)
2018-2024
Innovative Genomics Institute
2024
University of California, Berkeley
2024
University of Chinese Academy of Sciences
2017-2020
China National GeneBank
2018-2019
Citrus is a globally important, perennial fruit crop whose rhizosphere microbiome thought to play an important role in promoting citrus growth and health. Here, we report comprehensive analysis of the structural functional composition microbiome. We use both amplicon deep shotgun metagenomic sequencing bulk soil samples collected across distinct biogeographical regions from six continents. Predominant taxa include Proteobacteria, Actinobacteria, Acidobacteria Bacteroidetes. The core...
Abstract The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. microbial community structure has been extensively investigated by 16S/18S/ITS amplicons metagenomic sequencing crops model plants. However, the functional associations between host growth are poorly understood. This work investigates bacterial of foxtail millet (Setaria italica) its potential effects on productivity. We determined composition 2882 samples from rhizoplane,...
Bacterial indole-3-acetic acid (IAA), an effector molecule in microbial physiology, plays important role plant growth-promotion. Here, we comprehensively analyzed about 7282 prokaryotic genomes representing diverse bacterial phyla, combined with root-associated metagenomic data to unravel the distribution of tryptophan-dependent IAA synthesis pathways and quantify synthesis-related genes root environments. We found that 82.2% were potentially capable synthesizing from tryptophan (Trp) or...
The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a fundamental epigenomics approach and has been widely used in profiling the chromatin accessibility dynamics multiple species. A comprehensive reference of ATAC-seq datasets mammalian tissues important understanding regulatory specificity developmental abnormality caused by genetic or environmental alterations. Here, we report an adult mouse atlas producing total 66 profiles from 20 primary both male female mice....
Adequate calorie restriction (CR) as a healthy lifestyle is recommended not only for people with metabolic disorders but also adults. Previous studies have mainly focused on the beneficial effects of CR obese subjects, while its non-obese subjects are still scarce. Here, we conducted three-week non-controlled intervention in 41 approximately 40% fewer calories than daily energy intake. We measured BMI, and applied targeted profiling fasting blood samples shotgun metagenomic sequencing fecal...
Mangroves, as important and special ecosystems, create unique ecological environments for examining the microbial gene capacity potential producing bioactive compounds. However, little is known about biogeochemical implications of microbiomes in mangrove especially variations between pristine anthropogenic mangroves. To elucidate this, we investigated taxonomic functional shifts their compounds two different coastal ecosystems southern China. A catalogue, including 87 million genes, was...
Despite being the world’s third largest ocean, Indian Ocean is one of least studied and understood with respect to microbial diversity as well biogeochemical ecological functions. In this study, we investigated community its metabolic potential for nitrogen (N) acquisition in oligotrophic surface waters using a metagenomic approach. Proteobacteria Cyanobacteria dominated an average 37.85 23.56% relative abundance, respectively, followed by Bacteroidetes (3.73%), Actinobacteria (1.69%),...
Abstract The advent of next‐generation sequencing has revolutionized microbiome research, enabling in‐depth exploration microbial communities through amplicon sequencing. widespread adoption across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high‐throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility many...
Bacterial indole-3-acetic acid (IAA), an effector molecule in microbial physiology, plays important role plant growth-promotion. Here, we comprehensively analyzed about 7282 prokaryotic genomes representing diverse bacterial phyla, combined with root-associated metagenomic data to unravel the distribution of tryptophan-dependent IAA synthesis pathways and quantify synthesis-related genes root environments. We found that 82.2% were potentially capable synthesizing from tryptophan (Trp) or...
Introduction Citrus is one of the most important fruit crops worldwide, and root-associated microbiota can have a profound impact on tree health growth. Methods In collaborative effort, International Microbiome Consortium investigated global citrus root with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA ITS2 amplicon sequencing data to identify predominant prokaryotic fungal taxa in samples. Comparative analyses were conducted between...
Abstract Calorie restriction (CR), which has the potential effect to weight loss and blood amino acids, been demonstrated associate with gut microbiota in human, especially obese individuals. However, studies for simultaneously evaluating enterotype-dependent impacts of CR on acids nonobese individuals are still limited. Here, 41 received a 3-week diet approximately 50% fewer calories than normal diet. We measured their BMI acid concentration, along before after intervention. In this trial,...
Abstract The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a fundamental epigenomics approach and has been widely used in profiling the chromatin accessibility dynamics multiple species. A comprehensive reference of ATAC-seq datasets mammalian tissues important understanding regulatory specificity developmental abnormality caused by genetic or environmental alterations. Here, we report an adult mouse atlas producing total 66 profiles from 20 primary both male...