Where and Why: The Influence of Host Metabolism on Bacterial Niche Specificity

The aim of this work is to determine to how bacteria sense if their environment is optimal for colonisation. In previous work we have shown that the host metabolite, D-serine, affects if bacteria bind to host tissues. The present proposal is important because if these sensing mechanisms can be inhibited, there is the opportunity to develop novel ways of combating pathogens by interfering with their ability to occupy specific niches, and therefore to prevent pathogenesis. For example, our prediction is that strains that can use D-serine for growth are more likely to cause infections in organs where this amino acid is abundant, such as the urinary tract and brain. The diet of patients with a strong susceptibility to such infections (e.g. patients with catheters, women with recurrent bladder infections) could be modified to reduce the concentration of this amino acid in their urine. This push towards overall patient health through diet perfectly fits the BBSRC strategic priority "Food, Nutrition and Health".

Bacteria live and thrive in and on a huge variety of environments including all animals and plants, acting as both the most significant component of the microbiota and the cause of many diseases. The bacterial contribution to health and the environment is enormous with central roles in processes as diverse and important as immune development and nutrient cycling. Many of these roles require bacteria to colonise a defined location, a specific niche. Understanding how and why bacteria colonise particular sites is therefore a fundamental question with profound implications for health, biosecurity and food production. Our work has found that an unusual amino acid, D-serine is produced by humans in some tissues. This D-serine affects how bacteria respond to that environment, so it acts to either promote or discourage colonisation. In other words, D-serine strongly affects the bacteria that colonise particular niches within the human body.

We have discovered the proteins that acts collectively to sense and respond to D-serine. Fascinatingly, one core protein, the D-serine transporter as been shown to be one of the most commonly found sequences in nature. This highlights just how important the protein in for more complex animals, as well as the bacteria. We plan to use our bacteria as a model to help understand this system. We want to know how bacteria detect this amino acid as it will help in our basic understand of why particular diseases are caused. To do this we will dissect the molecular pathway involved using a combination of methods. We will look at how the amino acid is bound and what effects it has on the proteins that bind it. We will then work out how this causes changes in the production of the factors that affect where and how the bacteria colonise. We are confident that our work will provide a major step forward in our understanding of how bacteria cause specific diseases and, more generally, how they interact with humans and other animal hosts.

The bacterial contribution to health and the environment is enormous with critically important roles in processes as diverse and important as immune development and nutrient cycling. Many of these roles require bacteria to colonise a defined location, a specific niche. Understanding how and why bacteria colonise particular sites is therefore a fundamental question with profound implications for health, biosecurity and food production.

Our recent work has focused on analysing the roles of both bacterial and host metabolism in affecting bacterial gene expression. We have found that the amino acid D-serine drives niche adaptation and bacterial evolution by affecting gene selection in E. coli. How E. coli responds to D-serine can vary according to the specific subtype involved. Pathogenic strains of the bacterium, E. coli cause many serious diseases including hospital-acquired infections such as urinary tract infections (UTIs), meningitis, diarrhea and septicemia. These pathogenic E. coli can be classified as either ExPEC (extra-intestinal pathogenic E. coli) due to their ability to cause disease beyond the gastrointestinal tract and InPEC (intestinal pathogenic E. coli) that are highly niche-specific and are very rarely associated with the colonisation of distal sites. Our data indicate that ExPEC and InPEc strains respond very differently to D-serine, a trait we will investigate in this proposal.

We use E. coli as a model to study this D-serine system and its relevance to niche specificity. The key questions that we plan to address in this proposal are firstly, how do E. coli strains sense and respond to D-serine? And secondly, how does this response vary between different pathotypes to affect niche specificity? To address this we will use a combination of established techniques to understand the molecular and biochemical basis to D-serine sensing. We also plan to test if the same proteins are functional in different bacterial species.

The aims and objectives of the proposed research will contribute to advances in knowledge and understanding at the fundamental level. As our work on niche specificity develops, we will be able to more precisely define potential applications derived from this research. However, in the medium and long term this fundamental knowledge could have significant economic and societal impact as described below.
Health care providers and patients: understanding how these infections are influenced by host metabolism could have profound implications for prevention and treatment of these pathogens. For example, our prediction is that strains that can metabolise D-serine are more likely to cause specific infections of tissues abundant in this amino acid. One outcome might be that the diet of patients with a strong susceptibility to such infections (e.g. patients with catheters, women with recurrent infections) modulated be formulated to reduce the concentration of this amino acid in the urine. Furthermore, understanding the basis to how E. coli O157:H7 colonises disease in humans is very important. Children under five years of age have been shown to be particularly vulnerable to this organism with Shiga toxin (Stx) produced inducing hemolytic uremic syndrome (HUS), resulting in acute kidney injury in 50-70% of patients. Longer-term sequelae include ongoing chronic renal disease (usually requiring kidney replacement) and hypertension, as well as a variety of neuropsychiatric problems. There is no effective therapy that can alter progression from initial O157:H7 infection to HUS. Indeed, treatment with conventional antibiotics increases the likelihood of progression through the release of Stx. Our research will help in understanding the potential for this organism to colonise new sites and niches and the genetic factors involved.
Money saving to the economy and NHS: Research by the Centre for Foodborne Illness Research has found that, one-third of E. coli O157:H7 HUS survivors will suffer life-long medical problems, such as high blood pressure, diabetes, kidney failure and brain damage. These costs are estimated to be ten times greater than those associated with the initial infection alone. Based on data from Canadian studies we estimate that the cost to the UK health system is around £9 million per year. As our research progresses we will aim to develop partnerships with strategic partnerships with groups working on human metabolism to explore the relationship between diet formulation and levels of D-serine in the body. This push towards overall patient health through careful formulation of diets perfectly matches fits the BBSRC strategic priority "Food, Nutrition and Health".
Food manufacturers: As we understand the importance of diet and its influence on infection, there will be the opportunity to develop formulated dietary programs that will require interfacing with food and healthcare manufacturers. This sector is very important across Europe, with over 1750 health-product manufacturers represented by the European Federation of Associations of Health Product Manufacturers (EHPM) alone. The UK has become a leading source of new foods with health propositions. In 2007, 36% of new health product launches in the European Union originated in the UK. Our work will help maintain this competitive advantage.
Antibiotics development industry: There is a clear link between expression of the "sensory" system we have found and virulence factors. This provides a fantastic opportunity to develop novel compounds that block this pathway and effectively switch off key proteins used for attachment. New mechanisms to combat hard to treat infection, particularly gram negative infections are a cross council priority area that still has been sorely neglected despite the urgency of the issue.
Capacity building: the work will feed directly into training at the forefront of research (applied and basic) in respect of Food Security (a BBSRC priority area).