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A Systems biology approach to analyze
microbiome in soil and fish gut
03-03-2017
Biomedical Informatics
Suyeon Kim
Eat Ice-cream!
Image source: Kevin Barrett, project assistant; Terry Devitt, editor; S.V. Medaris, designer/illustrator; David J. Tenenbaum, feature writer
Two case studies
• Outside Environment : Soil.
• Composition of soil and impact on growth of plants.
• Inside Environment : Fish gut
• Composition of fish gut and impact on growth of fishes.
Research Goal
• Develop a method to study how the features in any
microbiome affect the health of organisms growing in
the same environment.
• Features ; Abundance level of bacteria (in the microbiome)
• Health of organisms
• Soil Microbiome: Plant growth parameters (Root biomass, Root nitrogen etc)
• Fish gut Microbiome: Phenotype (Height, Weight, Length, and Width)
Data-driven research
Rhizosphere microbial community
Image source : Who’s who in the plant root
microbiome?. Nature biotechnology, 30(10), 961.
Gut microbiome of Fishes
Big head(Zooplankton)
Silver carp(Phytoplankton)
Omnivore fish: Phytoplankton, zooplankton, Cyanobacteria
Fish gut
• The morphology of the gut is dependent on the evolutionary history of
the species and on diet.
- Herbivore(Plant eater) have little stomach and very long intestines.
- Carnivore(Meat eater) have large stomach and short intestines.
Data
Soil microbiome
Fish gut microbiome
• “phylum_abundance.csv”
• 31 bacterial phylum in 557 plants are
growing in different pots.
• Bacterial abundance
• “phylum_abundance.csv”
• 3 different portions of fish gut (Foregut,
Midgut, and Hindgut)
• Bacterial abundance
• 3 different fish types.
• 34 bacterial phylum in 65 fish
samples (Hybrid)
• 34 bacterial phylum in 104 fish
samples (Bighead)
• 34 bacterial phylum in 106 fish
samples (Silver carp)
• “ synetheses.csv” (16 parameters) ;
• growth parameters example of Total
biomass, Root biomass, and Root
nitrogen etc.
• “ phenotype.csv” (4 phenotypes) ; Body
weight, height, length, and width.
How does data look like?
Phylum_abundance (foregut_phylum)
Phenotypes
Fishes
Fishes
Phyla
Abundance level
of Bacteria
Phenotype
Systems biology approach
• “Proposed Model”
Correlation between every pair of organisms
• Edge to the left :
Correspond to correlation
among the bacteria in soil
and fish gut.
• Cross-edge : Correspond
to correlation between B1
and growth parameter
element.
• Subgroup(=Cliques) :
Correspond to the group
of elements are highly
correlated, that associated
with growth parameter.
Maximum Weighted Clique Model
High impact on the growth
High correlation
What can we expect ?
• Correlation : How often they co-exist..
Generate a co-occurring network
Soil Case ; Total biomass_VS3
Below 30%
Fish Case ; Foregut_Hybrid (Weight)
Below 30%
Fish Case ; Foregut_Hybrid (Weight)
Results
SOIL
FISH GUT - Weight
Fibrobacteria
Armatimonadetes
Elusimicrobia
Unknown
Total biomass
Fusobacteria
Nitrospirae
Weight
Conclusions
• Data driven research can make microbiome research possible.
• We can solve the problem with systems biology approach.
• Biology Study (Ontology) would be next steps.
Thank you for listening!