How to analyze a microbiome from edX

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.

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

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

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

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

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Organize your notes, assignments, quizzes, and exams to improve your retention and understanding of the course material.

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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

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Follow online tutorials to familiarize yourself with bioinformatics tools and software packages commonly used for microbiome analysis, such as QIIME and R.

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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

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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

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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

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Compare microbiome compositions

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Practice comparing the composition of microbial communities across different samples, using statistical and machine learning techniques to identify significant differences.

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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

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Create a computational pipeline using Python or other programming languages to automate the analysis of microbiome data, making your workflow more efficient and reproducible.

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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

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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.

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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 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.

See salaries and explore the career path for Research Scientist

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.

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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.

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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.

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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.

See salaries and explore the career path for Biostatistician

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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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How to analyze a microbiome

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