A5000391306- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Genomics and Phylogenetic Studies
- Plant Pathogens and Fungal Diseases
- Probiotics and Fermented Foods
- Plant-Microbe Interactions and Immunity
- Helicobacter pylori-related gastroenterology studies
- Microbial Community Ecology and Physiology
- Cancer Immunotherapy and Biomarkers
- Gastrointestinal motility and disorders
- Antimicrobial Resistance in Staphylococcus
- Seed and Plant Biochemistry
- Liver Disease Diagnosis and Treatment
- Plant Pathogens and Resistance
- Molecular Biology Techniques and Applications
- Colorectal Cancer Screening and Detection
- Spondyloarthritis Studies and Treatments
- Cancer, Stress, Anesthesia, and Immune Response
- Legume Nitrogen Fixing Symbiosis
- Microbial Metabolism and Applications
- Ocular Diseases and Behçet’s Syndrome
- Nematode management and characterization studies
- Oral microbiology and periodontitis research
- Protist diversity and phylogeny
- Diet and metabolism studies
Tongji University
2017-2025
Shanghai Tenth People's Hospital
2018-2025
Northwest Women's and Children's Hospital
2025
Shanxi University
2024
Shanxi Agricultural University
2020-2024
Liaoning Cancer Hospital & Institute
2024
China Medical University
2024
Sinotech Genomics (China)
2021-2022
Genomics (United Kingdom)
2019-2021
Second Military Medical University
2020
To understand the impact of gut microbes on human health and well-being it is crucial to assess their genetic potential. Here we describe Illumina-based metagenomic sequencing, assembly characterization 3.3 million non-redundant microbial genes, derived from 576.7 gigabases sequence, faecal samples 124 European individuals. The gene set, ∼150 times larger than complement, contains an overwhelming majority prevalent (more frequent) genes cohort probably includes a large proportion intestinal...
The organized societies of ants include short-lived worker castes displaying specialized behavior and morphology long-lived queens dedicated to reproduction. We sequenced compared the genomes two socially divergent ant species: Camponotus floridanus Harpegnathos saltator. Both contained high amounts CpG, despite presence DNA methylation, which in non-Hymenoptera correlates with CpG depletion. Comparison gene expression different identified up-regulation telomerase sirtuin deacetylases...
Checkpoint-blockade immunotherapy targeting programmed cell death protein 1 (PD-1) has recently shown promising efficacy in hepatocellular carcinoma (HCC). However, the factors affecting and predicting response to anti-PD-1 HCC are still unclear. Herein, we report dynamic variation characteristics specificities of gut microbiome during using metagenomic sequencing.Fecal samples from patients responding showed higher taxa richness more gene counts than those non-responders. For analysis...
The genetic diversity of Yersinia pestis , the etiologic agent plague, is extremely limited because its recent origin coupled with a slow clock rate. Here we identified 2,326 SNPs from 133 genomes Y. strains that were isolated in China and elsewhere. These define genealogy since most common ancestor. All but 28 these represented mutations happened only once within genealogy, they distributed essentially at random among individual genes. Only seven genes contained significant excess...
The assessment and characterization of the gut microbiome has become a focus research in area human autoimmune diseases. Ankylosing spondylitis is an inflammatory disease evidence showed that ankylosing may be microbiome-driven disease. To investigate relationship between spondylitis, quantitative metagenomics study based on deep shotgun sequencing was performed, using microbial DNA from 211 Chinese individuals. A total 23,709 genes 12 metagenomic species were shown to differentially...
Abstract The human microbiome is an integral component of the body and a co-determinant several health conditions 1,2 . However, extent to which interpersonal relations shape individual genetic makeup its transmission within across populations remains largely unknown 3,4 Here, capitalizing on more than 9,700 metagenomes computational strain-level profiling, we detected extensive bacterial strain sharing individuals (more 10 million instances) with distinct mother-to-infant, intra-household...
Microbes hold the key to life. They secrets our past (as descendants of earliest forms life) and prospects for future we mine their genes solutions some planet's most pressing problems, from global warming antibiotic resistance). However, piecemeal approach that has defined efforts study microbial genetic diversity over 20 years in 30,000 genome projects risks squandering promise. These have covered less than 20% cultured archaeal bacterial species, which represent just 15% overall known...
Behcet's disease (BD) is a recalcitrant, multisystemic inflammatory that can lead to irreversible blindness. Microbial agents have been considered contribute the pathogenesis of this disease, but underlying mechanisms remain unclear. In study, we investigated association gut microbiome composition with BD as well its possible roles in development disease. Fecal and saliva samples were collected from 32 active patients 74 healthy controls. DNA extracted fecal was subjected metagenomic...
// Zhigang Ren 1, 3, 4, * , Jianwen Jiang Haiyang Xie 3 Ang Li 2, 4 Haifeng Lu Shaoyan Xu Lin Zhou Hua Zhang Guangying Cui Xinhua Chen Yuanxing Liu Liming Wu Nan Qin Ranran Sun Wei Wang Lanjuan Weilin and Shusen Zheng 1 Department of Hepatobiliary Pancreatic Surgery, First Affiliated Hospital, School Medicine, Zhejiang University, Key Laboratory Combined Multi-organ Transplantation, Ministry Public Health, Hangzhou 310003, China 2 State for Diagnosis Treatment Infectious Disease,...
Bacterial biofilms are particularly problematic since they become resistant to most available antibiotics. Hence, novel potential antagonists inhibit biofilm formation urgent. Here the influences of two natural products, ursolic acid and resveratrol, on clinical methicillin-resistant Staphylococcus aureus (MRSA) isolate were investigated using RNA-seq differentially expressed genes analyzed Cuffdiff. The results showed that inhibition may reduce amino acids metabolism adhesins expression...
Abstract Chinese Rice Wine (CRW) is a common alcoholic beverage in China. To investigate the influence of microbial composition on quality CRW, high throughput sequencing was performed for 110 wine samples bacterial 16S rRNA gene and fungal Internal Transcribed Spacer II (ITS2). Bioinformatic analyses demonstrated that yeast starter final correlated with taxonomic composition, which exemplified by our finding spoilage resulted from proportion genus Lactobacillus . Subsequently, based...
Abstract Complex environmental conditions can significantly affect bacterial genome size by unknown mechanisms. The So0157-2 strain of Sorangium cellulosum is an alkaline-adaptive epothilone producer that grows across a wide pH range. Here, we show the this 14,782,125 base pairs, 1.75-megabases larger than largest from S. reported previously. total 11,599 coding sequences (CDSs) include massive duplications and horizontally transferred genes, regulated lots protein kinases, sigma factors...
Microbiota dysbiosis in inflammatory bowel disease (IBD) has been widely reported. The gut microbiota connect diet to the metabolism by producing small molecules via diverse metabolic pathways. In this study we aimed investigate dietary preferences of IBD patients, and explore interactions among composition, components, metabolites relation IBD.Dietary patients (including those with ulcerative colitis [UC] Crohn's [CD]) health controls were investigated, their analyzed using 16S rRNA gene...
Abstract The human gut microbiota varies considerably among world populations due to a variety of factors including genetic background, diet, cultural habits and socioeconomic status. Here we characterized 110 healthy Mongolian adults by shotgun metagenomic sequencing compared the intestinal microbiome Mongolians, Hans European cohorts. results showed that taxonomic profile cohorts revealed Actinobaceria Bifidobacterium were key microbes contributing differences Europeans at phylum level...
Abstract Between March and June, 2013, forty H7N9 patients were hospitalized in our hospital. Next-generation sequencing technologies have been used to sequence the fecal DNA samples of patient, within sample diversity analysis, enterotyping, functional gene metagenomic species analysis carried on both healthy controls. The influence associated treatment infected is dramatic was firstly revealed level due deep technology. We found that most MetaGenomic Species (MGS) enriched control...
Globally, dental caries is the most prevalent chronic oral disease and affects roughly half of all children. The aim this report was to use metagenomic analyses investigate relationship between microbiome in preschool A total 25 preschoolers, aged 3 5 years old with severe early childhood (ECC), 19 age-matched, caries-free children as controls were recruited. Saliva samples collected from participants subjected analyses, whereby microbial communities investigated. revealed substantial...
Abstract Background While the physical and chemical properties of airborne particulate matter (PM) have been extensively studied, their associated microbiome remains largely unexplored. Here, we performed a longitudinal metagenomic survey 106 samples PM 2.5 10 in Beijing over period 6 months 2012 2013, including those from several historically severe smog events. Results We observed that composition functional potential were conserved between , although considerable temporal variations...
Background Vogt-Koyanagi-Harada (VKH) disease is a multisystemic autoimmune disorder characterized by granulomatous panuveitis. Gut microbiome has been considered to play role in the pathogenesis of this but whether alternation gut was involved unclear. This study set up identify abnormalities composition VKH disease.Results Depleted butyrate-producing bacteria, lactate-producing bacteria and methanogens as well enriched Gram-negative were identified active patients, patients Mix enterotype...