Enrichment of gastrointestinal anaerobes by a novel technique

Author Title Number of Pages Date Kir Ülle Enrichment of gastrointestinal anaerobes by a novel technique 43 pages + 3 appendices 15.10.2017 Degree Bachelor of Engineering Degree Programme Biotechnology and Chemical Engineering Specialization option Biotechnology and Food Engineering Instructors Teemu Rinttilä, Senior scientist Carola Fortelius, Head of Degree Programme This thesis was commissioned by a Finnish company Alimetrics Ltd., which specializes in life sciences. The aim was to isolate bacterial communities of broiler chicken gastrointestinal tract while segregating them by their preferred source of carbon. Successful execution of this novel approach would allow for significant further research potential. During this thesis a novel method for isolating anaerobic bacteria was developed. The principal idea was to microbiologically enrich gastrointestinal bacteria by culturing them on specific growth medium. Anaerobic cultivation on selective medium was performed to enrich seven different cultures. Inoculum was gastrointestinal bacteria of broiler chicken. Bacteria was cultured in liquid growth media. Growth media was otherwise identical except the difference of included carbon source. Seven different carbon sources were used to enrich bacteria that could utilize them. Substrates used were various carbohydrates, protein, fat and lactic acid. Bacteria was propagated every day, which diluted the bacterial population that could not utilize the particular substrate. Enrichment cultures were subject to short-chain fatty acid composition, ammonium concentration, and bacterial composition analysis. The novel method proved to be adequate and multiple cultures with specific characteristics were isolated. To a surprise, the genus Bacteroides was abundant in most cultures, which could be explained by the composition of used substrates. Metabolite analyses indicated features that are widely associated with bacterial utilization of each carbon source in question. The enrichment part of experiment was successful and potential for further research is significant. However, a method for treating substrates to simulate digestion of small intestine before enrichment would be advantageous.