A study was conducted to isolate and identify bacteria from “amabere amaruranu” cultured-milk from Kenya and to evaluate the isolates’ potential to be used as probiotics. Isolates were identified using PCR sequence analysis of the 16S rRNA gene and the API® 50 identification system. Identified isolates included: Acetobacter tropicalis, Bacillus pumilus, Bacillus safensis, Lactobacillus paracasei, Lactobacillus rhamnosus, Staphylococcus aureus, Staphylococcus epidermidis and Staphylococcus sciuri. Their potential as probiotics was evaluated using their ability to survive in acid-then-bile conditions, antibacterial activity (against Escherichia coli, Klebsialla pneumonia, Enterococcus faecalis, Pseudomonas aeruginosa and Enterobacter cloacae), mucin degradation activity, and sensitivity to antibiotics (ampicillin, bacitracin, chloramphenicol, erythromycin, kanamycin, penicillin, streptomycin and tetracycline). Lactobacillus isolates were tolerant to acid-then-bile conditions, non-mucinolytic and inhibited growth of indicator strains but only L. rhamnosus was sensitive to all test antibiotics. Bacillus isolates were tolerant to acid-then-bile conditions, non-mucinolytic, lacked antibacterial activity and only B. safensis was sensitive to all test antibiotics. Acetobacter tropicalis isolates were non-mucinolytic but were intolerant to acid-then-bile conditions. In conclusion, both Lactobacillus rhamnosus and Bacillus safensis isolates that showed tolerance to digestive tract conditions, were sensitive to antibiotics and were non-mucinolytic would be recommended for further consideration as candidate probiotics.

Major depressive disorder (MDD) is rapidly growing and one of the most common causes of disability and mortality worldwide. People with MDD often display brain changes such as adisrupted balance in neurotransmitters, impaired neurogenesis and neuroplasticity. Traditionally has MDD been treated with medications and talking therapies (psychotherapy). Studies have shown that just around 50 % of people with MDD get improvements from common traditional treatments.Therefore is there a great need for a better understanding of MDD and new treatments. There is now an emerging field of research that indicates that the gut microbiota plays a crucial role in disturbing normal brain functioning in MDD. This connection between the gut and the brain is called the gutbrain axis.The thesis aims to investigate if there is a connection between gut microbiota disruption and MDD and if gut microbiota restoration can be a potential effective future treatment for MDD. Key findings of the thesis were, studies show that people with MDD often display gut microbiota disruption and chronic low grade inflammation. Studies also indicate that this inflammation can cause the specific brain change often displayed in people with MDD. One of the most critical findings in the thesis was that gut brain treatments affect tryptophan metabolism, which affects the risk of MDD. The research area of the gut brain axis is still new and many more studies are needed,particularly in humans.

Dans le côlon humain, le genre Faecalibacterium est le membre principal du groupe Clostridium leptum et comprend le deuxième genre représentatif le plus commun dans les échantillons fécaux, après Clostridium coccoides. Il a été reconnu comme une bactérie importante favorisant la santé intestinale et est aujourd'hui considéré comme un probiotique de prochaine génération. Jusqu'à récemment, on croyait qu'il n'y avait qu'une seule espèce dans ce genre, mais depuis 2012, certaines études ont commencé à suggérer l'existence de deux phylogroupes dans le genre. Cette nouvelle proposition de reclassification dans ce genre augmente l'importance de nouvelles études, toutes souches confondues, pour mieux comprendre la diversité, les interactions avec l'hôte et les aspects sécuritaires dans son utilisation comme probiotique. Brièvement, dans ce travail, nous introduisons les analyses de génomique comparative au genre Faecalibacterium en effectuant une étude phylogénétique profonde et en évaluant les aspects de sécurité pour son utilisation comme probiotique. Les analyses phylogénétiques comprenaient non seulement l'utilisation classique du gène de l'ARNr 16S, mais aussi l'utilisation de 17 génomes et techniques complets comme le typage de séquence multi-locus (wgMLST), l'identité nucléotidique moyenne (ANI), le synténie génique et le pangénome. C'est aussi le premier travail à combiner une analyse du développement du pangénome avec l'analyse ANI afin de corroborer l'attribution de souches à de nouvelles espèces. Les analyses phylogénétiques ont confirmé l'existence de plus d'une espèce dans le genre Faecalibacterium. De plus, l'évaluation de la sécurité impliquait (1) la prédiction des régions acquises horizontalement (îlots de résistance aux antibiotiques, îlots métaboliques et régions phagiques), (2) la prédiction des voies métaboliques, (3) la recherche de gènes liés à la résistance aux antibiotiques et des bactériocines. Ces analyses ont identifié des îlots génomiques dans tous les génomes, mais aucun d'entre eux n'est exclusif à une souche ou à une génospécie. En outre, ont été identifiés 8 gènes liés aux mécanismes de résistance aux antibiotiques répartis entre les génomes. 126 voies métaboliques ont été prédites et parmi certaines ont été mises en évidence: la dégradation du bisphénol A, le métabolisme du butanoate et la biosynthèse de la streptomycine. En outre, nous avons étudié le contexte génomique d'une protéine (molécule anti-inflammatoire microbienne - MAM) décrite pour la première fois par notre groupe. Cette recherche montre que la MAM apparaît proche des gènes liés au processus de sporulation et, dans certaines souches, proche d'un transporteur ABC. / Within the human colon, the genus Faecalibacterium is the main member of the Clostridium leptum cluster and comprises the second-most common representative genus in fecal samples, after Clostridium coccoides. It has been recognized as an important bacterium promoting the intestinal health and today is considered as a potential next generation probiotic. Until recently, it was believed that there was only one species in this genus, but since 2012, some studies have begun to suggest the existence of two phylogroups into the genus. This new proposition of reclassification into this genus increases the importance of new studies, with all strains, to better understand the diversity, the interactions with the host and the safety aspects in its use as probiotic. Briefly, in this work we introduce the comparative genomics analyzes to the genus Faecalibacterium performing a deep phylogenetic study and evaluating the safety aspects for its use as a probiotic. The phylogenetic analyzes included not only the classical use of 16S rRNA gene, but also the utilization of 17 complete genomes and techniques like whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome. Also, this is the first work to combine an analysis of pangenome development with ANI analysis in order to corroborate the assignment of strains to new species. The phylogenetic analyzes confirmed the existence of more than one species into the genus Faecalibacterium. Moreover, the safety assessment involved the (1) prediction of horizontally acquired regions (Antibiotic resistance islands, Metabolic islands and phage regions), (2) prediction of metabolic pathways, (3) search of genes related to antibiotic resistance and (4) search of bacteriocins. These analyzes identified genomic islands in all genomes, but none of than are exclusive to one strain or genospecies. Also, were identified 8 genes related to antibiotic resistance mechanisms distributed among the genomes. 126 metabolic pathways were predicted and among than some were highlighted: Bisphenol A degradation, Butanoate metabolism and Streptomycin biosynthesis. In addition, we studied the genomic context of one protein (Microbial Anti-inflammatory Molecule - MAM) first described by our group. This investigation shows that MAM appears close to genes related to sporulation process and, in some strains, close to an ABC-transporter.

Aging is associated with natural biological changes, which result in a decrease in the functional capacity of the body, which is also accompanied by an increased incidence of inflammatory processes that contribute to the development of neurodegeneration. The intestinal microbiota and its interaction with the intestine and the central nervous system play a key role in maintaining the function of biological homeostatic systems at an older age. This opens the possibility of influencing or modifying human microbiota for the development of therapeutic strategies. Based on the analysis of stool samples by HPLC MS / MS, the study confirmed the effect of selected probiotics on the modification of metabolic pathways and the proper functioning of the microbiota per se. The greatest effects were observed on tyrosine metabolism, tryptophan metabolism, arachidonic acid metabolism and bile acid biosynthesis metabolism. A positive effect of selected probiotic bacteria was found in the memory component of cognitive functions. Significant improvements were observed in verbal learning and verbal memory. In subjects with mild cognitive impairment, the progression of cognitive deficit has been slowed. Significant improvement was also observed for executive functions. These findings were not followed by a subjective...

Introduction: Physiological microflora is characterised by wide diversity. The microbial community is mostly composed of bacteria, but also includes fungi, archaea and viruses. Anaerobic commensal bacteria (Firmicutes and Bacteroidetes) dominate 90% of the colon. The composition and products of the gut microbiota have a significant effect on an individual's immune system, and their interactions may ultimately promote immune tolerance or inflammatory immune response. Blood cell transplantation (HSCT) and its associated standard procedures of conditioning, antibiotic exposure and dietary prophylaxis represent modification and disruption of the gut microbiota leading to the development of some serious post-transplant complications affecting the OS (overall survival) and TRM (treatment related mortality) of patients. Objectives: The aim of this work was to investigate the representation of individual bacterial strains in patients undergoing allogeneic HSCT, as well as the effect of transplantation on the composition and diversity of their gut microbiota. Methods: Stool samples were obtained from 52 patients who underwent an allogeneic hematopoietic cell transplant at the Institute of Hematology and Blood Transfusion in Prague. A cut-off date for the first sample was set for the start of...

Yeast probiotics and paraprobiotics, live and inactivated yeast cells, respectively, improve health and performance of livestock by stabilizing the intestinal microbial community. They have also been used for infection prevention and treatment. Despite much research already conducted, the mechanism of direct antagonism, or adhesion of bacteria to the probiotic/paraprobiotic, is under characterized. Additionally, it is unknown which probiotic/paraprobiotic is optimal to use for specific infections. The interactions between the yeast and certain pathogens were analyzed qualitatively with scanning electron microscopy (SEM) and quantitatively with membrane filtration assays. Gram-positive bacteria were found to exhibit specificity under SEM. Through membrane filtration, Listeria monocytogenes exhibited binding to all samples (P<0.05), while Salmonella Typhimurium exhibited binding (P<0.001) with all samples except with 2338. Escherichia coli O157:H7 only bound to the probiotics (P<0.001). With a better understanding of how specific yeast probiotics and paraprobiotics interact with bacteria, specific therapies can be administered to combat infections.

As one of the most common medications, it is reasonable to assume that the adverse effects from nonsteroidal anti-inflammatory drugs (NSAIDs) are well understood. While this is the case for NSAID-induced gastropathy, NSAID-induced enteropathy is often clinically overlooked and has a pathogenesis that is incompletely understood. The goal of this study was to determine how alterations in the microbiota impact NSAID-induced intestinal injury. Initial studies explore how gastric acid secretion suppression substantially decreases Bifidobacteria in the small intestine, and emphasize how replenishment of these bacteria results in an amelioration of NSAID-induced enteropathy. Follow-up studies involved pretreating rats with specific bacteria that have conferred protection in other models of small intestinal injury. We examined the role that acetate may play in reducing the damage by evaluating bacteria that had an acetate production gene knocked out via homologous recombination. Protection levels were similar between wildtype and knockout bacteria, and it did not appear that acetate had a key role in damage reduction. Moreover, we found that changes in intestinal damage were dependent not only on the strain of bacteria used but also on the NSAID administered. None of the bacterial pretreatments tested protected against indomethacin- or diclofenac-induced small intestinal injury, and pretreatment with one specific bacterial strain resulted in a significant worsening of damage. To gain further insight as to the potential role of the microbiota in exacerbation of injury, we conducted studies using single antibiotics and antibiotic cocktails. No single antibiotic treatment conferred protection against naproxen-induced small intestinal injury, but an antibiotic cocktail decreased damage scores by ~46%. Furthermore we explored the effects of L-lactic acid supplementation of drinking water but this was unable to reduce naproxen-induced intestinal damage. Collectively, the work presented in this thesis provides novel insights on the relationship between alterations in the microbiota and susceptibility to NSAID-induced enteropathy. / Dissertation / Doctor of Philosophy (Medical Science)

Type 2 diabetes is a worldwide and costly disease that requires complex cellular metabolic breakdown for its development. The onset of this disease is indicated by an abnormal elevated blood glucose level (hyperglycemia) and coexistence with hypertension. Apple and blueberry are the two popular fruits in the U.S. that are high in bioactive phenolic compounds. The objectives of this thesis were to investigate the synergistic health benefits of apple cider and blueberry juice for potential management of early stages of type 2 diabetes using in vitro enzyme assay models and enhance their synergistic effects through fermentation using probiotic strains of lactic acid bacteria. Apple cider and whole blueberry juice were combined at 5 different ratios. Synergistic interaction of the phenolic bioactives between the two juice sources was observed in all assays. For maintenance of high α-glucosidase, α-amylase and ACE inhibition activities, a proportion of 80% apple cider and 20% whole blueberry juice was selected as the optimum combination reflecting maximum health benefits to potentially manage hyperglycemia and hypertension associated with type 2 diabetes. The 80/20 apple cider and blueberry juice combination was fermented at 24 and 48 h using Lactobacillus helveticus R0052 and Bifidobacterium longum isolate. High inhibition of α-glucosidase, α-amylase and ACE enzymes was observed in apple cider/blueberry juice combination. Strong antimicrobial activity against H. pylori was exerted by L. helveticus- and B. longum-fermented sample at 48 h. A possible mode of action through the synergy between lactic acid and proline oxidation pathway was suggested.

Salmonella Enteritidis (SE) infections in laying hens is a significant cause of foodborne illness linked to the consumption of contaminated eggs. This dissertation encompasses novel strategies aimed to explore appropriate in-vitro and in-vivo models to evaluate the effects of these novel strategies to reduce SE in laying hens. Firstly, we investigated the potential probiotics, prebiotics, and essential oil combinations to reduce SE in-vitro. The results showed that probiotics and prebiotics are equally effective to reduce SE. In subsequent studies, we evaluated the role of vaccination history on cecal microbiota and SE infections with various doses of oral SE challenge. Our findings showed a dose-dependent response on fecal SE shedding in vaccinated and unvaccinated laying hens. Concurrently, we found an increased abundance of phylum Synergistota in the cecal microbiota following an SE infection, as well as a surge in the relative abundance of fatty-acid producing bacteria. The emphasizing the necessity to understand microbiota changes during SE infection for developing an effective intervention. We further researched the efficacy of a Bacillus-based probiotic and a glycan-based product to reduce SE infections in laying hens. These products were effective in reducing SE in the fecal and cecal content of laying hens. However, our research also underscored the necessity of developing a precise enumerate method to accurately measure the concentration of Salmonella in fecal and tissue samples. Overall, we expect this dissertation to contribute valuable insights into developing effective strategies to reduce SE infections in laying hens. These findings, while promising, underscore the ongoing challenge to develop a robust and effective solution to address the problem of SE in laying hens.

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