Human Microbiome Analysis: Computational techniques and challenges

Presented at BC2 Basel Computational Biology Conference, June 2015

Microbial communities in and on the human body represent a complex mixture of microbial eukaryotes bacteria, viruses and archaea containing in total more than ten times the number of genes found in the human genome. High-throughput sequencing offers a powerful culture-independent approach to study the underlying diversity of microbial communities in their natural habits across different human tissues and diseases. In this tutorial, we provide necessary knowledge and skills allowing researchers to use contemporary sequencing technologies to study human microbial comunities. The tutorial provides general introduction to computational techniques used to analyze human microbiome. We will summarize the main aspect of the human microbiome analyses highlighting the challenges and benefits of various approaches.  In particular we provide the overview of existing reference-based and reference-free method to compare microbial communities across samples. We will highlight challenges and benefits associated with various steps of the human microbiome analyses. The tutorial provides hands-on guide on available sequencing protocols and computational software tools for complete human microbiome analysis i.e. genomic and functional analysis of microbial communities; comparison of the microbial communities across samples and diseases.  Genomic analysis helps answers the question “Who is out there” by determining types of the microbial organisms and their proportions.  Functional analysis helps answers the question “What are they doing?” by establishing types of genes and metabolic pathways and their proportions.  In addition to hands-on guide the tutorial discusses current next-generation sequencing technologies and available computational tools for human microbiome analysis.  The main focus of the tutorial is to  enable researchers to acquire expertise necessary for using next‐generation sequence data for human microbiome analysis.  The tutorial is supplemented with many hands-on examples.

Motivation

Microbial communities in and on the human body represent a complex mixture of microbial eukaryotes, bacteria, viruses and archaea containing in total more than ten times the number of genes found in the human genome. Traditional cultured-based methods are able to culture only small portion of known microbial species present in the human body. High-throughput sequencing offer a powerful culture-independent approach to study the underlying diversity of microbial communities in their natural habits across different human tissues and diseases. The detailed genomic and functional profile of the microbial communities provides a better understanding of how the human microbiome is assembled and maintained. Ability to access human microbiome richness at the various taxa level offers a promise to improve our understanding of how microbiome is involved in human health and disease. Comparative microbial analyses for multiple subject groups has a potential to establish healthy and disease specific microbiome composition. Studying the human microbiome in health and disease and establishing an association between disease and microbial gene pool may have important medical implications, including treatment of diseases with behavioral abnormalities. Additionally ability to identify prevalent microbial communities in individuals with various disorders relative to the general population may contribute to development of the microbiome-based diagnostic, prognostic, and treatment strategies. Additionally, accurate characterization of the personal microbiome and ability to compare it across individuals and diseases opens new possibilities to investigate host-microbiome interactions.

Expected Goals

The tutorial provides general introduction to computational techniques used to analyze human microbiome. We will summarize the main aspect of the human microbiome analyses highlighting the challenges and benefits of various approaches.  In particular we provide the overview of existing reference-based and reference-free method to compare microbial communities across samples. We will highlight challenges and benefits associated with various steps of the human microbiome analyses.

During the tutorial we provide hands on expertise necessary to carry out microbiome analyses using next generation sequencing technologies.  Participants will be able to:

  • understand and apply next-generation sequencing technologies (including Illumina, 454, Ion Torrent,  Pac Bio)  for human microbiome analysis
  • manage, interpret and assess the quality of sequencing data
  • understand and apply protocols to extract candidate microbial reads from sequencing data
  • acquire expertise necessary for using next‐generation sequence data for human microbiome analysis including read alignment,  taxomic profiling, determining microbiota abundances and composition
  • understand main computational and statistical techniques used in human microbiome analysis
  • get hands on experience in working with UNIX command-line environment, allowing to use suggested human microbiome analysis pipelines
  • confidently use the available tools  for human microbime analyis on either a local or remote Unix system
  • interpret and visualize the results

Prerequisites and intended audience

The tutorial is aimed at general audience who need or planning to use next-generation sequencing to study human microbiome or would like to get a general background of the field.

Attendees are strongly encouraged to bring a laptop computer able to access WiFi network.  Attendees are encouraged to have cluster account (with UNIX OS). If cluster account is not available, personal laptop will be used for analysis, i.e. installing necessary computational tools, downloading the data and performing the analysis. Please reserve at least 20Gb of space on your laptop or cluster.

Tutorial Outline 

14:00-15:00 Welcome, Introduction to human microbiome analysis The first session will provide the basic background in sequencing technologies and computational techniques and challenges in human microbiome analysis. It includes introduction to next-generation sequencing technologies and provides comparison of available sequencing platforms used to profile the microbial communities.  Additionally the session provides the overview of computational steps in human microbiome analysis and discusses challenges and possible solutions.  Finally, overview of existing tools and underlying statistical and computational techniques is covered.

15:00 – 15:30 Hands on session 1:  Introduction to UNIX command-line This session will provide necessary background and skills for participants to be able to use UNIX command-line environment for human microbiome analysis. No previous experience with Unix or computational tools is required.

15:30-16:00 Coffee break 

16:00-17.30 Hands on session 2: Human microbiome analysis – Genomic analysis of the microbial communities  This session will provide detailed hand on tutorial on genomic analysis of microbial communities.  Genomic analysis answers the question “Who is out there” by determining types of the microbial organisms and their proportions. Session includes step-by-step guidance how to install and run computational tools for the genomic analysis. Additionally we discuss computational tools for comparison of the microbial communities across samples and diseases. We provide recommendations for the reference-based and reference-free computational techniques used to compare the microbial communities across samples. Scripts and commands allowing analyzing and managing sequencing data are provided.

17:30 – 17:45.  Discussion and conclusions

 
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