The Buckley Lab

Our group investigates the impacts that pharmaceuticals, such as antimicrobials, and nutrition have upon the intestinal microbiota, and how to overcome these negative effects. This research is very exciting as currently there is little known about functional relationship between antibiotic usage, gut dysbiosis and the microbiome. Addressing this gap in healthcare requires moving beyond correlative effects and discovering the causative agents underpinning the relationship between these factors.

Our resident microbiota act in symbiosis with various systems in our body to maintain homeostasis. We know that when in a healthy state, our microbiota acts to provide a level of competitive exclusion to exogenous microorganisms that could be detrimental to our health (colonisation resistance). Our microbiota also contributes to the conditioning and regulation of our immune system, food digestion, and manufacturing important vitamins. During dysbiosis, when the balance of microbiome is disrupted, these functions can fail, leading to functional gastrointestinal (GI) disorders.

It is already known that antimicrobials have the potential to impact the microbiome beyond their target organisms and that this can induce gut dysbiosis, causing negative side effects for the patient. For example, Clostridioides difficile infection (CDI) is strongly associated with dysbiosis caused by certain broad-spectrum antimicrobial treatments such as clindamycin. We also see that the treatments used to manage the initial CDI instance can in turn damage the gut microbiome further, leading to recurrences. We investigate the efficacy of different microbial consortia (biotherapeutics) to overcome gut dysbiosis, caused by antibiotic or certain foods, and re-establishing the homeostasis. We are also beginning to see links drawn between gut dysbiosis and conditions such as colorectal cancer, Crohn’s disease, and ulcerative colitis.

Currently, we know that there are certain biomarkers and metabolites that are important in the prevention of opportunistic pathogen growth, such as the presence of the bile acid cholate in initiating CDI. Therefore, our analysis involves a semi-targeted metabolomic approach to search for the presence of previously identified markers such as cholate, as well as identifying additional biomarkers resulting from antimicrobial exposure and disruption to the microbiome.

The GI tract is a very complex system to study. To overcome this, our lab models the GI tract using a triple-stage chemostat with conditions representative of different points along the human colon with different environmental and nutrient conditions. At the University of Leeds, we have been using and refining these models of the human colon for several years and have succeeded in producing a miniaturised version to allow us to increase capacity to investigate more variables. Our models have been shown to be clinically reflective of CDI and colonisation, expansion by carbapenemase-producing microbes, and efficacy of biotherapeutics to inform clinical trials. The model is inoculated with bacterial populations from faecal material and the effects caused by antimicrobials or nutrients directly on the microbes are assessed. While the models cannot incorporate host factors such as immunological or secretory events, they do provide us with a highly microbiologically reflective model of the human gut.

In our initial observations, clinical antimicrobial prescription practices often involved prescribing combinations of antibiotics or multiple sequential antibiotic treatments. This, unsurprisingly, is correlated with reduced diversity of the microbiota, potentially putting these individuals at increased risk of colonisation or disease with C. difficile or other organisms. Our initial experiments modelled these prescription practices in our in vitro system and noted fundamental changes to the microbiome. Even after five weeks without antibiotics and total levels of bacteria returning to levels seen before antimicrobial instillation, the microbiome failed to re-establish effective colonisation resistance when challenged with multiple opportunistic pathogens. This cements the idea that we must move beyond describing the microbiome and dysbiosis through the metric of population dynamics and begin to explore it as a collection of potentially functionally distinct pathologies.

Looking to the future, we believe that the research our group are undertaking could identify biomarkers which could potentially be used to de-risk the side effects of antimicrobial prescription for patients. Identification of certain biomarkers which give an insight in to the status of the patient’s gut microbiome could influence antibiotic prescription choices to spare the microbiome from further assault, whilst the antibiotic is still clinically effective. Ultimately, this will be an important step in the stratification of healthcare and prescribing behaviours.