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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!