This document discusses the fungal and bacterial microbiota present in the lungs of cystic fibrosis patients. It presents results from a pilot study that used metagenomic sequencing of sputum samples from 4 CF patients. The study found 24 fungal and bacterial species/genera, with only 4 identified by culture previously. Fungal and bacterial richness was correlated with poorer clinical status and lung function. A follow up study of 36 patients with or without pulmonary exacerbation is analyzing microbiota differences using sequencing and may provide insights into CF exacerbations. Preliminary PCA analysis of the data suggests correlations and anti-correlations between certain microorganisms like Pseudomonas and oral bacteria.
This document discusses research on the lung mycobiota (fungal microbiota) in cystic fibrosis (CF) patients. Deep sequencing was used to analyze fungal and bacterial communities in sputum samples from CF patients. 24 fungal species/genera were identified, only 4 of which had been previously isolated by culture. Fungal and bacterial diversity were found to be statistically associated with clinical status measures like lung function. A pilot study on 8 samples found that lower diversity was linked to poorer clinical status. Further research aims to better characterize lung microbial communities in CF and understand how they relate to disease exacerbation and response to treatment.
What can we learn from studying fungal microbiotaLaurence Delhaes
The document discusses analyzing the fungal microbiota (mycobiota) in the lungs of cystic fibrosis (CF) patients. It summarizes a study that used high-throughput sequencing to analyze sputum samples from CF patients. The study found greater fungal diversity than previous culture-based methods, identifying 24 fungal genera including Aspergillus. Preliminary results showed associations between decreased fungal diversity and poorer clinical outcomes in CF patients. Larger studies are still needed to better understand the role of the lung mycobiota in CF exacerbations and how it interacts with bacterial communities and clinical status.
Targeted RNA Sequencing, Urban Metagenomics, and Astronaut GenomicsQIAGEN
This document discusses targeted RNA sequencing and metagenomics projects including:
1. Using targeted RNA panels to profile gene expression in acute lymphoblastic leukemia patients to identify chemo-resistant clones hiding at low frequencies.
2. Conducting the first city-scale metagenomic profile of the New York City subway system, finding many bacterial species including those associated with skin.
3. Ongoing plans to conduct metropolitan-scale metagenomic profiling in several major cities around the world to better understand urban microbiomes and human-microbe interactions.
The Global Virome Project is a 10-year global effort to identify and characterize naturally occurring viruses with pandemic potential. It aims to build a comprehensive database of the estimated 1.6 million viral species circulating in mammals and waterfowl. This will allow researchers to develop broad-spectrum countermeasures against future zoonotic viruses and identify high-risk viruses to prevent spillover. The project will sample viruses in 108 sites across 63 countries over 10 years, prioritizing countries and species based on viral discovery rates and zoonotic risk prediction models. The goal is to capture over 85% of the global mammalian virome to transform virology and pandemic preparedness.
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
Phage adhere more strongly to mucus layers than surrounding environments across diverse animal species. In vitro experiments show that phage adhere specifically to mucin glycoproteins in mucus via interactions between Ig-like domains on phage capsids and glycan residues on mucins. Pretreating mucus-producing cells with phage reduces subsequent bacterial attachment and infection, protecting the underlying epithelium. The presence of Ig-like protein domains in phages from many environments suggests a widespread symbiotic relationship between phages and metazoans, whereby phage adherence to mucus provides a non-host-derived antimicrobial defense of mucosal surfaces.
This document discusses research on the lung mycobiota (fungal microbiota) in cystic fibrosis (CF) patients. Deep sequencing was used to analyze fungal and bacterial communities in sputum samples from CF patients. 24 fungal species/genera were identified, only 4 of which had been previously isolated by culture. Fungal and bacterial diversity were found to be statistically associated with clinical status measures like lung function. A pilot study on 8 samples found that lower diversity was linked to poorer clinical status. Further research aims to better characterize lung microbial communities in CF and understand how they relate to disease exacerbation and response to treatment.
What can we learn from studying fungal microbiotaLaurence Delhaes
The document discusses analyzing the fungal microbiota (mycobiota) in the lungs of cystic fibrosis (CF) patients. It summarizes a study that used high-throughput sequencing to analyze sputum samples from CF patients. The study found greater fungal diversity than previous culture-based methods, identifying 24 fungal genera including Aspergillus. Preliminary results showed associations between decreased fungal diversity and poorer clinical outcomes in CF patients. Larger studies are still needed to better understand the role of the lung mycobiota in CF exacerbations and how it interacts with bacterial communities and clinical status.
Targeted RNA Sequencing, Urban Metagenomics, and Astronaut GenomicsQIAGEN
This document discusses targeted RNA sequencing and metagenomics projects including:
1. Using targeted RNA panels to profile gene expression in acute lymphoblastic leukemia patients to identify chemo-resistant clones hiding at low frequencies.
2. Conducting the first city-scale metagenomic profile of the New York City subway system, finding many bacterial species including those associated with skin.
3. Ongoing plans to conduct metropolitan-scale metagenomic profiling in several major cities around the world to better understand urban microbiomes and human-microbe interactions.
The Global Virome Project is a 10-year global effort to identify and characterize naturally occurring viruses with pandemic potential. It aims to build a comprehensive database of the estimated 1.6 million viral species circulating in mammals and waterfowl. This will allow researchers to develop broad-spectrum countermeasures against future zoonotic viruses and identify high-risk viruses to prevent spillover. The project will sample viruses in 108 sites across 63 countries over 10 years, prioritizing countries and species based on viral discovery rates and zoonotic risk prediction models. The goal is to capture over 85% of the global mammalian virome to transform virology and pandemic preparedness.
Viral Metagenomics (CABBIO 20150629 Buenos Aires)bedutilh
This is a one-hour lecture about metagenomics, focusing on discovery of viruses and unknown sequence elements. It is part of a one-day workshop about metagenome assembly of crAssphage, a bacteriophage virus found in human gut. The hands-on workflow can be found at http://tbb.bio.uu.nl/dutilh/CABBIO/ and should be doable in one afternoon with supervision. There is also an iPython notebook about this here: https://github.com/linsalrob/CrAPy
Phage adhere more strongly to mucus layers than surrounding environments across diverse animal species. In vitro experiments show that phage adhere specifically to mucin glycoproteins in mucus via interactions between Ig-like domains on phage capsids and glycan residues on mucins. Pretreating mucus-producing cells with phage reduces subsequent bacterial attachment and infection, protecting the underlying epithelium. The presence of Ig-like protein domains in phages from many environments suggests a widespread symbiotic relationship between phages and metazoans, whereby phage adherence to mucus provides a non-host-derived antimicrobial defense of mucosal surfaces.
Tom Delmont: From the Terragenome Project to Global Metagenomic Comparisons: ...GigaScience, BGI Hong Kong
This document discusses challenges in comparing metagenomic data from different environments and studies. It argues that when exploring a new environment, multiple methodological approaches should be used to capture natural and methodological variations. When performing global comparisons, methodological variations should be considered for all environments. Defining ecosystems precisely at the microorganism level is important. The author's vision is for projects like the Earth Microbiome Project to use flexible experimental designs informed by different experts to best represent microbial communities.
Metagenomics is the study of microbial communities directly in their natural environments without isolating individual species in the lab. It involves sequencing DNA from environmental samples and analyzing the metagenomes. Some key points are that metagenomics can identify uncultivable microbes, bypassing the need for culture, and it has led to advances in understanding microbial ecology, evolution, and diversity. The rumen, home to a complex microbial community important for ruminant digestion, is a important target of metagenomics study. Next generation sequencing techniques now allow more accessible exploration of microbial systems through metagenomics.
The document describes a meta-analysis of microbial community samples collected by the Earth Microbiome Project (EMP) that used coordinated protocols and analytical methods to explore patterns of diversity at an unprecedented scale. By tracking individual bacterial and archaeal ribosomal RNA gene sequences across multiple studies, the analysis resulted in both a reference database providing global context to DNA sequence data and an analytical framework for incorporating future study data to further characterize Earth's microbial diversity. The meta-analysis found that standardized environmental descriptors and new analytical methods, particularly using exact sequences instead of clustered operational taxonomic units, enabled comparisons across studies and exploration of large-scale ecological patterns.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
This document describes a genomic study of Agaricus bisporus collected from the Tibetan Plateau in China. Key findings include:
1) The genome of the Tibetan Plateau strain ABM was sequenced and found to be 30.4 Mb with 8,562 genes. Comparative genomic analysis revealed conserved synteny with European strains H97 and H39 but also some genomic inversions.
2) Phylogenetic analysis of 1,276 single-copy orthologous genes from nine fungal species estimated that Tibetan Plateau and European A. bisporus diverged around 5.5 million years ago.
3) Population genomic analysis of 29 strains using genome resequencing identified significant genetic differentiation
This document summarizes a study that used PCR and cloning to analyze the 16S rRNA genes present in a natural marine bacterioplankton population from the Sargasso Sea. Researchers constructed a library of 51 small-subunit rRNA genes and sequenced five unique genes. In addition to genes from known marine Synechococcus and SAR11 lineages, they identified two new classes of genes belonging to alpha- and gamma-proteobacteria, confirming that many planktonic bacteria have not been previously recognized by microbiologists.
This document discusses the potentials and pitfalls of metagenomics. It begins with an introduction to metagenomics and its history. It describes some of the early applications of metagenomics including exploration of microbial communities and identification of specific functions. Potential pitfalls of metagenomics are then outlined, including issues related to DNA extraction, sequencing depth, and biases. The major pitfall discussed is the incompleteness of databases for assigning taxonomy and functions. The document concludes by describing some of the potentials of metagenomics, including hunting for novel antibiotic resistance genes using functional metagenomics and extracting genomes from metagenomes through reducing microdiversity and binning sequences from multiple related samples.
Metagenomics is a set of techniques used to study microbial communities through direct collection and analysis of environmental DNA samples. It allows researchers to study millions of microbial organisms and genetic fragments simultaneously without needing to culture individual microbes in the lab. The main procedures involve sampling an environment, filtering out particles by size, extracting and sequencing DNA fragments. Two common sequencing methods are shotgun sequencing and high-throughput sequencing using platforms like Illumina or SOLiD. Projects like MetaHIT use metagenomics to study the human gut microbiome and its role in health and disease. Potential applications include contributions to earth sciences, life sciences, biomedicine, bioenergy, biotechnology, and microbial forensics.
Replication Competent IAV and IBV with Timer Article.PDFMichael Breen
This document describes the generation of replication-competent influenza A and B viruses expressing the fluorescent dynamic Timer protein fused to the viral NS1 protein. Timer protein undergoes a time-dependent color change from green to red that can be used to track viral infections over time. The generated Timer-expressing influenza viruses displayed similar growth properties to wild-type viruses in cell culture. Using fluorescent microscopy and other techniques, the Timer protein allowed differentiation of primary and secondary infected cells and tracking of viral spread in vitro and in vivo. These Timer-expressing influenza viruses provide a tool to study the dynamics and chronology of viral infections.
Polyketide Synthase type III Isolated from Uncultured Deep-Sea Proteobacteriu...Hadeel El Bardisy
Screening and Isolation of possible bacterial PKS type III in Atlantis II deep brine pool using a metagenomic approach
and gaining a deeper insights into the evolutionary origin of PKS type III among Prokaryotes and Eukaryotes
The Phytobiomes Initiative proposes a systems-level approach to studying the entire microbial community associated with plants, including bacteria, viruses, and eukaryotes in the rhizosphere, phyllosphere, and within plants. Recent advances in metagenomic technologies now allow comprehensive analysis of both culturable and non-culturable microbes. Two recent studies using these methods revealed that root microbial communities are non-random and depend on host genotype and environment. The initiative aims to establish a foundation for understanding how phytobiomes influence plant health and productivity, with the goal of developing strategies to improve crop yields, reduce disease and environmental impacts, and enhance food safety and security.
Using Supercomputers and Supernetworks to Explore the Ocean of LifeLarry Smarr
The document summarizes Dr. Larry Smarr's presentation about the CAMERA project, which uses supercomputers and networks to explore microbial genomic data from ocean samples. The CAMERA infrastructure provides researchers worldwide with access to over 1 billion base pairs of metagenomic sequence data through an online portal. Analysis of this data has expanded knowledge of microbial biodiversity and gene families, providing insights into evolution and relationships between microbes and human health.
Metagenomics is the study of genetic material recovered directly from environmental samples. It provides a new approach to studying microbes that are not easily cultured in a laboratory and enables investigation of microbial communities in their natural habitats. Metagenomics involves directly extracting DNA from samples, sequencing it, and analyzing the genetic information obtained from entire communities of organisms simultaneously. This provides insights into uncultured microbes and their roles in various environments.
Clinical Metagenomics for Rapid Detection of Enteric Pathogens and Characteri...QIAGEN
High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.
This document summarizes key points from a class on microbial phylogenomics taught by Jonathan Eisen. It discusses reading scientific papers, specifically beginning with the introduction rather than the abstract. It also provides guidance on identifying the big question a field is trying to answer, summarizing the background and limitations of prior work, stating the specific questions authors are addressing, and identifying their experimental approach. The document does not summarize any specific paper.
Global surveillance One World – One HealthExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Global surveillance One World – One Health. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
The document provides information about the objectives and history of the Human Genome Project. It discusses:
- The goals of the project which were to identify all human genes, determine the DNA sequence, improve data analysis tools, and address ethical issues.
- Key dates and milestones from 1984 when it was proposed through completion of sequencing the human genome in 2003.
- Methods used to determine DNA sequences including Sanger dideoxy chain termination and shotgun sequencing.
- Outcomes of the project including ability to locate disease genes, advances in gene therapy, and providing benefits to medicine, energy, the environment, and risk assessment.
This document discusses the polymicrobial nature of biofilm infections. It summarizes that biofilms are usually polymicrobial communities that provide advantages like passive resistance, metabolic cooperation, and an enlarged gene pool through horizontal gene transfer. DNA methods using PCR and sequencing have demonstrated the ability to identify microorganisms in clinical biofilm infections. A robust model of polymicrobial biofilm infection along with accurate diagnosis is improving clinical outcomes.
Mold and cystic fibrosis : what can we learn from studying fungal microbiota ?Laurence Delhaes
This document discusses studying the fungal microbiota (mycobiota) in the lungs of cystic fibrosis (CF) patients. It begins by providing background on human microbial diversity and the emerging importance of studying the lung mycobiota. The authors aim to characterize the lung mycobiota in CF patients using deep sequencing techniques and analyze how the mycobiota relates to clinical status and bacterial composition. Preliminary results on 36 sputum samples from CF patients with and without pulmonary exacerbation show no association between common fungi like Aspergillus fumigatus and exacerbation. Principal component analysis of bacterial and fungal genera indicates some correlations and lack of correlation between certain microorganisms. Further statistical analysis is ongoing.
This document outlines Dalia Abd El_Mohsen Mohamed's proposed master's degree work plan. The plan aims to investigate the relationship between concentrations of cyanobacterial hepatotoxins (microcystins and cylindrospermopsin) in drinking water and human blood in Egypt for the first time. Water and blood samples will be collected from patients and healthy individuals and analyzed for hepatotoxin levels using ELISA. Liver enzyme levels will also be measured and correlated with hepatotoxin levels to assess potential liver impacts. The study aims to provide insights into health risks from cyanobacterial toxins in drinking water in Egypt.
Tom Delmont: From the Terragenome Project to Global Metagenomic Comparisons: ...GigaScience, BGI Hong Kong
This document discusses challenges in comparing metagenomic data from different environments and studies. It argues that when exploring a new environment, multiple methodological approaches should be used to capture natural and methodological variations. When performing global comparisons, methodological variations should be considered for all environments. Defining ecosystems precisely at the microorganism level is important. The author's vision is for projects like the Earth Microbiome Project to use flexible experimental designs informed by different experts to best represent microbial communities.
Metagenomics is the study of microbial communities directly in their natural environments without isolating individual species in the lab. It involves sequencing DNA from environmental samples and analyzing the metagenomes. Some key points are that metagenomics can identify uncultivable microbes, bypassing the need for culture, and it has led to advances in understanding microbial ecology, evolution, and diversity. The rumen, home to a complex microbial community important for ruminant digestion, is a important target of metagenomics study. Next generation sequencing techniques now allow more accessible exploration of microbial systems through metagenomics.
The document describes a meta-analysis of microbial community samples collected by the Earth Microbiome Project (EMP) that used coordinated protocols and analytical methods to explore patterns of diversity at an unprecedented scale. By tracking individual bacterial and archaeal ribosomal RNA gene sequences across multiple studies, the analysis resulted in both a reference database providing global context to DNA sequence data and an analytical framework for incorporating future study data to further characterize Earth's microbial diversity. The meta-analysis found that standardized environmental descriptors and new analytical methods, particularly using exact sequences instead of clustered operational taxonomic units, enabled comparisons across studies and exploration of large-scale ecological patterns.
Microbiome Isolation and DNA Enrichment Protocol: Pathogen Detection Webinar ...QIAGEN
This slidedeck presents an easy-to-use workflow that allows selective isolation of microbial DNA from samples that are intrinsically rich in host DNA. This protocol includes steps for efficient depletion of host DNA while providing optimized conditions specific for bacterial lysis. This workflow is also specific for the identification of live bacteria, avoiding false results due to nucleic acids from dead bacteria. Enriched microbial DNA can be directly used in other molecular methods such as whole genome sequencing, qPCR and microarray assays.
This document describes a genomic study of Agaricus bisporus collected from the Tibetan Plateau in China. Key findings include:
1) The genome of the Tibetan Plateau strain ABM was sequenced and found to be 30.4 Mb with 8,562 genes. Comparative genomic analysis revealed conserved synteny with European strains H97 and H39 but also some genomic inversions.
2) Phylogenetic analysis of 1,276 single-copy orthologous genes from nine fungal species estimated that Tibetan Plateau and European A. bisporus diverged around 5.5 million years ago.
3) Population genomic analysis of 29 strains using genome resequencing identified significant genetic differentiation
This document summarizes a study that used PCR and cloning to analyze the 16S rRNA genes present in a natural marine bacterioplankton population from the Sargasso Sea. Researchers constructed a library of 51 small-subunit rRNA genes and sequenced five unique genes. In addition to genes from known marine Synechococcus and SAR11 lineages, they identified two new classes of genes belonging to alpha- and gamma-proteobacteria, confirming that many planktonic bacteria have not been previously recognized by microbiologists.
This document discusses the potentials and pitfalls of metagenomics. It begins with an introduction to metagenomics and its history. It describes some of the early applications of metagenomics including exploration of microbial communities and identification of specific functions. Potential pitfalls of metagenomics are then outlined, including issues related to DNA extraction, sequencing depth, and biases. The major pitfall discussed is the incompleteness of databases for assigning taxonomy and functions. The document concludes by describing some of the potentials of metagenomics, including hunting for novel antibiotic resistance genes using functional metagenomics and extracting genomes from metagenomes through reducing microdiversity and binning sequences from multiple related samples.
Metagenomics is a set of techniques used to study microbial communities through direct collection and analysis of environmental DNA samples. It allows researchers to study millions of microbial organisms and genetic fragments simultaneously without needing to culture individual microbes in the lab. The main procedures involve sampling an environment, filtering out particles by size, extracting and sequencing DNA fragments. Two common sequencing methods are shotgun sequencing and high-throughput sequencing using platforms like Illumina or SOLiD. Projects like MetaHIT use metagenomics to study the human gut microbiome and its role in health and disease. Potential applications include contributions to earth sciences, life sciences, biomedicine, bioenergy, biotechnology, and microbial forensics.
Replication Competent IAV and IBV with Timer Article.PDFMichael Breen
This document describes the generation of replication-competent influenza A and B viruses expressing the fluorescent dynamic Timer protein fused to the viral NS1 protein. Timer protein undergoes a time-dependent color change from green to red that can be used to track viral infections over time. The generated Timer-expressing influenza viruses displayed similar growth properties to wild-type viruses in cell culture. Using fluorescent microscopy and other techniques, the Timer protein allowed differentiation of primary and secondary infected cells and tracking of viral spread in vitro and in vivo. These Timer-expressing influenza viruses provide a tool to study the dynamics and chronology of viral infections.
Polyketide Synthase type III Isolated from Uncultured Deep-Sea Proteobacteriu...Hadeel El Bardisy
Screening and Isolation of possible bacterial PKS type III in Atlantis II deep brine pool using a metagenomic approach
and gaining a deeper insights into the evolutionary origin of PKS type III among Prokaryotes and Eukaryotes
The Phytobiomes Initiative proposes a systems-level approach to studying the entire microbial community associated with plants, including bacteria, viruses, and eukaryotes in the rhizosphere, phyllosphere, and within plants. Recent advances in metagenomic technologies now allow comprehensive analysis of both culturable and non-culturable microbes. Two recent studies using these methods revealed that root microbial communities are non-random and depend on host genotype and environment. The initiative aims to establish a foundation for understanding how phytobiomes influence plant health and productivity, with the goal of developing strategies to improve crop yields, reduce disease and environmental impacts, and enhance food safety and security.
Using Supercomputers and Supernetworks to Explore the Ocean of LifeLarry Smarr
The document summarizes Dr. Larry Smarr's presentation about the CAMERA project, which uses supercomputers and networks to explore microbial genomic data from ocean samples. The CAMERA infrastructure provides researchers worldwide with access to over 1 billion base pairs of metagenomic sequence data through an online portal. Analysis of this data has expanded knowledge of microbial biodiversity and gene families, providing insights into evolution and relationships between microbes and human health.
Metagenomics is the study of genetic material recovered directly from environmental samples. It provides a new approach to studying microbes that are not easily cultured in a laboratory and enables investigation of microbial communities in their natural habitats. Metagenomics involves directly extracting DNA from samples, sequencing it, and analyzing the genetic information obtained from entire communities of organisms simultaneously. This provides insights into uncultured microbes and their roles in various environments.
Clinical Metagenomics for Rapid Detection of Enteric Pathogens and Characteri...QIAGEN
High-throughput sequencing, combined with high-resolution metagenomic analysis, provides a powerful diagnostic tool for clinical management of enteric disease. Forty-five patient samples of known and unknown disease etiology and 20 samples from health individuals were subjected to next-generation sequencing. Subsequent metagenomic analysis identified all microorganisms (bacteria, viruses, fungi and parasites) in the samples, including the expected pathogens in the samples of known etiology. Multiple pathogens were detected in the individual samples, providing evidence for polymicrobial infection. Patients were clearly differentiated from healthy individuals based on microorganism abundance and diversity. The speed, accuracy and actionable features of CosmosID bioinformatics and curated GenBook® databases, implemented in the QIAGEN Microbial Genomics Pro Suite, and the functional analysis, leveraging the QIAGEN functional metagenomics workflow, provide a powerful tool contributing to the revolution in clinical diagnostics, prophylactics and therapeutics that is now in progress globally.
This document summarizes key points from a class on microbial phylogenomics taught by Jonathan Eisen. It discusses reading scientific papers, specifically beginning with the introduction rather than the abstract. It also provides guidance on identifying the big question a field is trying to answer, summarizing the background and limitations of prior work, stating the specific questions authors are addressing, and identifying their experimental approach. The document does not summarize any specific paper.
Global surveillance One World – One HealthExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Global surveillance One World – One Health. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
The document provides information about the objectives and history of the Human Genome Project. It discusses:
- The goals of the project which were to identify all human genes, determine the DNA sequence, improve data analysis tools, and address ethical issues.
- Key dates and milestones from 1984 when it was proposed through completion of sequencing the human genome in 2003.
- Methods used to determine DNA sequences including Sanger dideoxy chain termination and shotgun sequencing.
- Outcomes of the project including ability to locate disease genes, advances in gene therapy, and providing benefits to medicine, energy, the environment, and risk assessment.
This document discusses the polymicrobial nature of biofilm infections. It summarizes that biofilms are usually polymicrobial communities that provide advantages like passive resistance, metabolic cooperation, and an enlarged gene pool through horizontal gene transfer. DNA methods using PCR and sequencing have demonstrated the ability to identify microorganisms in clinical biofilm infections. A robust model of polymicrobial biofilm infection along with accurate diagnosis is improving clinical outcomes.
Mold and cystic fibrosis : what can we learn from studying fungal microbiota ?Laurence Delhaes
This document discusses studying the fungal microbiota (mycobiota) in the lungs of cystic fibrosis (CF) patients. It begins by providing background on human microbial diversity and the emerging importance of studying the lung mycobiota. The authors aim to characterize the lung mycobiota in CF patients using deep sequencing techniques and analyze how the mycobiota relates to clinical status and bacterial composition. Preliminary results on 36 sputum samples from CF patients with and without pulmonary exacerbation show no association between common fungi like Aspergillus fumigatus and exacerbation. Principal component analysis of bacterial and fungal genera indicates some correlations and lack of correlation between certain microorganisms. Further statistical analysis is ongoing.
This document outlines Dalia Abd El_Mohsen Mohamed's proposed master's degree work plan. The plan aims to investigate the relationship between concentrations of cyanobacterial hepatotoxins (microcystins and cylindrospermopsin) in drinking water and human blood in Egypt for the first time. Water and blood samples will be collected from patients and healthy individuals and analyzed for hepatotoxin levels using ELISA. Liver enzyme levels will also be measured and correlated with hepatotoxin levels to assess potential liver impacts. The study aims to provide insights into health risks from cyanobacterial toxins in drinking water in Egypt.
To form the basis of a respiratory disease model in rats by investigating the microbial distribution and composition in the lower respiratory tracts of normal rats. Methods: DNA was extracted from the intestine, trachea, bronchus and lung samples collected from healthy rats under sterile conditions. The 16S rDNA V4-V5 region was sequenced using Illumina high-throughput technology. Results: The sequencing results showed that there was no significant difference in abundance and species diversity of microbiota between the lower respiratory and the intestine. The microbiota structure analysis showed samples from lungs and intestinal shared similarity. However, the dominant species at the levels of phylum, family, and genus diverged. The similarity analysis showed that the lung microbiota were different from the intestines. The linear discriminant analysis showed significantly different species in different tissues; function prediction also showed different microbiota function in different tissues. Conclusions: These results suggest that bacterial colonization depends on the sample’s anatomical location. The human pathogen Acinetobacter lwoffii was also detected in the rat lower respiratory tract samples.
This document provides information on using the Coriolis μ air sampler for monitoring biocontamination in veterinary environments. It includes two application notes summarizing studies that used the Coriolis μ to: 1) assess fungal contamination in Portuguese poultry facilities using cultural and molecular methods, finding some toxigenic strains not detected by culture; and 2) demonstrate airborne transmission of swine influenza virus between pigs in an experimental setting, detecting the virus in air samples before infected pigs showed symptoms. It also lists two publications using the Coriolis μ to study Streptococcus suis in swine confinement buildings and Coxiella burnetii in sheep farms. The document encourages joining an online community for sharing Coriolis application
The transformational role of polymerase chain reaction (pcr) in environmental...Alexander Decker
This document discusses the transformational role of polymerase chain reaction (PCR) in environmental health research. PCR allows for exponential amplification of target DNA sequences, which has enabled rapid and sensitive detection of pathogens in environmental samples as an alternative to traditional culture methods. While PCR is widely used in developed countries, its benefits have yet to be fully realized in developing countries like Nigeria. The document provides background on DNA replication and the basics of how PCR works to exponentially amplify DNA. It argues that PCR could greatly aid environmental health monitoring and disease diagnosis in Nigeria.
This document summarizes a presentation on applying systems biology approaches to epidemiology and personalized medicine. It discusses how epidemiology has evolved from studying single risk factors to investigating complex interactions between genes, environments and diseases. Systems approaches integrate multiple levels of data to gain insights into disease mechanisms. Large consortia now apply these methods to conditions like asthma and COPD to understand their complexity. Epidemiology contributes a population perspective and helps develop evidence-based systems medicine frameworks.
Purpose: To investigate the effect of sulfur dioxide on the lung microbiota of healthy rats. Methods Fifteen male rats were randomly divided into high dose and low dose exposure group and control group. After 7 days of SO2 exposure, the lung tissues were obtained and the lung microbiota was identified by Illumina high-throughput sequencing. Results The microbial community of lung microbiota was significantly alternated in the exposure group and the dominant phylum changed from Firmicutes to Proteobacteria. In addition, the SO2 exposure caused the bronchial wall thickening and a large number of inflammatory cell infiltration in the lungs of rats in exposure groups. Conclusions The results suggest that SO2 can significantly alter the lung microbiota and pathological structure of the lungs.
1) TB is caused by Mycobacterium tuberculosis and is one of the top infectious disease killers.
2) It is transmitted through the air and one-third of the world's population is infected with latent TB.
3) Diagnosis involves sputum smear microscopy, culture, tuberculin skin test, chest x-ray and PCR. Treatment requires a minimum of 6 months of multiple antibiotic drugs.
Function Of Defense Responses And Developmental ProgramsKaren Oliver
The document discusses chorismate mutase, an enzyme involved in the shikimate pathway that converts primary metabolites into chorismate. Chorismate is then converted to prephenate and other aromatic amino acids important for controlling defense responses and development. Chorismate mutase catalyzes the rearrangement of chorismate to prephenate through a Claisen rearrangement. It exists in active and inactive states, and binding of transition state analogues keeps it in the active state.
This document describes the development of a fluorescence-based assay called "ProteAl" to detect the volatile biomarker 2-methylbutanal produced by Proteus bacteria. Gas chromatography-mass spectrometry and Fourier transform infrared spectroscopy were used to identify 2-methylbutanal in the headspace of Proteus cultures. A fluorescent dye, 5-dimethylaminonaphthalene-1-sulfonylhydrazine, was found to react specifically with 2-methylbutanal, producing a distinct green fluorescence. Testing of 95 bacterial strains showed the ProteAl assay can identify Proteus with 100% specificity and sensitivity, providing a simple method for rapid surveillance of this pathogen.
Genomic epidemiology of mayor Mycobacterium tuberculosis outbreak retrospective cohort stdy in a low incidence setting using sparse time series sampling.
The document describes experiments conducted to identify an unknown microorganism. Samples from two patients, labeled Culture A and Culture B, were tested using a Gram stain. Culture A showed pink rod-shaped bacteria, while Culture B showed round purplish-pink bacteria. An antibiotic test found that chloramphenicol and tetracycline were most effective at inhibiting the growth of both bacterial cultures. Based on the morphological and antibiotic test results, the unknown microorganism was identified as Citrobacter Freundii.
2017 - Environmental Ordination of Filamentous Bacteria in Activated SludgeWALEBUBLÉ
Reference:
Zornoza, A., Serrano, S. and Alonso, J.L. (2017) Environmental Ordination of Filamentous Bacteria in Activated Sludge. In: Abstracts of the 7th congress of European microbiologists FEMS 2017, Valencia, Spain, 9-13 July 2017.
Indicator role and monitoring of microorganisms in life [autosaved]Maryam Idris
an overview of the role of microbes in determining the health and safety of life support systems including the crew members, rapid diagnostic methods and real time monitoring of enclosed ecosystems using microbes as indicators of the health statues of such systems
Rick Stevens: Prospects for a Systematic Exploration of Earths Microbial Dive...GigaScience, BGI Hong Kong
Rick Stevens presented information about the Earth Microbiome Project (EMP), which aims to systematically characterize microbial life on Earth through a combination of extremely deep metagenomic sequencing and large-scale horizontal surveys. The EMP will establish common standards and coordinate independent projects proposed by the research community to advance large-scale microbial ecology research. It will generate over 1 petabase of sequencing data from around 1 million samples to map microbial habitats and discover new microbial diversity, genomes, and proteins.
This document discusses molecular microbiology and some of its techniques. It begins by defining molecular microbiology as the study of the molecular basis of physiological processes in microorganisms and manipulation of DNA. It then discusses several molecular techniques used, including polymerase chain reaction (PCR) and its applications such as quantitative real-time PCR and multiplex PCR. The document also discusses uses of molecular microbiology such as detection of pathogens and its role in fields like environmental microbiology.
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2013 escf metagenome fungal and bacterial interactions
1. Metagenome: Fungal and Bacterial
interactions
Laurence Delhaes
laurence.delhaes@pasteur-lille.fr
1
BDEEP – EA4547 (CIIL), Institut Pasteur de Lille, Université de Lille 2 – France
2
Département de Microbiologie, Service de Parasitologie-Mycologie, CHU de Lille - France.
2. Microorganisms (bacteria, archaea, yeasts, moulds, viruses) are
colonizing all ecological systems
Such microorganisms are present even in extreme environments
A majority of these microorganisms remains to be identified
1-4 106
bacteria / g of soil
(tropical rain forest)
2 108
cells / g of soil
(desert)
1,04 1020
cells / cm3
of water
(hypersaline water)
Introduction: Global microbial diversity
3. Micromycetes: are present in various ecosystems
(but poorly studied/analyzed)
Playing an important role within soil regeneration
(nutriment - metabolism of plant decomposition)
Of note: Fungi (especially ascomycetes) have/fulfill
along with bacteria a central role in most land-based
ecosystems, as they are important decomposers,
breaking down organic substances.
1 500 000 represents the number of fungus species
estimated for the entire earth/world
But only 97 000 have been identified
[Hibbett et al. 2007, Mycol Res , 111: 509-
547]
Introduction - Microbial diversity: Place of the
fungi
4. As other ecological systems, there is a microbial community /diversity
of human organisms
Introduction: Human Microbial diversity
Species number (bacteria)
Acid mine See Termite hindgut Human gut Soil
Proctor LM (2011) The Human Microbiome
Project in 2011 and Beyond. Cell Host & Microbe
10:287-91
Recently, the Common Fund's Human
Microbiome Project (HMP) has been
developed.
It aims to characterize the microbial
communities found at several different
sites on the human body, including nasal
passages, oral cavities, skin, gastrointestinal
tract, and urogenital tract, and to analyze
the role of these microbes in human
health and disease.
5. The main bacteria isolated in Humans are belonging 4 phyla (among the 50 known phyla). There are
Firmicutes (in blue), Bacteroidetes (in pink), Actinobacteria (in green), and Proteobacteria (in
purple).
http://www.larecherche.fr/content/recherche/article?id=25319
Human beings: Which bacteria are living in us (The genomes in our genome)?
[La Recherche – a 2011 up-date: 1st
panorama drawn from 7 studies realised from 2004 to 2007]
Introduction: Human Microbial diversity
2 Missing
Elements
6. Respiratory function: A major issue for Public Heath
In relation with the outdoor environment As for the other
air-breathing animals, human lungs are dealing with gas exchange
(drawing and expulsion of air; 15m3
of air / day / adult; with a fungal
contamination from to 108
to 103
spores/m3
in working to domestic usual
exposure [OMS 2009]
Lungs: Sterile organs: an old dogma?
[Morris et al. 2013; Beck et al. 2012; Erb-Downward et al. 2011; Huang et al.
2011]
-Respiratory disorders: 1st
cause of worldwide consultations
-Chronic obstructive pulmonary disease (COPD): 4th
origin in
worldwide decease by 2030 (WHO)
-Cystic Fibrosis (CF): Most common serious hereditary disorder in the
Caucasian population[Rabe et al. « The year of the lung ». Lancet 2010]
Introduction: Human Microbial diversity and Lung
7. Lung microbial diversity in Cystic Fibrosis (CF):
- Lung diversity = Bacterial microbiota
exists in healthy people [Morris et al. 2013; Beck
et al. 2012; Erb-Downward et al. 2011; Huang et al.
2011]
- This bacterial community has been largely
studied in CF, and seems to be associated
with the evolution of the respiratory function
in CF [Maughan et al. 2012; Guss et al. 2011; van der
Gast et al. 2011; Rogers et al. 2010; Armougom et al.
2009; Bittar et al. 2008; Sibley et al. 2008; Tunney et al.
2008; Harris et al. 2007Goddard et al. 2012; Madan et
al. 2012; Fodor et al. 2012]
Introduction: Human Microbial diversity and Lung
8. Purpose: What is the fungal microbiota (or
Mycobiota) of CF patients?
Is the fungal microbiota stable?
Are the mycobiota diversity and
richness associated to the clinical
status of CF patient? …
What is the fungal composition of lung
microbiota in CF?
⇒ Mycobiota analysis by developping and using high
throughput sequencing approach
Which relation we observed between the
mycobiota and the bacterial composition?
Introduction: Human Microbial diversity and Lung
9. DNA Extraction depends on matrix/substrate
PCRs targeted conserved genes that allow the
amplification of species distant/different
phylogenetically (V3 of 16s rDNA – ITS2)
Massive sequencing (multi-parallelized) – getting
hundreds of thousands of reads
Bio-informatic analysis
Identification by local blast to 2 databases: BLASTN ≠
- Silva SSU rRNA database release 102
- ITS2dbScreen that we designed de novo
Read assignments and clustering
(at the species or genus level)
To allow a biologic analysis of the data,
comparison between samples
(diversity analysis using MEGAN, U-clust, MEGANE5 progamms)
Collectd sputum samples of CF patients
Materials & Methods: Metagenomic approach
10. -Bacteria [16s rDNA region V3] : 326,277
pyrosequences (with 93% : 450-500 bp)
-Fungi [ITS2] : 133,317 pyrosequences
(with 85% : 300-450 bp)
-With adequate rarefaction curves
(confirming we have a good evaluation of
the sample diversity)
Lung mycobiota in CF: Results of the pilot study
Determine:
• Bacterial diversity (comparable to published data)
• Fungal diversity
Evaluate the relation between fungal/bacterial community
structure and patient clinical status
8 sputum samples (4 patients) using
454 FLX system
11. Lung mycobiota in CF: Results of the pilot study
Fungal diversity
- Among the 24 species /genera
identified as fungi using deep-
sequencing, only 4 have been
isolated by cultures.
- Genomic methods allowed the
identification of additional species
that are recognized as
microorganismsinvolved in respiratory or
infectious diseases
- The median [IQ] number
of microorganism genera
per sputum sample was
3.5 [3; 7.5] micromycetes
[Bouchara et al. 2009].
12. Fungal richness
(Choa1 index)
S-K score= Shwachman-Kulczycki Score (overall clinical
status, activity, lung function, pulnmonary radiography)
Body Mass
Index
(kg/m2
)
Lung mycobiota in CF: Results of the pilot study
Relation between species richness & clinical status
13. Body Mass
Index
(kg/m2
)
Lung mycobiota in CF: Results of the pilot study
Relation between species richness & clinical status
Prokaryote richness
(Choa1 index)
S-K score= Shwachman-Kulczycki Score (overall clinical
status, activity, lung function, pulnmonary radiography)
14. Body Mass
Index
(kg/m2
)
Lung mycobiota in CF: Results of the pilot study
Relation between species richness & clinical status
Choa1 indexes
S-K score= Shwachman-Kulczycki Score (overall clinical
status, activity, lung function, pulnmonary radiography)
Pat. 3 (09/2007)
Pat. 3 (09/2008)
Patients 2
Patient 1 (01/2008)
Patient 1 (01/2009)
Patient 4 (10/2008)
Patient 4 (08/2008)
- Chao1 indexes of fungi
and bacteria are
statistically (p<0.05)
associated with S-K
score and BMI.
- For bacteria, these
results are in agreement
with published data [van
der Gast et al. 2011; Klepas-
Ceraj et al. 2010].
15. % Forced Vital Capacity (FVC)
% Forced Expiratory Volume
(FEV1)
Pat. 3 (09/2007)
Pat. 3 (09/2008)
Patient 1 (01/2008)
Patient 1 (01/2009)
Patient 4 (10/2008)
Patient 4 (08/2008)
Patients 2 (03/2008)
Patients 2 (03/2009)
- Chao1 indexes of
fungi and bacteria are
statistically (p<0.05)
associated with FVC
and FEV1.
Lung mycobiota in CF: Results of the pilot study
Relation between species richness & clinical status
16. ⇒ Validation of the molecular
approach (ITS2 DB+++)
⇒ We observed a decrease of
diversity and richness for
fungal and bacterial
communities significantly
associated with poor clinical
status (S-K score and BMI)
and decreased lung function
(FEV1 and FVC)
⇒ Our results documented the
complexity of fungal and
bacterial communities in CF,
with potential interaction
between species (biofilm)
[Delhaes et al. 2012]
Lung mycobiota in CF: Results of the pilot study
17. ⇒ 36 sputum samples From patients with (18) and without (18)
pulmonary exacerbation were compared (clinical, radiological,
biological data – 40 variables per patient)
⇒ Microbial analysis is under process:
(i) using deep-sequencing fungal/bacterial analysis
(ii) using RT-PCR targeting RNA respiratory viruses
(iii) using q-PCR targeting DNA respiratory viruses
⇒ Mathematical approach under process
a first PCA (principal component analysis) taking into account
the whole set of variables (40 per patient) for analyzing
Mycobiota versus bacterial microbiota at the genus level - We
limited our analyses to the number of genera that were present
at least in 3 patients and the number of OTU present at 1%.
Lung mycobiota in CF: Relevance in CF
exacerbation
18. Lung mycobiota in CF: Relevance in CF
exacerbation
According to PCA graph:
Addition of the 2 axes = the
explained part of the variability →
33% [42% in Zemanick et al. 2013]
For each variable, arrow lengh
is proportional to the load of the
corresponding variable on the
first 2 principal components
(Dim/axes 1-2) (the longer the arrow
is = the more the axes explained the
variable)
Our model and axes explained a
lot of microorganisms
19. Lung mycobiota in CF: Relevance in CF
exacerbation
Key point to read a PCA graph:
Interpreting a correlation
between microorganisms as
follow
Right angle =
No correlation
Acute angle =
Positive correlation
180° angle =
Negative correlation
20. Lung mycobiota in CF: Relevance in CF
exacerbation
Pseudomonas
- is alone [Zemanick et al. 2013]
- not correlated with
“Malassezia plus Prevotella
group” [Zemanick et al 2013]
- neither with the “Candida
plus Rothia group” (which is
not well explained by our axes
since the arrows are short)
- but is negatively correlated
with the “group of oral flora
plus some environmental
fungi”, as well as FEV1 –
SK-score[Zemanick et al. 2013]
21. Lung mycobiota in CF: Relevance in CF
exacerbation Aspergillus
- Unfortunately, our PCA model
doesn’t explained this mold
Malassezia
- As some anaerobes, M. furfur and
M. sympodialis are difficult to
culture, both obligatory lipophilic,
and skin flora yeasts of humans
Classically, they are associated with
superficial infections of the skin
(pityriasis versicolor - folliculitis)
They appear
+ correlated
with
anaerobes in
agreement with
their lipophyly
(since anaerobes
ChromAgar
Malassezia
→ Integrate virus data
→ Continue mathematical analysis
22. ⇒ Muco-Bac-Myco: Ecology & dynamics of fungal and bacterial communities
of sputum samples from CF patients under antimicrobial treatment: A
French prospective study based on deep-sequencing
Lung mycobiota in CF: To conclude
Validation of mycobiota analysis based on ITS2 (ITS2DB)
→ Candida et A. fumigatus = Main species/genus
isolated [Charlson et al. 2012; Delhaes et al. 2012]
→ Role in the decrease of pulmonary function
→ Which place for fungi in CF exacerbation?
→ What is mycobiota evolution and role when
ATB treatment are managed? [Muco-Bac-Myco project]
- F Botterel & L Delhaes under process]
Mycobiota = dynamic event, part of the overall lung microbiome
23. Determining exhaustively the microbial community
composition in CF patient sputa.
Developing new approaches based on deep-sequencing,
(standardization)
Larger studies are now required to better understand CF
associated communities
Improving management/survival of CF patients
Development of ex vivo model biofilm to adapt drug
treatment (anti-bacterial/fungal)
Predict the efficiency of drug treatment
Lung mycobiota
Improving our knowledge of microbiome by
Lung mycobiota in CF: Perspectives
24. Institut Pasteur-Lille / Université de Lille 2
• Laurence Delhaes
• Eric Viscogliosi
• Eduardo Dei-Cas
• Anne Goffard
• Magali Chabé
Université Littoral Côte d’Opale
• Sébastien Monchy
• Christine Hubans / Stéphanie Ferreira
Faculté de Médecine de Lille
• Benoit Wallaert
• Anne Prévotat
• Julia Salleron
• Fréderic Wallet
• Rodrigues Dessein
• Sylvie Leroy
Société Genoscreen-Lille
Département de Microbiologie
AP-HP Créteil
•Françoise Botterel
•Odile Cabaret
•Jean-Winoc Decousser
•Jean-Philippe Barnier
Consortium Pegase
• Christophe Audebert / Romain Dassonneville
Requiring multidisciplinary approaches
(due to the massive data generated)
Acknowledgments
Editor's Notes
Good morning everyone.
1st, I would like to thank ESCF committee, Mister Moss and Mac Elvaney for giving this opportunity to share with you our data.
Microorganisms (bacteria, archaea, yeasts, moulds, viruses) are able to colonize all ecological systems, even extreme environments (such as tropical rain forest, desert or hypersaline water for which the concentration of bacteria ranged from the million to thousands of millions)
A majority of these microorganisms remains to be identified
Regarding fungi,
They are also present in various ecosystems (but poorly studied or analysed)
They are playing an important role in soil regeneration.
Fungi/molds (especially ascomycetes such as Aspergillus) have (along with bacteria) a key role in most land-based ecosystems – they are important decomposers, breaking down organic substances.
One million and a half represents the number of fungus species currently estimated for the entire world.
But only 6% have been identified
Microbes et environnement: grand intérêt+++
Microorganismes: impliqués dans de nombreux processus globaux
Microorganismes: Rôle fondamental en biotechnologie (ATB, fermentation, expression, biomatériaux)
the Ascomycota are heterotrophic organisms that require organic compounds as energy sources
ils ne peuvent pas, comme les plantes, synthétiser leur matière organique à partir du CO2 atmosphérique. Ils doivent donc puiser dans le milieu ambiant l’eau et les substances organiques et minérales nécessaires à leurs propres synthèses ; ils sont hétérotrophes (Kendrick 2001).
As other ecological systems mine, see, animal and soil, there is a microbial diversity of human organisms.
Especially a gut microbiota
La recherche sur le microbiome du poumon est un domaine relativement nouveau pouvant conduire à modifier notre vision des maladies respiratoires [1]. Les poumons des sujets en bonne santé ont longtemps été considérés comme stériles sur la base de données obtenues par les méthodes classiques, principalement fondées sur la culture bactérienne. De fait, le grand projet américain initié par le National Institute of Health (NIH) sur le microbiome humain n’incluait pas, jusqu’à récemment, les poumons comme un site de recherche [2]. Cependant, des données récemment publiées, basées sur des méthodes indépendantes des cultures bactériennes, ont démontré que les poumons de sujets sains non fumeurs étaient habitées par une population bactérienne, peu abondante mais diversifiée [3].
La fonction respiratoire est l’un des plus grands enjeux de demain en matière desanté publique: - Les troubles…
-la BPCO sera la 4ème
-la prévalence de l’asthme est en augmentation dans Pays développés (25 millions d’américains atteints asthme)
-la mucoviscidose, pathologie à laquelle nous nous intéressons plus particulièrement, est la maladie génétique la plus fréquente dans la population caucasienne. (1/3000 -4000 Nnés en France).
L’épaississement du mucus observé dans la mucoviscidose, a comme conséquence directe une accumulation (un piégeage) des microorganismes (bactérie champ) au niv pulmonaire, ce qui entrave fortement la fonction respiratoire, est responsable d’infection/ sur-infections pulmonaires (notamment les infections à Pseudomonas aeruginosa)
= cause majeure de mortalité dans la mucoviscidose
Au même titre que les sols, les océans (et autres milieux), il existe un microbiote de l’organisme humain: le plus étudié et documenté étant le microbiote intestinal . environ 100 000 milliards, soit au moins deux fois plus que le nombre moyen de cellules de l&apos;organisme
Mais de la même façon, il existe un microbiote cutané, vaginal, et biensur pulmonaire
A ce jour c’est essentiellement le microbiote bactérien qui est étudié
Rationnel: Aspergillus scedos : 2 plus frequent champ chez la muco
P jiroveci: portage très fréquent muco + BPCO - Portage Pj associé aux stades sévères (III, et IV) de BPCO: role dans la réponse inflammatoire ?; 2.5% d’API chez les patients atteints de BPCO avec une mortalité très élévée 70-95%: signifcation de la colonisation sensibilisation ?
We have genomes in our genome, bacteria are living in us (1 human being = 1 thousand million of bacteria).
… with a repartition depending on the sites .
But (As you guess) there were two missing elements :
One missing mucosa and tract: the lung microbiota which is now included in this project
And the fungal micobiota
Recently (about 2011-12), lungs have been included in the Human Microbiome NIH project as a site of microbiota analysis. But, exclusively bacterial microbiota analysis have been assessed
la majorité des bactéries humaines appartiennent à 4 grands embranchements, sur les cinquante connus. Il s&apos;agit des : Firmicutes (en bleu), Bacteroidetes (en rose), Actinobacteria (en vert) et Proteobacteria (en violet).
-Nov 2010
BIEN QU&apos;ENCORE TRÈS PRÉLIMINAIRE, l&apos;analyse du microbiote humain a déjà fourni plusieurs résultats marquants [1]. Comme on le voit sur le schéma ci-dessus, la majorité des bactéries humaines appartiennent à quatre grands embranchements, sur les cinquante connus. Il s&apos;agit des Firmicutes (en bleu), Bacteroidetes (en rose), Actinobacteria (en vert) et Proteobacteria (en violet). Leur abondance respective varie selon les organes considérés. Ainsi, le côlon abrite en majorité des Firmicutes et des Bacteroidetes, et il semble que cette caractéristique se retrouve chez tous les individus (même si les proportions relatives peuvent varier). Le vagin, lui, est essentiellement peuplé de Firmicutes chez une majorité de femmes (ci-dessus), mais chez une minorité, il abrite majoritairement des Actinobacteria.
- MÊME SI LES BACTÉRIES de notre microbiote appartiennent majoritairement à seulement 4 embranchements, elles n&apos;en sont pas moins très diverses. Cette diversité apparaît au niveau des espèces (ci-dessus, chiffres entre parenthèses), et plus encore au niveau des souches (non montré). Si l&apos;on compare les organes étudiés à ce jour, on constate, ainsi que l&apos;indique la taille de chaque diagramme, que le côlon possède la plus grande diversité : 195 espèces par individu en moyenne. Or on estime que 80 % des espèces bactériennes présentes chez un individu donné lui sont propres. À l&apos;échelle de la planète, la diversité de nos bactéries atteindrait donc plusieurs milliards d&apos;espèces...
La concentration dans un environnement intérieur sans contamination fongique est généralement en dessous de 103 spores/m3 d’air (OMS 2009).
La fonction respiratoire est l’un des plus grands enjeux de demain en matière desanté publique: - Les troubles…
-la BPCO sera la 4ème
-la prévalence de l’asthme est en augmentation dans Pays développés (25 millions d’américains atteints asthme)
-la mucoviscidose, pathologie à laquelle nous nous intéressons plus particulièrement, est la maladie génétique la plus fréquente dans la population caucasienne. (1/3000 -4000 Nnés en France).
L’épaississement du mucus observé dans la mucoviscidose, a comme conséquence directe une accumulation (un piégeage) des microorganismes (bactérie champ) au niv pulmonaire, ce qui entrave fortement la fonction respiratoire, est responsable d’infection/ sur-infections pulmonaires (notamment les infections à Pseudomonas aeruginosa)
= cause majeure de mortalité dans la mucoviscidose
Au même titre que les sols, les océans (et autres milieux), il existe un microbiote de l’organisme humain: le plus étudié et documenté étant le microbiote intestinal . environ 100 000 milliards, soit au moins deux fois plus que le nombre moyen de cellules de l&apos;organisme
Mais de la même façon, il existe un microbiote cutané, vaginal, et biensur pulmonaire
A ce jour c’est essentiellement le microbiote bactérien qui est étudié
Rationnel: Aspergillus scedos : 2 plus frequent champ chez la muco
P jiroveci: portage très fréquent muco + BPCO - Portage Pj associé aux stades sévères (III, et IV) de BPCO: role dans la réponse inflammatoire ?; 2.5% d’API chez les patients atteints de BPCO avec une mortalité très élévée 70-95%: signifcation de la colonisation sensibilisation ?
La fonction respiratoire est l’un des plus grands enjeux de demain en matière desanté publique: - Les troubles…
-la BPCO sera la 4ème
-la prévalence de l’asthme est en augmentation dans Pays développés (25 millions d’américains atteints asthme)
-la mucoviscidose, pathologie à laquelle nous nous intéressons plus particulièrement, est la maladie génétique la plus fréquente dans la population caucasienne. (1/3000 -4000 Nnés en France).
L’épaississement du mucus observé dans la mucoviscidose, a comme conséquence directe une accumulation (un piégeage) des microorganismes (bactérie champ) au niv pulmonaire, ce qui entrave fortement la fonction respiratoire, est responsable d’infection/ sur-infections pulmonaires (notamment les infections à Pseudomonas aeruginosa)
= cause majeure de mortalité dans la mucoviscidose
Au même titre que les sols, les océans (et autres milieux), il existe un microbiote de l’organisme humain: le plus étudié et documenté étant le microbiote intestinal . environ 100 000 milliards, soit au moins deux fois plus que le nombre moyen de cellules de l&apos;organisme
Mais de la même façon, il existe un microbiote cutané, vaginal, et biensur pulmonaire
A ce jour c’est essentiellement le microbiote bactérien qui est étudié
Rationnel: Aspergillus scedos : 2 plus frequent champ chez la muco
P jiroveci: portage très fréquent muco + BPCO - Portage Pj associé aux stades sévères (III, et IV) de BPCO: role dans la réponse inflammatoire ?; 2.5% d’API chez les patients atteints de BPCO avec une mortalité très élévée 70-95%: signifcation de la colonisation sensibilisation ?
Nous nous sommes attachés à déterminer la composition du microbiote fongique du patient atteint de muco, en prenant également en compte les bactéries,
Avec comme questions biologiques sous-jacentes (aux quelles nous avons essayé de répondre) :
-Le microbiote du patient atteint de muco est-il différent de celui du patient sain?
-Quelle est sa stabilité dans le temps?
-Est-il corrélé à l’état clinique/évolution du patient?
Et nous avons utilisé les outils qui nous semblaient les plus adaptés au contexte càd les approches DE SEQUENCAGE HAUT-DEBIT
Notre stratégie méthodologique était basée sur le pyroséq sur automate 454 (roche)
Je vais en donner les grandes étapes de cette méthodologie
Si vous souhaitez nous pourrons en reparler après.
-aà partir des expecto (8 de 4 patients adultes stables cliniquement), nous avons extrait l’AND total OU métagenome (kit Hight pure Kit – Roche)
-2 PCR ciblant l’ADN16 (V3) des bactéries et le locus ITS2 des champignons ont été réalisées (grâce à 2 couples d’amorces)
-Séquençage multi-parallélisé, obtention de plusieurs milliers de pyroséquences
Elles ont été identifiées par comparaisosn à 2 banques de données la banque SILVA en accès libre pour les seq de 16S et une banque spécifique des séquences ITS2 que nous avons créé et validé pour cette étude en collaboration avec Genoscreen à IPL
Après plusieurs étapes de bioinformatique, les pyroséquences sont groupées en fonction de leur identité puis attribuées à une espèce quand c’est possible ou sinon à un genre conformément aux données de nos 2 banques et selon les critères choisis.
Puis nous avons réalisé une analyse phylogénétique des différents taxons permettant de comparer les 2 échantillons d’un même patient = grâce au logiciel MEGAN,
- Pseudomonas reads were highly similar to P. aeruginosa strains isolated from CF patients or endotracheal tube biofilms.
Notre stratégie méthodologique était basée sur le pyroséq
Je vais en donner les grandes étapes de cette méthodologie
Si vous souhaitez nous pourrons en reparler après.
-a partir des expecto, nous avons extrait l’AND total
-2 PCR ciblant l’ADN16 des bacteries et le locus ITS2 des champignons ont été réalisées (grace à 2 couples d’amorces)
-Plusieurs milliers de pyroséquences ont été obtenus,
Elles ont été identifiées par comparaisosn à 2 banques de données la banque SILVA en accès libre pour les seq de 16S et une banque specifique des séquences ITS2 que nous avons créé et validé pour cette étude en collaboration avec Genoscreen à IPL
Après plusieurs étapes de bioinformatique, les pyroséquences sont groupées en fonction de leur identité puis attibuées à une espèce quand c’est possible ou sinon à un genre conformément aux données de nos 2 banques et selon les critères choisis.
Puis nous avons réalisé une analyse phylogénétique des differents taxons permettant de comparer les 2 échantillons d’un même patient,
(1/3000 Nnés en France)
(1/3000 Nnés en France)
Rationel
Aspergillus scedos : 2 plus frequent champ chez la muco
P jiroveci: portage très fréquent muco + BPCO
2.5% d’API chez les patients atteints de BPCO avec une mortalité très élévée 70-95%: siginifcation de la colonisation sensibilisation ?
Portage Pj associé aux stades sévères (III, et IV) de BPCO: role dans la réponse inflammatoire ?
(1/3000 Nnés en France)
(1/3000 Nnés en France)
Rationel
Aspergillus scedos : 2 plus frequent champ chez la muco
P jiroveci: portage très fréquent muco + BPCO
2.5% d’API chez les patients atteints de BPCO avec une mortalité très élévée 70-95%: siginifcation de la colonisation sensibilisation ?
Portage Pj associé aux stades sévères (III, et IV) de BPCO: role dans la réponse inflammatoire ?
(1/3000 Nnés en France)
(1/3000 Nnés en France)
Rationel
Aspergillus scedos : 2 plus frequent champ chez la muco
P jiroveci: portage très fréquent muco + BPCO
2.5% d’API chez les patients atteints de BPCO avec une mortalité très élévée 70-95%: siginifcation de la colonisation sensibilisation ?
Portage Pj associé aux stades sévères (III, et IV) de BPCO: role dans la réponse inflammatoire ?
(1/3000 Nnés en France)
(1/3000 Nnés en France)
Rationel
Aspergillus scedos : 2 plus frequent champ chez la muco
P jiroveci: portage très fréquent muco + BPCO
2.5% d’API chez les patients atteints de BPCO avec une mortalité très élévée 70-95%: siginifcation de la colonisation sensibilisation ?
Portage Pj associé aux stades sévères (III, et IV) de BPCO: role dans la réponse inflammatoire ?
At the physiology level,
Mucus composition in CF provides conditions suitable for chronic co-infection:
- Reduced oxygen tension in CF lung favourable for growth of P. aeruginosa, anaerobes (i.e. SMG members), C. albicans, and A. fumigatu
- All are known to be able to form biofilm consortia, and to produce direct and indirect microbe-microbe interactions including quorum-sensing phenomenon
Establishing microbiota in CF airways = dynamic event managed (we can supppose) to be beneficial to all members of the microbial population, probably with some “synergene” phenomenon
Principal component analysis (PCA) is a mathematical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components. The number of principal components is less than or equal to the number of original variables. This transformation is defined in such a way that the first principal component has the largest possible variance (that is, accounts for as much of the variability in the data as possible), and each succeeding component in turn has the highest variance possible under the constraint that it be orthogonal to (i.e., uncorrelated with) the preceding components. Principal components are guaranteed to be independent only if the data set is jointly normally distributed. PCA is sensitive to the relative scaling of the original variables.
The Addition of the 2 axes represents the explained part of the variance
Principal component analysis (PCA) is a mathematical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components. The number of principal components is less than or equal to the number of original variables. This transformation is defined in such a way that the first principal component has the largest possible variance (that is, accounts for as much of the variability in the data as possible), and each succeeding component in turn has the highest variance possible under the constraint that it be orthogonal to (i.e., uncorrelated with) the preceding components. Principal components are guaranteed to be independent only if the data set is jointly normally distributed. PCA is sensitive to the relative scaling of the original variables.
The Addition of the 2 axes represents the explained part of the variance
Principal component analysis (PCA) is a mathematical procedure that uses an orthogonal transformation to convert a set of observations of possibly correlated variables into a set of values of linearly uncorrelated variables called principal components. The number of principal components is less than or equal to the number of original variables. This transformation is defined in such a way that the first principal component has the largest possible variance (that is, accounts for as much of the variability in the data as possible), and each succeeding component in turn has the highest variance possible under the constraint that it be orthogonal to (i.e., uncorrelated with) the preceding components. Principal components are guaranteed to be independent only if the data set is jointly normally distributed. PCA is sensitive to the relative scaling of the original variables.
Kappamyces is a new genus for a chytrid member of the Rhizophydium clade is described
zoospore in the Chytridiales
Granulicatella species, along with the genus Abiotrophia, were originally known as ‘nutritionally variant streptococci’. They are a normal component of the oral flora, but have been associated with a variety of invasive infections in man and are most noted as a cause of bacterial endocarditis. It is often advised that Granulicatella endocarditis should be treated in the same way as enterococcal endocarditis.
Atopobium= Anearobie bacteria, involved in vaginosis. This inability to prevent recurrences reflects our lack of knowledge on the origins of BV. Atopobium vaginae has been recently reported to be associated with BV
Gemella bacteria are primarily found in the mucous membranes of humans and other animals, particularly in the oral cavity and upper digestive tract.
Definition of NECTRIACEAE. : a family of ascomycetous fungi (order Hypocreales) that are close to fusarium and currently environmental /phytopathogen
Capnocytophaga is a genus of Gram-negative bacteria. Normally found in the oropharyngeal tract of mammals, they are involved in the pathogenesis of some animal bite wounds as well as periodontal diseases.[1]
OW: raisonnable mais pas parfait
(tobramycine n’impacterait pas la diversité)
Pour conclure, cette étude est modeste : 8 echantillons mais à mon sens très prometteuse elle a clairement mis en évidence une correlation entre la diversité du microbiote et le statut du patient en utilisant le séquençage haut-débit et les outils de bioinfo correspondant(elle vient d’être publiée)
Sur le plan physiopathologique, dans la mucoviscidose, la composition du mucus représente des conditions favorables au développement des co-infection / co-colinisation
Il a été montré que
La réduction de tension en oxygène (observée dans la muco) favorise la croissance de …
De plus tous ces microorganismes sont capables de former des biofilms avec de potentielles interactions intra mais aussi inter-spécifiques
La formation du microbiote est donc un évement dynamique,
pour mieux le comprendre, il nous faut maintenant
(1/3000 Nnés en France)
(1/3000 Nnés en France)
Rationel
Aspergillus scedos : 2 plus frequent champ chez la muco
P jiroveci: portage très fréquent muco + BPCO
2.5% d’API chez les patients atteints de BPCO avec une mortalité très élévée 70-95%: siginifcation de la colonisation sensibilisation ?
Portage Pj associé aux stades sévères (III, et IV) de BPCO: role dans la réponse inflammatoire ?
(1/3000 Nnés en France)
(1/3000 Nnés en France)
Rationel
Aspergillus scedos : 2 plus frequent champ chez la muco
P jiroveci: portage très fréquent muco + BPCO
2.5% d’API chez les patients atteints de BPCO avec une mortalité très élévée 70-95%: siginifcation de la colonisation sensibilisation ?
Portage Pj associé aux stades sévères (III, et IV) de BPCO: role dans la réponse inflammatoire ?