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Microbial ecology of food fermentations and intestinal ecosystems Open Access


Other title
Type of item
Degree grantor
University of Alberta
Author or creator
Supervisor and department
Gaenzle, Michael (AFNS)
Examining committee member and department
Guan, Leluo (AFNS)
Lacroix, Christophe (Institute of Food Science and Nutrition, ETH, Zurich)
Gaenzle, Michael (AFNS)
Baracos, Vickie (AFNS)
Madsen, Karen (Medicine)
Department of Agricultural, Food, and Nutritional Science
Food Science and Technology
Date accepted
Graduation date
Doctor of Philosophy
Degree level
Microbiota are ubiquitous in nature. Similarities as well as differences are present between microbiota in animals and fermentation systems. The aim of the PhD project was to investigate factors affects microbial ecology in rodent and sourdough models. To determine how compromised health of the host by tumor and CPT-11 therapies affects intestinal microbiota in tumor bearing rats, qualitative and quantitative taxonomic analyses were combined to characterize intestinal microbiota during CPT-11-based chemotherapy. Both tumor and CPT-11 chemotherapy increased cecal Clostridium cluster XI and Enterobacteriaceae. The effect of dietary fibre was evaluated in the same model. Cecal butyrate concentrations and feed intake were highly correlated. Moreover, a positive correlation of the host expression of MCT1 with body weight as well as a positive correlation of the abundance of bacterial butyryl-CoA gene with cecal butyrate concentrations were obeserved. These correlations support the interpretation that the influence of dietary fibre on CPT-11 toxicity is partially mediated by an increased cecal production of butyrate. Similar to intestinal microbiota, in sourdough, cereal substrates contain various compounds that may have selective effect on sourdough microbiota. The effect of growth rate and acid resistance on microbial competitiveness in sourdoughs was evaluated by assessing competitiveness of glycerol-dehydratase (gupCDE) positive and glutamate-decarboxylase (gadB) positive strains of L. reuteri relative to the corresponding null mutants. Both glycerol and glutamate metabolism determine the competitiveness of L. reuteri in sourdough fermentations. Besides competition over shared energy source, microbes also compete with each other by producing antimicrobial compounds. Reutericyclin is an antibiotic produced by sourdough-originated L. reuteri which is bactericidal against most gram-positive bacteria. A combination comparative genomics, bioinformatics analysis, and the characterization of null-mutants was used to determine the genetic determinants of reutericyclin biosynthesis. A gene cluster unique to reutericyclin producers was identified on a genomic island acquired through lateral gene transfer. It includes genes coding for a nonribosomal peptide synthetase (NRPS), a polyketide synthase (PKS), homologues of phlABC, and putative transport and regulatory proteins. The combination of PhlABC homologues with both a NRPS and PKS is exclusive to the lactic acid bacteria Streptococcus mutans, L. plantarum and L. reuteri, indicating that the genes in these organisms share a common evolutionary origin.
Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.
Citation for previous publication
Lin XB, Dieleman LA, Ketabi A, Bibova I, Sawyer MB, Xue H, Field CJ, Baracos VE, Gänzle MG (2012) Irinotecan (CPT-11) chemotherapy alters intestinal microbiota in tumour bearing rats. PLoS One 7: e39764Lin XB, Farhangfar A, Valcheva R, Sawyer MB, Dieleman L, Schieber A, Gänzle MG, Baracos VE (2014) The role of intestinal microbiota in development of irinotecan toxicity and in toxicity reduction through dietary fibres in rats. PLoS One 9: e83644Lin XB, Gänzle MG (2014) Quantitative high-resolution melting PCR analysis for monitoring of fermentation microbiota in sourdough. Int J Food Microbiol 186C: 42–48Lin XB, Gänzle MG (2014) Effect of lineage-specific metabolic traits of Lactobacillus reuteri on sourdough microbial ecology. Appl Environ Microbiol 80:5782-9

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