Introduction to Systems Biology Project 9 In silico

Introduction to Systems Biology Project 9 In silico symbiosis of Strepptococcus Thermophilus and Musculus

Strepptococcus Thermophilus • “Streptococcus thermophilus is an essential lactic acid bacterium used for commercial purposes, which includes the production of milk, cheese, and other dairy products. ” • „Lactic acid bacteria (LAB) are of great importance in the food industry because of their lactic acid production and their characteristic impact (e. g. , texture, flavor) on the final product. ”

Symbiosis • We study the metabolic interactions of a mouse and it‘s gut microbe, Strepptococcus Thermophilus. • Matlab is used to model the metabolic networks and the corresponding interactions between the organisms. • Optimization techniques are used to compare biomass growth on different diets. • We study how the presence of one organism effects biomass growth in the other.

Biomass growth rate (BGR) • Biomass growth rate is optimized for the organisms on four different diets, both biassociated (in symbiosis) and monoassociated (without symbiosis). High protein Low fat / high carb Low carb / high fat Western diet Diet composition CHO Fat Protein High-CHO High-Fat Western 5% 20% 75% 5% 75% 20% 50% 35% 15% 75% 5% 20%

High protein diet • • Mouse BGR is highest on the high protein diet Presence of Strepptococcus greatly increases mouse BGR Monoassociated Biassociated Mouse 1. 32 2. 69 Strepptococcus 0. 04 2. 24

High carb diet • • Strepptococcus BGR is highest on high carb diet Presence of Strepptococcus greatly increases mouse BGR Monoassociated Biassociated Mouse 0. 35 1. 39 Strepptococcus 1. 65 2. 50

High fat diet • • Presence of Strepptococcus greatly increases mouse BGR Same maximum growth rates for mouse as high carb. Mammals need protein and protein is limited to 20% in both cases. Monoassociated Biassociated Mouse 0. 35 1. 39 Strepptococcus 0. 02 2. 03

Western diet • • Mouse BGR is lowest on western diet. Probably due to low amount of protein in the diet selected (15%). Presence of Strepptococcus greatly increases mouse BGR Monoassociated Biassociated Mouse 0. 26 1. 04 Strepptococcus 0. 11 2. 12

Metabolic interactions • • • The main part of the project is the study of the metabolite exchange between the two organisms – the symbiotic interactions. Flux Variability Analysis is used to study which metabolites are exchanged under given, extreme conditions. (e. g. max mouse growth, max streppto growth and when they are competing for resources) The metabolic system is divided into the microorganism, the mouse and the mutual lumen. • A lumen (Lat. lūmen, an opening) in biology is the inside space of a tubular structure, such as an artery or intestine. By extension, a lumen can also be the inside space of a cellular component or structure, such as the endoplasmic reticulum. • The goal is to study both nutrient intake and secretion of the organisms and also the interactions between the lumen and microorganism/mouse.