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Karoline Faust,
Sam Röttjers,
and
Anna Krzynowek
Microorganisms play a major role in the biosphere and within our bodies, but only a tiny fraction has been cultured so far. Microbiome data, that is the genetic information of microorganisms, is therefore an important window into the hidden microbial world.
Microbiome data analysis elucidates the composition of microbial communities and how it changes in response to the environment. When analyzing sequencing data, we learn whether microbial diversity differs across conditions and identify links between microbes. In brief, microbiome data analysis gives us a first idea of how a microbial ecosystem works.
Read more
Microorganisms play a major role in the biosphere and within our bodies, but only a tiny fraction has been cultured so far. Microbiome data, that is the genetic information of microorganisms, is therefore an important window into the hidden microbial world.
Microbiome data analysis elucidates the composition of microbial communities and how it changes in response to the environment. When analyzing sequencing data, we learn whether microbial diversity differs across conditions and identify links between microbes. In brief, microbiome data analysis gives us a first idea of how a microbial ecosystem works.
Read more
Microorganisms play a major role in the biosphere and within our bodies, but only a tiny fraction has been cultured so far. Microbiome data, that is the genetic information of microorganisms, is therefore an important window into the hidden microbial world.
Microbiome data analysis elucidates the composition of microbial communities and how it changes in response to the environment. When analyzing sequencing data, we learn whether microbial diversity differs across conditions and identify links between microbes. In brief, microbiome data analysis gives us a first idea of how a microbial ecosystem works.
This course will illustrate with the help of real-world example data how to carry out typical analysis tasks, such as comparing microbial composition and diversity, clustering samples and computing associations. If you plan to work with microbiome data, this course will get you up to speed.
The instructors are experienced bioinformaticians who are internationally known for their analysis of large-scale microbiome data sets.
Register for this course and see more details by visiting:
OpenCourser.com/course/nxeya7/how
What's inside
Learning objectives
- How and why microbiome data are collected
- How to extract species and function counts from sequencing data
- The definitions of richness, evenness and diversity
- How to compare diversity and microbial composition across conditions
- How to compute and interpret taxon and function associations
- How and why microbiome data are collected
- How to extract species and function counts from sequencing data
- The definitions of richness, evenness and diversity
- How to compare diversity and microbial composition across conditions
- How to compute and interpret taxon and function associations
Syllabus
Module 0: Introduction Study guide, R basics and a help forum for programming questions
Module 1: Introduction to microbiome data Sequencing techniques, data types (16S, WGS, metadata), example applications
Read more
Syllabus
Module 0: Introduction Study guide, R basics and a help forum for programming questions
Module 1: Introduction to microbiome data Sequencing techniques, data types (16S, WGS, metadata), example applications
Read more
Module 2: From sequences to counts Quality control of reads, taxonomic and functional assignment
Module 3: Comparing microbiomes Relative versus absolute abundance, taxonomic and functional richness, evenness and diversity
Module 4: Ordination Dimension reduction: arranging samples according to their taxonomic and functional composition in two-dimensional space
Module 5: Taxon/function associations Network construction: computing and interpreting associations between taxa and functions
Module 6: Your favourite microbiome Databases and journals for microbiome data and guidelines for doing your own analysis
Module 7: Final exam Complete the course by passing the quiz or by completing a microbiome analysis
Good to know
Good to know
Know what's good ,
what to watch for , and
possible dealbreakers
Explores microbiome analysis using real-world example data
Taught by experts in microbiome data analysis
Suitable for individuals interested in working with microbiome data
Covers the basics of microbiome analysis, making it suitable for beginners
Provides a comprehensive overview of microbiome data analysis techniques
Assumes prior knowledge in basic programming
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Activities
Be better prepared
before
your course. Deepen your understanding
during
and
after
it. Supplement your coursework and achieve mastery of the topics covered
in How to analyze a microbiome with these
activities:
Gather and organize course resources
Show steps
Organize your notes, assignments, quizzes, and exams to improve your retention and understanding of the course material.
Show steps
-
Collect and organize all course-related materials
-
Create a system for easy access and retrieval
-
Review and revise the materials regularly
Explore microbiome analysis tools
Show steps
Follow online tutorials to familiarize yourself with bioinformatics tools and software packages commonly used for microbiome analysis, such as QIIME and R.
Show steps
-
Identify the most suitable tools for your analysis задачи
-
Complete tutorials and exercises provided by the tool developers
-
Apply the tools to practice data analysis on real-world microbiome datasets
Visualize microbial diversity
Show steps
Create visualizations that illustrate the diversity of microbes in different environments, helping you understand the patterns and relationships within microbial communities.
Browse courses on
Microbial Diversity
Show steps
-
Gather microbiome data from public databases
-
Use bioinformatics tools to analyze and visualize the data
-
Create graphs and charts to represent microbial diversity
Three other activities
Expand to see all activities and additional details
Show all six activities
Compare microbiome compositions
Show steps
Practice comparing the composition of microbial communities across different samples, using statistical and machine learning techniques to identify significant differences.
Show steps
-
Obtain microbiome data from different environments or conditions
-
Perform statistical tests to compare microbial abundance
-
Use machine learning algorithms to classify and group samples based on their microbial composition
Develop a microbiome analysis pipeline
Show steps
Create a computational pipeline using Python or other programming languages to automate the analysis of microbiome data, making your workflow more efficient and reproducible.
Browse courses on
Data Analysis
Show steps
-
Design the pipeline architecture and workflow
-
Implement data preprocessing, analysis, and visualization modules
-
Test and optimize the pipeline's performance
-
Document the pipeline and make it available to others
Build a microbiome data repository
Show steps
Contribute to the field by compiling and organizing a comprehensive data repository of microbiome data, metadata, and analysis tools, making it easier for researchers to access and utilize.
Browse courses on
Data Curation
Show steps
-
Identify and collect microbiome data from various sources
-
Standardize and annotate the data with relevant metadata
-
Develop a user-friendly interface for data exploration and retrieval
-
Promote the repository and encourage contributions from the community
Gather and organize course resources
Show steps
Organize your notes, assignments, quizzes, and exams to improve your retention and understanding of the course material.
Show steps
Show steps
Show steps
- Collect and organize all course-related materials
- Create a system for easy access and retrieval
- Review and revise the materials regularly
Explore microbiome analysis tools
Show steps
Follow online tutorials to familiarize yourself with bioinformatics tools and software packages commonly used for microbiome analysis, such as QIIME and R.
Show steps
Show steps
Show steps
- Identify the most suitable tools for your analysis задачи
- Complete tutorials and exercises provided by the tool developers
- Apply the tools to practice data analysis on real-world microbiome datasets
Visualize microbial diversity
Show steps
Create visualizations that illustrate the diversity of microbes in different environments, helping you understand the patterns and relationships within microbial communities.
Browse courses on
Microbial Diversity
Show steps
Show steps
Show steps
- Gather microbiome data from public databases
- Use bioinformatics tools to analyze and visualize the data
- Create graphs and charts to represent microbial diversity
Three other activities
Expand to see all activities and additional details
Show all six activities
Compare microbiome compositions
Show steps
Practice comparing the composition of microbial communities across different samples, using statistical and machine learning techniques to identify significant differences.
Show steps
Show steps
Show steps
- Obtain microbiome data from different environments or conditions
- Perform statistical tests to compare microbial abundance
- Use machine learning algorithms to classify and group samples based on their microbial composition
Develop a microbiome analysis pipeline
Show steps
Create a computational pipeline using Python or other programming languages to automate the analysis of microbiome data, making your workflow more efficient and reproducible.
Browse courses on
Data Analysis
Show steps
Show steps
Show steps
- Design the pipeline architecture and workflow
- Implement data preprocessing, analysis, and visualization modules
- Test and optimize the pipeline's performance
- Document the pipeline and make it available to others
Build a microbiome data repository
Show steps
Contribute to the field by compiling and organizing a comprehensive data repository of microbiome data, metadata, and analysis tools, making it easier for researchers to access and utilize.
Browse courses on
Data Curation
Show steps
Show steps
Show steps
- Identify and collect microbiome data from various sources
- Standardize and annotate the data with relevant metadata
- Develop a user-friendly interface for data exploration and retrieval
- Promote the repository and encourage contributions from the community
Career center
Learners who complete How to analyze a microbiome will develop knowledge and skills
that may be useful to these careers:
Research Scientist
Research Scientist
Research Scientists who study biological processes at the microbial level may take **How to analyze a microbiome** to enhance their foundational knowledge of how to read and process sequencing data for microbiome analysis. This course can lead to success for the Research Scientist's role in analyzing data to make discoveries in microbial populations.
Microbiologist
Microbiologist
Microbiologists study microorganisms, including those in the microbiome, and their applications in fields like medicine, agriculture, and environmental science. **How to analyze a microbiome** can help build a foundation for Microbiologists to strengthen their data analysis skills.
Bioinformatician
Bioinformatician
Bioinformaticians work with large biological datasets, including microbiome data. **How to analyze a microbiome** helps build a foundation for Bioinformaticians by teaching the skills needed to interpret microbiome sequencing data.
Data Scientist
Data Scientist
Data Scientists who specialize in biology or healthcare may take **How to analyze a microbiome** to strengthen their knowledge of microbiome analysis techniques. This course can help Data Scientists in these fields contribute to research and development of microbiome-based applications.
Biostatistician
Biostatistician
Biostatisticians who work with microbiome data may take **How to analyze a microbiome** to gain specialized knowledge in microbiome analysis techniques. This course can supplement their statistical expertise with domain-specific knowledge, enhancing their ability to analyze and interpret microbiome data.
Epidemiologist
Epidemiologist
Epidemiologists who study the distribution and determinants of microbiome-related diseases may take **How to analyze a microbiome** to enhance their understanding of microbiome analysis methods. This course can help Epidemiologists strengthen their ability to design and conduct microbiome-focused epidemiological studies.
Physician
Physician
Physicians who specialize in fields like gastroenterology, infectious diseases, or dermatology may take **How to analyze a microbiome** to gain a better understanding of the role of the microbiome in health and disease. This course can help Physicians stay up-to-date on the latest microbiome research and its clinical implications.
Registered Dietitian
Registered Dietitian
Registered Dietitians who work with clients to improve their health through nutrition may take **How to analyze a microbiome** to gain knowledge of the role of the microbiome in nutrition and health. This course can help Registered Dietitians make more informed recommendations to their clients based on the latest microbiome research.
Science Writer
Science Writer
Science Writers who specialize in health or science may take **How to analyze a microbiome** to gain a better understanding of the microbiome and its role in health and disease. This course can help Science Writers effectively communicate microbiome-related research to a wider audience.
Healthcare Consultant
Healthcare Consultant
Healthcare Consultants who work with healthcare providers to improve patient care may take **How to analyze a microbiome** to gain knowledge of the role of the microbiome in health and disease. This course can help Healthcare Consultants make more informed recommendations to their clients based on the latest microbiome research.
Environmental Scientist
Environmental Scientist
Environmental Scientists who study the microbiome's role in environmental processes may take **How to analyze a microbiome** to gain specialized knowledge in microbiome analysis techniques. This course can help Environmental Scientists contribute to research and development of microbiome-based environmental solutions.
Educator
Educator
Educators who teach biology, health, or environmental science may take **How to analyze a microbiome** to gain a better understanding of the microbiome and its role in health and the environment. This course can help Educators develop engaging lesson plans and activities for their students.
Science Policy Analyst
Science Policy Analyst
Science Policy Analysts who work on health or environmental policy may take **How to analyze a microbiome** to gain knowledge of the role of the microbiome in health and the environment. This course can help Science Policy Analysts make informed recommendations based on the latest microbiome research.
Laboratory Technician
Laboratory Technician
Laboratory Technicians who work in microbiology labs may take **How to analyze a microbiome** to gain specialized knowledge in microbiome analysis techniques. This course can help Laboratory Technicians enhance their skills in processing and analyzing microbiome samples.
Quality Assurance Manager
Quality Assurance Manager
Quality Assurance Managers in the healthcare or food industry may take **How to analyze a microbiome** to gain knowledge of microbiome analysis techniques and their applications in quality control. This course can help Quality Assurance Managers ensure the safety and quality of products and services related to the microbiome.
For more career information including salaries, visit:
OpenCourser.com/course/nxeya7/how
Reading list
We've selected six books
that we think will supplement your
learning. Use these to
develop background knowledge, enrich your coursework, and gain a
deeper understanding of the topics covered in
How to analyze a microbiome.
Provides a comprehensive overview of the microbiome in health and disease. It valuable resource for researchers who are interested in learning more about this topic.
Provides a detailed overview of the statistical methods used in bioinformatics. It valuable resource for anyone who wants to learn more about this topic.
Save
Provides a gentle introduction to bioinformatics. It good starting point for anyone who wants to learn more about this field.
Save
A classic textbook in microbial ecology that provides a broad overview of the field. Covers topics such as microbial diversity, community structure, and ecosystem functioning.
Provides a comprehensive overview of the field of bioinformatics. It covers all the major topics, including sequence analysis, protein structure prediction, and gene expression analysis.
Provides a comprehensive overview of statistical methods for clinical trials. It covers all the major topics, including study design, data analysis, and interpretation.
For more information about how these books relate to this course, visit:
OpenCourser.com/course/nxeya7/how
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Effort
1 to 3 hours per week for 7 weeks
Level
Intermediate
Via
edX
Institution
KU Leuven
Instructors
Karoline Faust
Sam Röttjers
Anna Krzynowek
Language
English
Transcript
English
Good to know
Explores microbiome analysis using real-world example data
Taught by experts in microbiome data analysis
Suitable for individuals interested in working with microbiome data
Covers the basics of microbiome analysis, making it suitable for beginners
Provides a comprehensive overview of microbiome data analysis techniques
Assumes prior knowledge in basic programming
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