Potential for enriching next-generation health-promoting gut bacteria through prebiotics and other dietary components

The human intestinal commensal microbiota and associated metabolic products have long been regarded as contributors to host health. As the identity and activities of the various members of this community have become clearer, newly identified health-associated bacteria, such as Faecalibacterium prausnitzii, Akkermansia muciniphila, Ruminococcus bromii and Roseburia species, have emerged. Notably, the abundance of many of these bacteria is inversely correlated to several disease states. While technological and regulatory hurdles may limit the use of strains from these taxa as probiotics, it should be possible to utilize prebiotics and other dietary components to selectively enhance their growth in situ. Dietary components of potential relevance include well-established prebiotics, such as galacto-oligosaccharides, fructo-oligosaccharides and inulin, while other putative prebiotics, such as other oligosaccharides, polyphenols, resistant starch, algae and seaweed as well as host gut metabolites such as lactate and acetate, may also be applied with the aim of selectively and/or differentially affecting the beneficial bacterial community within the gastrointestinal environment. The present review provides an overview of the dietary components that could be applied in this manner

Evaluating substrate utilisation to target newly identified health-promoting gut bacteria

Promoting the growth and/or activity of potentially beneficial human gut microorganisms through the provision of specific substrates has been the subject of many studies over recent decades. Such substrates can include prebiotics, which promote growth in a targeted manner, but prebiotics can also be combined with other less target-specific nutrients to further enhance the growth of these targets. This field has continued to advance in recent years and has also expanded in response to the identification of new target species, such as Akkermansia muciniphila, Eubacterium rectale, Faecalibacterium prausnitzii, Roseburia inulinivorans, and Ruminococcus bromii, many of which produce metabolites that can contribute to host health. These developments have been in part due to improvements in culture-based techniques, advances in DNA sequencing-based approaches and improved computational pipelines. The combined use of these tools has enormous potential with respect to elucidating substrates that can be applied to specifically target microbes of interest and is the focus of this thesis. Chapter 1 reviews the literature relating to prebiotics, and potential prebiotics, with a focus on more recently identified health-promoting gut bacteria. Building on this, in Chapter 2 we applied both in silico and in vitro techniques to predict and assess substrate utilisation for seven strains across five species of interest. The bioinformatics-based component of Chapter 2 is expanded in Chapter 3 through the analysis of publicly available microbial genomes of the same species of interest and, through the creation of metabolic models, predicting the substrates that these microorganisms could consume. Finally, in Chapter 4 we employ an ex vivo model to evaluate, through shotgun metagenomic sequencing, the impact different substrates, including simple sugars, oligosaccharides, and whey protein concentrate had on the taxonomic composition and functional potential of a colonic microbiome. Thus, facilitating the design and testing of a functional prototype beverage comprised of some substrates assessed here. Overall, this thesis explores different substrates that could be applied to target the growth and/or activity of recently identified health modulating microbes within the human gut. Combining in silico, in vitro, and ex vivo approaches have the potential to identify and assess a variety of substrates that may be applied to bring about microbiome-mediated enhancements of host health

Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health

peer-reviewedOver the last two decades our understanding of the gut microbiota and its contribution to health and disease has been transformed. Among a new ‘generation’ of potentially beneficial microbes to have been recognized are members of the genus Eubacterium, who form a part of the core human gut microbiome. The genus consists of phylogenetically, and quite frequently phenotypically, diverse species, making Eubacterium a taxonomically unique and challenging genus. Several members of the genus produce butyrate, which plays a critical role in energy homeostasis, colonic motility, immunomodulation and suppression of inflammation in the gut. Eubacterium spp. also carry out bile acid and cholesterol transformations in the gut, thereby contributing to their homeostasis. Gut dysbiosis and a consequently modified representation of Eubacterium spp. in the gut, have been linked with various human disease states. This review provides an overview of Eubacterium species from a phylogenetic perspective, describes how they alter with diet and age and summarizes its association with the human gut and various health conditions

Methods to mitigate Escherichia coli blooms in human ex vivo colon model experiments using the high throughput micro-Matrix bioreactor fermentation system

Ex vivo colon model experiments are frequently employed as a means to assess the gut microbiome modulating potential of different foods, food ingredients and dietary supplements. A number of useful models already exist; however, they tend to be relatively low in terms of throughput (3–4 samples per experiment) with a long experiment duration of one to a number of weeks. Therefore, a need for a high-throughput system with a short duration time is required to enable screening of large numbers of samples. Therefore, we report here on the development of a system based on the Applikon micro-Matrix bioreactor which has the capacity to run 24 samples with an experiment duration of 48 h. However, Escherichia coli blooms are a common problem encountered in this model. Here, we describe the factors that contribute to such blooms and provide approaches to address them, providing: • Step by step optimisation of processes involved in conducting ex vivo distal colon experiments using the micro-Matrix bioreactor fermentation platform • Recommended steps for users on how to attenuate E. coli blooms in such ex vivo colon model experiments

Initial Teacher Education: Enriching and Extending Partnerships

The current publication, Initial Teacher Education: Enriching and Extending Partnerships is fifth in a series of publications that report on the projects of this initiative. Foundational to this series is the belief that the combined wisdom of field practitioners and university educators can transform new teacher preparation. High quality teacher education programs depend on such partnerships because collective efforts are vital for educators to be able to continually examine and develop successful ways to reach the diverse learners in today’s classrooms. Through mutually enhancing the intersecting school-university communities, educators can better address complex challenges that are confronting schools—especially while they seek to deepen and improve student understanding and achievement