Introduction to the Laboratory for Integrated Bioinformatics
Todd Taylor Team Leader
RIKEN Center for Integrative Medical Sciences
Metagenomics is the culture-independent cloning and analysis of bacterial DNA
• Environmental or community genomics • Often we cannot isolate individual bacteria, so
must study their genomes as a mixture • DNA is extracted directly from the
environmental sample, no culturing
Why the interest in metagenomics?
• Bacteria account for the vast majority of life forms on Earth
• Only 1-2% of microbes can be cultured • Most species do not survive in isolation • Widespread applications
• Identification and synthesis of novel drugs and chemicals
• Human health - probiotics • Biodegradation - sewage, ocean pollutants, plastics,
garbage, nuclear waste, etc. • Energy generation - production of clean “green” fuels
Metagenomics differs radically from traditional genomics
Ocean: Microbes floating in vast sea
Human Gut: Closed system for microbes
Whale Fall: Microbes come together to degrade whale mass
Soil: Dry environment with numerous microbes
Complex environmental systems have millions of microbes
Several microbes interact together to complete biochemical pathways
Vast numbers of bacteria colonize different parts of the body
Numbers represent the number of organisms per gram of homogenized tissue or fluid or per square centimeter of skin surface
Some of the mechanisms by which the normal flora competes with invading pathogens
We aim to reconstruct the combined community metabolic model
We can compare phylogenetic trees from multiple metagenomic samples
• A spore forming gram-positive bacteria found in mammalian gut.
• Induce the appearance of CD4+ T helper cells that produce IL-17 and IL-22
(Th17 cells).
• Colonization leads to increased expression of inflammatory and
antimicrobial defense related genes, such as Serum Amyloid A.
SFB monocolonized mice and rat
Feces and cecal content collected,
microbial DNA extracted*
Genome sequencing by whole-genome shotgun
strategy using Sanger and 454
pyrosequencing
SFB Genome: Unculturable bacteria that induces the differentiation of Th17 cells in mice gut
Accepted in Cell Host & Microbe 2011
Pathway construction in SFB-rat-Yit
Conservation of TLR5-binding motifs in SFB flagellin proteins
Flagellins are the agonists of TLR5, which in turn directs Th17 cell production
Chemotaxis and Flagellar assembly genes in SFB
Expression of flagellin genes in mouse SFB
There are many computational & bioinformatic challenges & bottlenecks to overcome
• Data management & storage – In-house & off-site
• Data transfer – Current internet is not capable
• Metagenomic sequence assembly – Diverse, complex, huge datasets – Huge memory is required
• Data analysis and massive parallel processing – Unprecedented scale
• Highly fragmented & incomplete data – How to make sense of it?
• Data integration – Comparison with other datasets and information resources
• More sure to come...
What do we hope to achieve? • Use bioinformatic approaches to: • Model entire ecosystems
– Environment – Health
• Predict and understand – Fluctuations over time – Impact from external forces – Modifications at genetic level – Manipulation of environments for benefit of living
species and long-term sustainability of the earth • Develop tools and pipelines
– Support other labs with high-throughput analyses
