Project description:Today, swine is regarded as promising biomedical model, however, its gastrointestinal microbiome dynamics have been less investigated than that of humans or murine models . The aim of this study was to establish a high-throughput multi-omics pipeline to investigate the healthy fecal microbiome of swine and its temporal dynamics as basis for future infection studies. To this end, a homogenization protocol based on deep-frozen feces followed by integrated sample preparation for different meta-omics analyses was developed. Subsequent data integration linked microbiome composition with function, i.e. expressed proteins and secreted metabolites.
Project description:Interactions between intracellular bacteria and mononuclear phagocytes give rise to diverse cellular phenotypes that may determine the outcome of infection. Recent advances in single-cell RNA-seq (scRNA-seq) have identified multiple subsets within the mononuclear population, but implications to their function during infection remain unknown. Here, we applied microscopy, flow cytometry and scRNA-seq to survey the mononuclear niche of intracellular Salmonella Typhimurium (S.Tm) during early systemic infection in mice. We describe eclipse-like growth kinetics in the spleen, with a first phase of bacterial control mediated by tissue-resident red-pulp macrophages. A second phase involved extensive bacterial replication within a newly identified macrophage population characterized by CD9 expression. Using Nr4a1e2-/- mice we established that CD9+ macrophages originated from non-classical monocytes (NCM), and NCM-depleted mice were more resistant to S.Tm infection. Our study defines a novel host-pathogen interface, with macrophage subset-specific interactions that determines early infection dynamics and the infection outcome of the entire organism.
Project description:Interactions between intracellular bacteria and mononuclear phagocytes give rise to diverse cellular phenotypes that may determine the outcome of infection. Recent advances in single-cell RNA-seq (scRNA-seq) have identified multiple subsets within the mononuclear population, but implications to their function during infection remain unknown. Here, we applied microscopy, flow cytometry and scRNA-seq to survey the mononuclear niche of intracellular Salmonella Typhimurium (S.Tm) during early systemic infection in mice. We describe eclipse-like growth kinetics in the spleen, with a first phase of bacterial control mediated by tissue-resident red-pulp macrophages. A second phase involved extensive bacterial replication within a newly identified macrophage population characterized by CD9 expression. Using Nr4a1e2-/- mice we established that CD9+ macrophages originated from non-classical monocytes (NCM), and NCM-depleted mice were more resistant to S.Tm infection. Our study defines a novel host-pathogen interface, with macrophage subset-specific interactions that determines early infection dynamics and the infection outcome of the entire organism.
Project description:Interactions between intracellular bacteria and mononuclear phagocytes give rise to diverse cellular phenotypes that may determine the outcome of infection. Recent advances in single-cell RNA-seq (scRNA-seq) have identified multiple subsets within the mononuclear population, but implications to their function during infection remain unknown. Here, we applied microscopy, flow cytometry and scRNA-seq to survey the mononuclear niche of intracellular Salmonella Typhimurium (S.Tm) during early systemic infection in mice. We describe eclipse-like growth kinetics in the spleen, with a first phase of bacterial control mediated by tissue-resident red-pulp macrophages. A second phase involved extensive bacterial replication within a newly identified macrophage population characterized by CD9 expression. Using Nr4a1e2-/- mice we established that CD9+ macrophages originated from non-classical monocytes (NCM), and NCM-depleted mice were more resistant to S.Tm infection. Our study defines a novel host-pathogen interface, with macrophage subset-specific interactions that determines early infection dynamics and the infection outcome of the entire organism.
Project description:To understand the current situation of the postoperative gastrointestinal dysfunction in patients with colorectal cancer effect a radical cure, and analyze the risk factors, and build the colorectal cancer radical surgery in patients with gastrointestinal dysfunction risk prediction nomogram model decision tree classification and regression tree model, through internal validation evaluation the performance of the two models in the modeling data set and dividing the postoperative gastrointestinal dysfunction risk level.Two risk prediction models were used to carry out external verification, evaluate the clinical practicability and effectiveness of the model, and provide reference for further promotion of the model.
Project description:Clostridioides difficile can cause severe infections in the gastrointestinal tract and affects almost half a million people in the U.S every year. Upon establishment of infection, a strong immune response is induced. We sought to investigate the dynamics of the mucosal host response during C. difficile infection.
Project description:Rationale: Lower respiratory tract infections continue to exact unacceptable worldwide mortality, often because the infecting pathogen cannot be identified. The respiratory epithelia provide protection from pneumonias through organism-specific generation of antimicrobial products, offering potential insight into the identity of infecting pathogens. Objective: This study assesses the capacity of the host gene expression response to infection to predict lower respiratory pathogens without reliance on culture data. Methods: Mice were inhalationally challenged with S. pneumoniae, P. aeruginosa, A. fumigatus or PBS prior to whole genome gene expression microarray analysis of their pulmonary parenchyma. Characteristic gene expression patterns for each condition were identified, allowing the derivation of prediction rules for each pathogen. After confirming the predictive capacity of gene expression data in blinded challenges, a computerized algorithm was devised to predict the infectious conditions of subsequent subjects. Measurements and Main Results: We observed robust, pathogen-specific gene expression patterns as early as 2 h after infection. We were able to develop a predictive model that used a limited number of specifically regulated transcripts to discriminate perfectly among infecting pathogens in the training data. Validation trials using an algorithmic decision tree revealed 94.4% diagnostic accuracy when discerning the presence of bacterial infection. The model subsequently differentiated between bacterial pathogens with 71.4% accuracy and between non-bacterial conditions with 70.0% accuracy, both far exceeding the expected diagnostic yield of standard culture-based bronchoscopy with bronchoalveolar lavage. Conclusions: These data substantiate the specificity of the pulmonary innate immune response and support the feasibility of a gene expression-based clinical tool for pneumonia diagnosis. Keywords: pathogen- and time-dependent host lung gene expression changes in pneumonia Mouse lungs were removed 6 h after challenge with P. aeruginosa, S. pneumoniae, A. fumigatus or sham (PBS), RNA was collected from leukoreduced lung homogenates, then cRNA was amplified and hybridized to Illumina Sentrix mouse-6 gene expression arrays v1.1. Gene expression data was analyzed to determine if there were distinct patterns of host trasnscription that corresponded with a specific infection.
Project description:Here we report comprehensive transcriptomic profiles from Fusobacterium nucleatum (Fn) under conditions that mimic the first stages of bacterial infection in a highly-differentiated adenocarcinoma epithelial cell line. Our transcriptomic in vitro adenocarcinoma approach allows us to measure the expression dynamics and regulation of bacterial virulence and response factors in real time and is a novel strategy for clarifying the role of Fn infection in CRC progression. Our data shows that: (1) infection alters metabolic and functional pathways in Fn, allowing the bacterium to adapt to the host-imposed milieu; (2) infection also stimulates the expression of genes required to help induce and promote a hypoxic and inflammatory microenvironment in the host; and (3) Fn invasion occurs by a hematogenous route of infection. Our study identifies novel gene targets from Fn that are activated during invasion and which may aid in determining how this species invades and promotes disease within the human gastrointestinal tract. These invasion-specific genes may be useful as biomarkers for colorectal cancer progression in a host and could also assist in the development of new diagnostic tools and treatments (such as vaccines or small molecule drug targets), which will be able to combat infection and inflammation in the host while circumventing the potential problem of Fn tolerisation.
Project description:We report the application of RNA sequencing to assess the expression dynamics of miRNAs and their isoforms over time upon infection with a panel of six intracellular bacteria (Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis Beijing strain GC1237, Mycobacterium bovis BCG, Salmonella typhimurium strain Keller, Staphloccocus epidermidis and Yersinia pseudotuberculosis) Study of miRNA expression dynamics of monocyte-derived dendritic cells upon bacterial infection using RNA sequencing
Project description:Secondary bacterial pneumonia following influenza infection is a significant cause of mortality worldwide. Upper respiratory tract pneumococcal carriage is important as both determinants of disease and population transmission. The immunological mechanisms that contain pneumococcal carriage are well-studied in mice but remain unclear in humans. Loss of this control of carriage following influenza infection is associated with secondary bacterial pneumonia during seasonal and pandemic outbreaks. We used a human type 6B pneumococcal challenge model to show that carriage acquisition induces early degranulation of resident neutrophils and recruitment of monocytes to the nose. Monocyte function associated with clearance of pneumococcal carriage. Prior nasal infection with live attenuated influenza virus induced inflammation, impaired innate function and altered genome-wide nasal gene responses to pneumococcal carriage. Levels of the cytokine IP-10 promoted by viral infection at the time of pneumococcal encounter was positively associated with bacterial density. These findings provide novel insights in nasal immunity to pneumococcus and viral-bacterial interactions during co-infection.