Metagenomics

and
eDNA Analysis

Training Module 5

of
Subhanil Chakraborty

Bioinformatics Internship
Smart farming India (Pvt.) Limited
2024
 METAGENOMICS

• The term "metagenomics" was first used by Jo Handelsman in 1998.

• Metagenome referes to the idea, that a collection of genes
sequenced from the environment could be analyzed in way analogous
to the study of a single genome .
• Application of techniques to the study of communities of microbial
organisms directly in their natural environments, by passing the need
for isolation and lab cultivation of individual species.
 Why Do We Do METAGENOMICS?
Understanding Cell Understanding
Structure & Function Host Interactions

Understanding
Expression
Understanding (RNA/Protein)
Metabolism
Discover DNA
Genome Variation, Genotyping
Engineering Forensics

Defining the
Drug/Vaccine Minimal
Development Understanding Gene Set
Protein-Protein
TIGR: The Institute for Genomic Research Interactions The J. Craig Venter Institute
Compositional view of human intestinal microbiomes
Specific aims of a Metagenomics Study
• Examining phylogenetic diversity using 16S rRNA

• Examining metabolic pathways, diversity patterns of microorganisms can be

used for monitoring and predicting environmental conditions and change.

• Examining genes/operons for desirable enzyme candidates (e.g., cellulases,

chitinases, lipases, antibiotics, other natural products these may be
exploited for industrial or medical applications.

• Examining secretory, regulatory, and signal transduction mechanisms

associated with samples or genes of interest.
Continued..
• Examining bacteriophage or plasmid sequences. These potentially influence diversity and
structure of microbial communities.

• Examining potential lateral gene transfer events. Knowledge of genome plasticity may give
us an idea of selective pressures for gene capture and evolution within a habitat.

• Directed approach towards designing culture media for the growth of previously-
uncultured microbes.

• Examining genes that predominate in a given environment compared to others.

• Finally, metagenomic data and metadata can be leveraged towards designing low- and
high-throughput experiments focused on defining the roles of genes and microorganisms in
the establishment of a dynamic microbial community.
Metagenomics analyses challenges
• More expensive and computationally demanding
• Require high performance compute clusters and parallelization
• More complex pipeline that needs to be tailored to study
• The challenge of correct binning – which read belongs to which
organism?
• For highly diverse communities (soil, gut) – coverage may be
insufficient to characterize low abundance organisms
• Host DNA (human, plant etc.) needs to be removed – mostly simple
but may require PCR-based enrichment of microbial DNA if majority
of DNA is host-derived (e.g. certain human samples; plants)
• Contaminant removal tricky – which genes were generated by the
contaminant?
Thank You