Omnivore, Vegetarian and Vegan Diets: Microbial Diversity in Foods and Prevalence of Antibiotic-Resistant Lactic Acid Bacteria in the Human Intestinal Microbiota

The human intestinal microbiota plays a huge role in the functional homeostasis and health of the human body. Diet and antibiotics are the most important factors, among others, known to influence the human intestinal microbiota. Overuse of antibiotics in aquaculture and agriculture as growth hormones; and in humans and animals for prophylaxis and therapy has, through the food chain, contributed to the dissemination and spread of antibiotic resistance (AR). The main aim of this PhD project was to study the effect of different diets, namely; omnivorous, vegetarian and vegan on the incidence of antibiotic-resistant bacteria in the human gastrointestinal tract (GIT). Initially, the microbial diversity and abundance of the microorganisms in the different foods consumed by subjects taking the three different diets was determined. Secondly, the prevalence of antibiotic-resistant lactic acid bacteria (LAB) in the GIT was investigated through isolation and characterisation of antibiotic-resistant LAB in the faeces of volunteers taking the three types of diets. Thirdly, transferability of AR genes was assessed. The results revealed an E. faecium strain carrying erythromycin, streptomycin and tetracycline resistant genes, isolated from an omnivore subject, that transferred its antibiotic-resistant genes, through conjugation, to E. faecium [64/3], E. faecalis (JH2-2), L. ivanovii (7842RF) and L. welshimeri (11857RF), all plasmid-free reference strains at frequencies of 5.7 x 10-4, 1.7 x 10-6, 4.3 x 10-7 and 8.5 x 10-8, respectively. Plasmid extraction revealed two plasmids of more than 24Kb in the donor and transconjugants. Sanger sequencing of the plasmids revealed several ORFs annotated to bacterial enzymes involved in multiple ARs. Findings from this study, affirm that the GIT harbours a mobilizable reservoir of antibiotic genes but the effects of different diets on the prevalence of AR bacteria in the GIT are not conclusive. Further experiments need to be duplicated in vivo.