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.
Microbiology has experienced a transformation during the last 25 years that has altered microbiologists' view of microorganisms and how to study them. The realization that most microorganisms cannot be grown readily in pure culture forced microbiologists to question their belief that the microbial world had been conquered. We were forced to replace this belief with an acknowledgment of the extent of our ignorance about the range of metabolic and organismal diversity.
Metagenomics research is a vast field which studies about the genetic system of the
environmental samples. Binning is a bioinformatics tool. Binning tool helps to analyses the
genomic analysis of the environmental samples.The
Microbiology has experienced a transformation during the last 25 years that has altered microbiologists' view of microorganisms and how to study them. The realization that most microorganisms cannot be grown readily in pure culture forced microbiologists to question their belief that the microbial world had been conquered. We were forced to replace this belief with an acknowledgment of the extent of our ignorance about the range of metabolic and organismal diversity.
Metagenomics research is a vast field which studies about the genetic system of the
environmental samples. Binning is a bioinformatics tool. Binning tool helps to analyses the
genomic analysis of the environmental samples.The
Targeted RNA Sequencing, Urban Metagenomics, and Astronaut GenomicsQIAGEN
Dr. Chris Mason’s presentation will cover the QIAseq Targeted RNA Panel beta testing, Qiagen’s Sample-to-Insight solution for Metagenomics sequencing as demonstrated in the Metasub project, as well as Chris latest endeavor the, “Twins Study”, which will be a comprehensive genomic study of the impact of spaceflight on the human body. Astronaut Scott Kelly will be studied during the course of his year-long stay at the ISS as will his twin brother, Mark Kelly, a former NASA astronaut who will remain on earth.
http://www.npr.org/sections/thetwo-way/2015/03/27/395536140/nasa-to-study-a-twin-in-space-and-his-brother-on-earth
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
Metagenomics as a tool for biodiversity and healthAlberto Dávila
A talk on the applications of metagenomics for the study of biodiversity and health, presented during the inaugural symposium of the Peruvian Society of Biochemistry and Molecular Biology. Lima, March 2018
Molecular pathology in microbiology and metagenomicsCharithRanatunga
INTRODUCTION
HISTORY
Steps
Analysis
Metagenomic Process
Sequence-based analysis
Function-based analysis
Application of metagenomics
Future Directions of metagenomics
Examples for metagenomics projects
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
Metagenomics is the study of genetic material recovered directly from environmental samples. Metagenomics is a molecular tool used to analyse DNA acquired from environmental samples, in order to study the community of microorganisms present, without the necessity of obtaining pure cultures.
Metagenomics is the study of a collection of genetic material (genomes) from a mixed community of organisms. Metagenomics usually refers to the study of microbial communities.
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICSLubna MRL
After billions of years of evolution, prokaryotes have developed a huge diversity of regulatory mechanisms, many of which are probably uncharacterized. Now that the powerful tool of whole-transcriptome analysis can be used to study the RNA of bacteria and archaea, a new set of un expected RNA-based regulatory strategies might be revealed.
Metagenomics, together with in vitro evolution and high-throughput screening technologies, provides industry with an unprecedented chance to bring biomolecules into industrial application.
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.
Targeted RNA Sequencing, Urban Metagenomics, and Astronaut GenomicsQIAGEN
Dr. Chris Mason’s presentation will cover the QIAseq Targeted RNA Panel beta testing, Qiagen’s Sample-to-Insight solution for Metagenomics sequencing as demonstrated in the Metasub project, as well as Chris latest endeavor the, “Twins Study”, which will be a comprehensive genomic study of the impact of spaceflight on the human body. Astronaut Scott Kelly will be studied during the course of his year-long stay at the ISS as will his twin brother, Mark Kelly, a former NASA astronaut who will remain on earth.
http://www.npr.org/sections/thetwo-way/2015/03/27/395536140/nasa-to-study-a-twin-in-space-and-his-brother-on-earth
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
Metagenomics as a tool for biodiversity and healthAlberto Dávila
A talk on the applications of metagenomics for the study of biodiversity and health, presented during the inaugural symposium of the Peruvian Society of Biochemistry and Molecular Biology. Lima, March 2018
Molecular pathology in microbiology and metagenomicsCharithRanatunga
INTRODUCTION
HISTORY
Steps
Analysis
Metagenomic Process
Sequence-based analysis
Function-based analysis
Application of metagenomics
Future Directions of metagenomics
Examples for metagenomics projects
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
Metagenomics is the study of genetic material recovered directly from environmental samples. Metagenomics is a molecular tool used to analyse DNA acquired from environmental samples, in order to study the community of microorganisms present, without the necessity of obtaining pure cultures.
Metagenomics is the study of a collection of genetic material (genomes) from a mixed community of organisms. Metagenomics usually refers to the study of microbial communities.
PROKARYOTIC TRANSCRIPTOMICS AND METAGENOMICSLubna MRL
After billions of years of evolution, prokaryotes have developed a huge diversity of regulatory mechanisms, many of which are probably uncharacterized. Now that the powerful tool of whole-transcriptome analysis can be used to study the RNA of bacteria and archaea, a new set of un expected RNA-based regulatory strategies might be revealed.
Metagenomics, together with in vitro evolution and high-throughput screening technologies, provides industry with an unprecedented chance to bring biomolecules into industrial application.
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.
Course: Bioinformatics for Biologiacl Researchers (2014).
Session: 3.1- Introduction to Metagenomics. Applications, Approaches and Tools.
Statistics and Bioinformatisc Unit (UEB) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.
QIAseq Technologies for Metagenomics and Microbiome NGS Library PrepQIAGEN
In this slide deck, learn about the innovative technologies that form the basis of QIAGEN’s portfolio of QIAseq library prep solutions for metagenomics and microbiome sequencing. Whether your research starts from single microbial cells, 16s rRNA PCR amplicons, or gDNA for whole genome analysis, QIAseq technologies offer tips and tricks for capturing the genomic diversity of your samples in the most unbiased, streamlined way possible.
VHIR Seminar led by Joel Doré. Research Director. Institut National de la Recherche Agronomique (INRA). Jouy-en-Josas, France.
Abstract: The human intestinal tract harbours a complex microbial ecosystem which plays a key role in nutrition and health. Interactions between food constituents, microbes and the host organism derive from a long co-evolution that resulted in a mutualistic association.
Current investigations into the human faecal metagenome are delivering an extensive gene repertoire representative of functional potentials of the human intestinal microbiota. The most redundant genomic traits of the human intestinal microbiota are identified and thereby its functional balance. These observation point towards the existence of enterotypes, i.e. microbiota sharing specific traits but yet independent of geographic origin, age, sex etc.. It also shows a unique segregation of the human population into individuals with low versus high gene-counts. In the end, it not only gives an unprecedented view of the intestinal microbiota, but it also significantly expands our ability to look for specificities of the microbiota associated with human diseases and to ultimately validate microbial signatures of prognostic and diagnostic value in immune mediated diseases.
Metagenomics of the human intestinal tract was applied to specifically compare obese versus lean individuals as well as to explore the dynamic changes associated with a severe calory-restricted diet. Microbiota structure differs with body-mass index and a limited set of marker species may be used as diagnostic model with a >85% predictive value. Among obese subjects; the overall phenotypic characteristics are worse in individuals with low gene counts microbiota, including a worse evolution of morphometric parameters over a period of 10 years, a low grade inflammatory context also associated with insulin-resistance, and the worst response to dietary constraints in terms of weight loss or improvement of biological and inflammatory characteristics. Low gene count microbiota is also associated with less favourable conditions in inflammatory bowel disease, such as higher relapse rate in ulcerative colitis patients.
Finally, microbiota transplantation has seen a regain of interest with applications expanding from Clostridium difficile infections to immune mediated and metabolic diseases.
The human intestinal microbiota should hence be regarded as a true organ, amenable to rationally designed modulation for human health.
Tools for Metagenomics with 16S/ITS and Whole Genome Shotgun SequencesSurya Saha
Presented at Cornell Symbiosis symposium. Workflow for processing amplicon based 16S/ITS sequences as well as whole genome shotgun sequences are described. Slides include short description and links for each tool.
DISCLAIMER: This is a small subset of tools out there. No disrespect to methods not mentioned.
Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research...Larry Smarr
06.06.27
Invited Talk
ONR Review
Scripps Institution of Oceanography, UCSD
Title: Creating a Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA)—Taking Metagenomics to Light Speed
La Jolla, CA
Hervé Blottiere-El impacto de las ciencias ómicas en la medicina, la nutrició...Fundación Ramón Areces
El 29 de marzo de 2016 celebramos un Simposio Internacional sobre el 'Impacto de las ciencias ómicas en la medicina, nutrición y biotecnología'. Organizado por la Fundación Ramón Areces en colaboración con la Real Academia Nacional de Medicina y BioEuroLatina, abordó cómo un mejor conocimiento del genoma humano está permitiendo notables avances hacia una medicina de precisión.
Human nutrition, gut microbiome and immune system S'eclairer
Dr Zahida Chaudnary talks with the students about nutrition, gut microbiomes, and nutrition as we look at diseases and how your body reacts to what you eat.
Check out the slideshow by itself here.
Want an audio version? Subscribe to our Podcast on iTunes!
Want to join us for the live discussion? Check out our Social Media in the noon hour every Monday as we sit down on Google Hangout OnAir! Follow us on Twitter, Facebook, or Google+ to get updated with the link when we start!
Single Cell Insights: Studying Environmental Microbial Communities Cell by CellQIAGEN
Dissecting complex microbial communities has incredible potential in the quest to decipher the world around us and find new sources of enzymes, antibiotics and other drugs. The challenge that remains is how to gain a deeper understanding of the roles and interactions of individual microbes. Single cell sequencing has emerged as an innovative investigational approach that provides a view of the cell-by-cell community by separating out individual microbes prior to sequencing. This issue of Single Cell Insights reviews peer-reviewed journal articles that describe applications and methodologies for single cell sequencing of environmental microbial communities.
A brief introduction to amplicon sequencing of the 16S rRNA gene for the analysis of microbial diversity. This talk was presented originally at the Workshop: Introduction to Systems Biology, Aalborg Denmark. 2013-10-29
Sample Prep Solutions for Microbiome ResearchQIAGEN
An accurate molecular analysis of the microbial constituents of a particular community is contingent upon high-yielding and non-biased nucleic acid extraction methodologies. Only by ensuring that all species and classes of microorganisms present in a sample are effectively lysed during extraction will one be able to reliably assess the composition of that sample. An additional challenge faced in nucleic acid extraction is the presence of persistent, co-purifying polymerase inhibitors endogenous to one’s sample. This presentation will focus on nucleic acid extraction tools developed by MO BIO Laboratories that facilitate accurate non-biased community analysis and eliminate common amplification problems via the depletion of endogenous polymerase inhibitors using our patented Inhibitor Removal Technology.
The benefits of environment specific curation of the public databases for tax...Aaron Marc Saunders
A presentation from the Workshop: Principles, potential, and limitations of novel molecular methods in water engineering; from amplicon sequencing to omics methods. Held at the Microbial Ecology and Water Engineering 2013 (MEWE 2013) July 7 – 10, 2013.
El lunes 23 de octubre de 2017 celebramos una jornada en la Fundación Ramón Areces sobre Microbiota Intestinal: Implicaciones en la Salud y Enfermedad.
In this short presentation I highlight the major advantages of using modern Amplicon Sequencing Variants (ASVs) instead of the traditional Operational Taxonomic Units (OTUs) for 16S rRNA amplicon sequencing data analysis. Please keep in mind that the slides are only a supplement to the talk and does not include all important aspects itself.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
UiPath Test Automation using UiPath Test Suite series, part 4DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 4. In this session, we will cover Test Manager overview along with SAP heatmap.
The UiPath Test Manager overview with SAP heatmap webinar offers a concise yet comprehensive exploration of the role of a Test Manager within SAP environments, coupled with the utilization of heatmaps for effective testing strategies.
Participants will gain insights into the responsibilities, challenges, and best practices associated with test management in SAP projects. Additionally, the webinar delves into the significance of heatmaps as a visual aid for identifying testing priorities, areas of risk, and resource allocation within SAP landscapes. Through this session, attendees can expect to enhance their understanding of test management principles while learning practical approaches to optimize testing processes in SAP environments using heatmap visualization techniques
What will you get from this session?
1. Insights into SAP testing best practices
2. Heatmap utilization for testing
3. Optimization of testing processes
4. Demo
Topics covered:
Execution from the test manager
Orchestrator execution result
Defect reporting
SAP heatmap example with demo
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
Slack (or Teams) Automation for Bonterra Impact Management (fka Social Soluti...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on the notifications, alerts, and approval requests using Slack for Bonterra Impact Management. The solutions covered in this webinar can also be deployed for Microsoft Teams.
Interested in deploying notification automations for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
As AI technology is pushing into IT I was wondering myself, as an “infrastructure container kubernetes guy”, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefit’s both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Software Delivery At the Speed of AI: Inflectra Invests In AI-Powered QualityInflectra
In this insightful webinar, Inflectra explores how artificial intelligence (AI) is transforming software development and testing. Discover how AI-powered tools are revolutionizing every stage of the software development lifecycle (SDLC), from design and prototyping to testing, deployment, and monitoring.
Learn about:
• The Future of Testing: How AI is shifting testing towards verification, analysis, and higher-level skills, while reducing repetitive tasks.
• Test Automation: How AI-powered test case generation, optimization, and self-healing tests are making testing more efficient and effective.
• Visual Testing: Explore the emerging capabilities of AI in visual testing and how it's set to revolutionize UI verification.
• Inflectra's AI Solutions: See demonstrations of Inflectra's cutting-edge AI tools like the ChatGPT plugin and Azure Open AI platform, designed to streamline your testing process.
Whether you're a developer, tester, or QA professional, this webinar will give you valuable insights into how AI is shaping the future of software delivery.
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Here’s what you’ll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
- Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy.
- Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency.
- Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity.
We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
Encryption in Microsoft 365 - ExpertsLive Netherlands 2024Albert Hoitingh
In this session I delve into the encryption technology used in Microsoft 365 and Microsoft Purview. Including the concepts of Customer Key and Double Key Encryption.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
Elevating Tactical DDD Patterns Through Object CalisthenicsDorra BARTAGUIZ
After immersing yourself in the blue book and its red counterpart, attending DDD-focused conferences, and applying tactical patterns, you're left with a crucial question: How do I ensure my design is effective? Tactical patterns within Domain-Driven Design (DDD) serve as guiding principles for creating clear and manageable domain models. However, achieving success with these patterns requires additional guidance. Interestingly, we've observed that a set of constraints initially designed for training purposes remarkably aligns with effective pattern implementation, offering a more ‘mechanical’ approach. Let's explore together how Object Calisthenics can elevate the design of your tactical DDD patterns, offering concrete help for those venturing into DDD for the first time!
UiPath Test Automation using UiPath Test Suite series, part 3DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 3. In this session, we will cover desktop automation along with UI automation.
Topics covered:
UI automation Introduction,
UI automation Sample
Desktop automation flow
Pradeep Chinnala, Senior Consultant Automation Developer @WonderBotz and UiPath MVP
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
4. Introduction
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Metagenome = Parts list of the community
Photo: D. Kunkel; color, E. Latypova
5. Introduction
”...functional analysis of the collective genomes of soil
microflora, which we term the metagenome of the soil.”
- J. Handelsman et al., 1998
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
7. Introduction
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
”...functional analysis of the collective genomes of soil
microflora, which we term the metagenome of the soil.”
- J. Handelsman et al., 1998
PubMed: metagenom*[Title/Abstract]
Sequencing costs
http://www.genome.gov/sequencingcosts/
11. What have metagenomics been used for?
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Rusch et al., 2007 Plos Biology
Exploration
Qin et al., 2010 Nature
• 6.3 Gbp of sequence (2x Human genomes,
2000 x Bacterial genomes)
• Most sequences were novel compared to
the databases
• 127 Human gut metagenomes
• 600 Gbp sequence (200 x Human genomes)
• 3.3 million genes identified
• Minimal gut metagenome definded
12. What have metagenomics been used for?
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
• A characteristic microbial fingerprint for
each of the nine different ecosystem types
Dinsdale et al., 2008 Nature
Comparative Specific functions
Hess et al., 2011 Science
• Identified 27.755 putative carbohydrate-active
genes from a cow rumen metagenome
• Expressed 90 candidates of which 57% had
enzymatic activity against cellulosic substrates
13. What have metagenomics been used for?
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
• Genome extraction from low complexity
metagenome
• Candidatus Accumulibacter phosphatis
• The first genome of a polyphosphate
accumulating organism (PAO) with a major
role en enhanced biological phosphorus
removal
Extracting genomes
• Genome extraction of low abundant species
(< 0.1%) from metagenomes
• First complete TM7 genome
• Access to genomes of the ”uncultured
majority”
Garcia Martin et al., 2006 Nat. Biotechnol. Albertsen et al., 2013 Nat. Biotechnol.
21. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Pitfalls
Is your DNA extraction OK?
... and the samples you want to compare with?
Did you sequence enough?
Did you know the GC bias of your protocol?
Did you normalize for sequencing depth?
Did you use the same sequencing platform?
Assembly = data not quantitative!
Are you comparing assembled data with reads?
22. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Databases
Contigs
Databases
...you only see what is in the database
Annotated metagenome
23. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
What is in the databases?
Phyla
Class
Order
Species
29
46
100
1268
90
249
405
99322
Genomes 16S
Finshed Genomes in IMG
Vs.
Greengenes 16S rRNA database
Note: only including 1 strain pr. species
*97% clustering
*
24. MG-RAST example
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Contigs
650.000 EBPR proteins with taxonomy assigned
How similar are they to the
genomes in the database?
25. Sludge microbes vs. Database genomes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
650.000 EBPR proteins
Note: not abundance weighted
26. Sludge microbes vs. Database genomes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
650.000 EBPR proteins
1.260.000 Human gut
Qin et al., 2010 Nature
RAST ID: 4448044.3
Note: not abundance weighted
27. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Sludge microbes vs. Database genomes
The 7 genera with most EBPR proteins assigned
28. Effect of missing genomes
What is the effect of not having closely related
genomes in the database?
1. Remove a genome from the database
2. Search the removed genome against the database
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
29. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Effect of missing genomes
Best hit
Bacteria 1268
Proteobacteria 564
Betaproteobacteria 84
Rhodocyclales 5
Rhodocyclaceae 5
Accumulibacter phosphatis
blastp
Related genomes
4326 proteins
30. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Effect of missing genomes
Best hit
Accumulibacter phosphatis
blastp
Related genomes
4326 proteins
Azoarcus
Bacteria 1268
Proteobacteria 564
Betaproteobacteria 84
Rhodocyclales 5
Rhodocyclaceae 5
31. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Effect of missing genomes
MEGAN LCA
Accumulibacter phosphatis
blastp
Lowest common ancester (LCA) approach:
Hit 1: Beta-proteobacteria 80% ID
Hit 2: Gamma-proteobacteria 79% ID
Hit 3: Actinobacteria 59% ID
Assigned to Proteobacteria
Related genomes
4326 proteins
Bacteria 1268
Proteobacteria 564
Betaproteobacteria 84
Rhodocyclales 5
Rhodocyclaceae 5
32. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Effect of missing genomes
MEGAN LCA
Accumulibacter phosphatis
blastp
Genus
No hits 261
Bacteria 325
Proteobacteria 860
Beta- 853
Rhodocyclaceae 1149
4326 proteins:
• 27% correctly
classified on
genus level
• 54% not
assigned the
correct class
• 101 genera
identified
Related genomes
Lowest common ancester (LCA) approach:
Hit 1: Beta-proteobacteria 80% ID
Hit 2: Gamma-proteobacteria 79% ID
Hit 3: Actinobacteria 59% ID
Assigned to Proteobacteria
4326 proteins
Bacteria 1268
Proteobacteria 564
Betaproteobacteria 84
Rhodocyclales 5
Rhodocyclaceae 5
33. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Effect of missing genomes
MEGAN LCA
Nitrospira defluvii
Bacteria 1268
Nitrospirae 3
blastp
Related genomes
4268 proteins:
• 1% correctly
classified on
phylum level
Phylum
34. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Effect of missing genomes
MEGAN LCA
+
KEGG
Nitrospira defluvii
blastp
Related genomes
Bacteria 1268
Nitrospirae 3
What about function?
35. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Effect of missing genomes
MEGAN LCA
+
KEGG
Nitrospira defluvii
blastp
Related genomes
Bacteria 1268
Nitrospirae 3
36. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Effect of missing genomes
Nitrospira defluvii
blastp
Related genomes
MEGAN LCA
+
KEGG
Bacteria 1268
Nitrospirae 3
37. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Implication of missing genomes
Function A
Function B
Function C
Function D
40. Potentials
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
1. Hunting novel antibiotic resistance genes
2. Extracting genomes from metagenomes
41. Hunting novel antibiotic resistance genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
What if you want to find
something that is not in the
database?
42. Hunting novel antibiotic resistance genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Functional metagenomics
M. Sommer, DTU, Denmark (in prep)
43. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Hunting novel antibiotic resistance genes
89 different antibiotic
resistance genes
19 novel
M. Sommer, DTU, Denmark (in prep)
44. Hunting novel antibiotic resistance genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
How abundant are the
antibiotic genes in the
environment?
45. Hunting novel antibiotic resistance genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
The number of
metagenome reads
reflect the abundance of
the bacteria.
Bacteria Reads
46. Hunting novel antibiotic resistance genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Bacteria Reads
47. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Hunting novel antibiotic resistance genes
Bacteria Reads
48. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Hunting novel antibiotic resistance genes
Metagenomes
Antibioticgenes
89 different antibiotic
resistance genes
M. Sommer, DTU, Denmark (in prep)
50. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
≈3.000.000 bp
pr. genome
≈1000 bp+
contigs
150 bp reads
Why not full
genomes?
Extracting genomes
51. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
≈3.000.000 bp
pr. genome
≈1000 bp+
contigs
150 bp reads
Why not full
genomes?
1. Micro-diversity
2. Separation of genomes (Binning)
Extracting genomes
52. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Not 1 strain
Many closely related strains
AAAAAAAAAAAAAA
AAAAAAAAATAAAA
AAAAAAAAACAAAA
AAAAAAAAA
TAAAA
CAAAA
What you get
AAAAA
Assembly
Extracting genomes
53. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Extracting genomes
Metagenome assembly
is not quantitative!
54. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Reduce microdiversity
Low micro-diversityHigh micro-diversity
Short term
enrichment
55. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
≈3.000.000 bp
pr. genome
≈1000 bp+
contigs
150 bp reads
Why not full
genomes?
1. Micro-diversity
2. Separation of genomes (Binning)
Extracting genomes
56. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Binning
Genomic signatures:
- GC / Codon usage
- Tetranucleotide frequency + statistical method
Complex sample
PhD student
”Binning”
57. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Binning
Genomic signatures:
- GC / Codon usage
- Tetranucleotide frequency + statistical method
Complex sample
PhD student
”Binning”
Problems:
- Short pieces of sequence (1-10kbp)
- Local sequence divergence
60. 1. Reduce micro-diversity
2. Use multiple related samples
Abundance Sample 1
AbundanceSample2
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Binning
61. 1. Reduce micro-diversity
2. Use multiple related samples
Abundance Sample 1
AbundanceSample2
Abundance Sample 1
AbundanceSample2
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Binning
62. Simple reactors
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYH. Daims & C. Dorninger, DOME, University of Vienna
• Nitrospira enrichment
running for years
• 3 dominant species
• No micro-diversity
63. Short term
enrichment
Full-scale EBPR plant
SBR reactor
Days 1. Reduction of (micro)-diversity
Competibacter
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
64. Short term
enrichment
Full-scale EBPR plant
SBR reactor
2. Two
different
DNA
extraction
methods
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
65. Colored using a set of 100 phylogenetic marker genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
66. Colored using a set of 100 phylogenetic marker genes
TM7-1 (1.6%)
TM7-2 (0.7%)
TM7-3 (0.2%)
TM7-4 (0.06%)
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
67. Zoom on target
TM7-2 (0.7%)
Colored using a set of 100 phylogenetic marker genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
68. Zoom on target
PC2
PC1
TM7-2
PCA on genomic
signatures
TM7-2 (0.7%)
Colored using a set of 100 phylogenetic marker genes
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
69. Colored using a set of 100 phylogenetic marker genes
TM7-1 (1.6%)
Candidate phylum TM7
Saccharibacteria
Candidatus Saccharimonas aalborgensis
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
71. Genome assembly validation
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
Phyla
Genes (HMM model)
Essential single copy genesAssembly inspection
72. Multi-metagenome
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITYAlbertsen et al., 2013 Nat. Biotech.
http://madsalbertsen.github.io/multi-metagenome/
Short: goo.gl/0ctA3
• Guides
• Workflow scripts
• Example data
• All the code
• Reccomendations
74. Potentials
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Metabolites
Proteins
mRNA
DNA
Meta-bolomics
Meta-proteomics
Meta-transcriptomics
Meta-genomics
In Situ methods
Community structure Microbial functions
Extraction
P-Removal:
N-Removal:
-Removal:
Foaming:
Ethanol production:
Microbial needs
75. Recommendations
• Do you really need metagenomics?
• Are the databases usefull in your environment?
• Unless human related they are not...
• Metagenomics is just the parts list
... of the DNA that could be extracted
... and the functions that could be annotated
• Validation, validation validation!
• Bioinformatic
• In situ
• Genome extraction from simple reactors is possible
• Enables comprehensive transcriptomics
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY