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Mapping Metabolic Interactions between S. cerevisiae and Lactic Acid Bacteria

Ponomarova, Olga

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Microorganisms in nature live in interconnected communities, where the language of biochemistry creates means for communicating, fighting, and cooperating with each other. This work investigates one of the ways for microbial interactions - nutrient exchange. It is focus ed primarily on co - metabolism of Saccharomyces cerevisiae and lactic acid bacteria - Lactococcus la ctis and Lactobacillus plantarum - community whose composition was inspired by co - occurrence of yeast and LAB in a multitude of naturally fermented foods. Specifically, I w as interested in detecting metabolic interactions between budding yeast and lactic a cid bacteria, identifying transferred molecules, exploring metabolic mechanisms of their biosynthesis and excretion, and understanding possible causes behind them. A c ombination of experimental and computational methods was used to understand how nutritio nal dependencies shape communit ies of microorganisms. First step involved compos ing a synthetic community of common laboratory strains of yeast and lactic acid bacteria . Following a series of experiments with chemically defined media, LAB revealed their me tabolic dependency on yeast for growth and survival. This m ixed species community appears to be stable and is sustained through the flow of small nitrogenous molecule s from yeast to bacteria. Nutrient cross feeding was found to be a result of overflow meta bolis m in yeast, which release excess catabolit es under particular combinations of available nitrogen sources. The o bserved nutrient excretion involve s a set of genes that regulate yeast nitrogen metabolism when depleted of preferred nitrogen sources. We h ave recreated co - metabolism of yeast - LAB community, as well as multiple natural bacterial communities, with multi - species genome - scale metabolic modeling. Simulation results demonstrated a link between metabolic cross - feeding and species co - occurrence, and proved its high potential of the method for predicting metabolite exchange in microbial communities. In this project, the inter - kingdom model community of wild type microorganisms has been established and characterized. Peculiarities of yeast regulatory n etwork, in certain media compositions, cause “wasteful” excretion of amino acids and other metabolites. This in turn cr e ates a stable niche for growth of lactic acid bacteria , which are auxotro phic for multiple amino acids. D escribed scenario of metabolic dependency between yeast and lactic acid bacteria demonstrates how survival of one species can be driven by metabo lic idiosyncrasy of the other. The y east - LAB interaction is established instantly, and thus can serve as a first step in evolution of cooperat ion.

Item Type: Dissertation
Supervisor: Patil, Dr. Kiran
Date of thesis defense: 18 November 2015
Date Deposited: 08 Dec 2015 08:30
Date: 2015
Faculties / Institutes: The Faculty of Bio Sciences > Dean's Office of the Faculty of Bio Sciences
Subjects: 500 Natural sciences and mathematics
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