A5040756224- Gut microbiota and health
- Mycobacterium research and diagnosis
- SARS-CoV-2 and COVID-19 Research
- Single-cell and spatial transcriptomics
- Antibiotic Resistance in Bacteria
- Dermatology and Skin Diseases
- Viral gastroenteritis research and epidemiology
- Vibrio bacteria research studies
- Tryptophan and brain disorders
- Animal Virus Infections Studies
- Tuberculosis Research and Epidemiology
- Cancer therapeutics and mechanisms
- Clostridium difficile and Clostridium perfringens research
- Enterobacteriaceae and Cronobacter Research
- Antimicrobial Resistance in Staphylococcus
- Probiotics and Fermented Foods
- Animal Nutrition and Physiology
- Livestock and Poultry Management
- Bacterial biofilms and quorum sensing
- Bacterial Genetics and Biotechnology
- Microbial Metabolism and Applications
- Infectious Diseases and Tuberculosis
- Salmonella and Campylobacter epidemiology
- RNA Interference and Gene Delivery
- Immune responses and vaccinations
Shanghai Jiao Tong University
2020-2025
Institute of Immunology
2024
To understand the dynamic interplay between human microbiome and host during health disease, we analyzed microbial composition, temporal dynamics, associations with multi-omics, immune, clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that stability individuality are body-site specific heavily influenced by host. The stool oral more stable than skin nasal microbiomes, possibly due to their interaction environment. identify individual-specific...
The aims of this study were to evaluate the safety and probiotic characteristics newly isolated Enterococcus lactis strain JDM1.Safety assessment E. JDM1 was accomplished by combination whole genome sequence information analysis phenotypic assays, including antimicrobial susceptibility test, haemolysis assay, biogenic amine production cytotoxicity assay. bacteriostatic experiment gastrointestinal tolerance also conducted its applicability.E. possesses good can inhibit growth pathogenic...
We developed an analysis pipeline that can extract microbial sequences from spatial transcriptomic (ST) data and assign taxonomic labels, generating a abundance matrix in addition to the default host expression matrix, enabling simultaneous of distribution. called metatranscriptome (SMT) applied it on both human murine intestinal sections validated information with alternative assays. Biological insights were gained these novel showed host-microbe interaction at various scales. Finally, we...
Adaptation to various stresses during infection is important for Salmonella Typhimurium virulence, while the fitness determinants under infection-relevant stress conditions remain unknown. Here, we simulated encountered within host or in environment by 15 individual as well two model cell lines (epithelium and macrophage) decipher genes pathways required fitness. By high-resolution Tn-seq analysis, a total of 1242 were identified essential at least one condition. The comparative analysis 17...
Summary To understand dynamic interplay between the human microbiome and host during health disease, we analyzed microbial composition, temporal dynamics, associations with multi-omics, immune clinical markers of microbiomes from four body sites in 86 participants over six years. We found that stability individuality are body-site-specific heavily influenced by host. The stool oral were more stable than skin nasal microbiomes, possibly due to their interaction environment. Also, identified...
Fundamental to viral biology is identification and annotation of genes their function. Determining the level coronavirus gene expression inherently difficult due positive stranded RNA genome subgenomic RNAs (sgRNAs) that are required for most genes. We developed a bioinformatic pipeline analyze metatranscriptomic data from 20 independent studies encompassing 588 individual samples 10 species. This comparative analysis defined core sgRNA repertoire SARS-CoV-2 found novel sgRNAs could encode...
ABSTRACT Background Fundamental to viral biology is identification and annotation of genes their function. Determining the level coronavirus gene expression inherently difficult due positive stranded RNA genome sub-genomic RNAs (sgRNAs) that are required for most genes. In COVID-19 epidemic so far, few genomic studies have looked at sgRNAs none systematically examined sgRNA profiles large numbers SARS-CoV2 datasets in conjuction with data other coronaviruses. Results We developed a...
ABSTRACT Salmonella could survive and replicate in macrophages, where it encounters multiple stresses. Deficiency of a DNA adenine methyltransferase impairs the survival enterica serovar Typhimurium ( S . Typhimurium) hydrogen peroxide. To investigate whether methylation is involved expression oxidative stress-responsive genes, we combined RNA-seq single-molecule real-time sequencing to integrate transcriptome methylome analysis. Here, show that (i) entire amount m6A GATC remains stable...
ObjectiveTo evaluate the levels and patterns of drug resistance in initially treated smear-negative pulmonary tuberculosis (TB) patients Ningbo, provide scientific evidence for prevention control drug-resistant TB. MethodsSputum samples 1 434 TB enrolled from March to December 2017 were isolated by liquid culture method. Strain identification susceptibility tests performed all positive with proportion ResultsA total 378 sputum positive, which 60 non-tuberculosis mycobacterium positive. Eight...
Abstract We developed an analysis pipeline that can extract microbial sequences from Spatial Transcriptomic (ST) data and assign taxonomic labels, generating a spatial abundance matrix in addition to the default host expression matrix, enabling simultaneous of distribution. called Meta-transcriptome (SMT) applied it on both human murine intestinal sections validated information with alternative assays. Biological insights were gained this novel demonstrated host-microbe interaction at...