Episode 17: Using metabolomics to learn about the activities of gut microbes


The Science, Microbes & Health Podcast 

This podcast covers emerging topics and challenges in the science of probiotics, prebiotics, synbiotics, postbiotics and fermented foods. This is the podcast of The International Scientific Association for Probiotics and Prebiotic (ISAPP), a nonprofit scientific organization dedicated to advancing the science of these fields.

Using metabolomics to learn about the activities of gut microbes, with Dr. Anisha Wijeyesekera

Episode summary:

In this episode, the ISAPP podcast hosts address the topic of metabolomics with Dr. Anisha Wijeyesekera, PhD, a Lecturer in the Department of Food and Nutritional Sciences at the University of Reading, United Kingdom. Dr. Wijeyesekera gives an overview of how metabolic profiling works, including the information provided by different biological samples, and discusses how metabolomics can be used to piece together the contributions of microbes to host health.


Key topics from this episode:

  • Dr. Wijeyesekera introduces the field of metabolomics and describes it as an essential part of systems biology. Metabolic profiling provides a real-time snapshot of the multiple metabolic processes going on in a system at the time the sample was collected.
  • Metabolites are the end products of metabolism; the gut microbiota is the most metabolically active of the microbiomes in the human body.
  • Methodology depends on what information you hope to uncover from your samples. Different biological samples (e.g. stool, urine, plasma) provide different pieces of information; this is cross-referenced with information on metabolic pathways.
  • One application of metabolomics is in identifying biomarkers that can predict patient outcomes. Identifying differences in microbes as well as metabolites could lead to the development of dietary-based supplements for patients to take alongside clinical treatments.
  • Changes in microbial composition may not be that meaningful if the bugs that change are doing the same thing in the end; this is what metabolomics helps uncover.
  • Metabolomics gives you insights into mechanisms when you have a probiotic or prebiotic trial with clinical outcomes. 
  • Short-chain fatty acids are metabolites that are frequently associated with health; changes in these is a clue that the gut microbiota has been impacted by the intervention.
  • Bile acids are metabolites that come from diet. Microbes convert primary bile acids to secondary, which circulate throughout the body. You can measure bile acids to see how gut microbiota are affected by an intervention.
  • Metabolomics is very promising and may be used in more probiotic and prebiotic studies in the future.


Episode abbreviations and links:


About Dr. Anisha Wijeyesekera:

Anisha is a Lecturer in the Department of Food and Nutritional Sciences at the University of Reading, United Kingdom. She previously worked at Imperial College London, where she also obtained her PhD (in Biochemistry). Anisha’s research applies a combined microbial and metabolic phenotyping approach, to better understand the tripartite relationship between diet, gut microbiota and human health. At the University of Reading, she conducts in vitro and in vivo studies for functional assessment of the gut microbiota, particularly in response to prebiotics and probiotics. The ultimate aim is to use this information to tailor nutritional or other interventional therapy to improve health outcomes.

How metabolites help us to understand the effect of gut microbes on health

By Dr. Anisha Wijeyesekera, University of Reading, UK

Much literature relating to the gut microbiota has focused on microbial composition (for example, using culture-dependent and -independent molecular biology approaches). Composition is important; knowing which microbes are present in a community enables us to gain insight into population dynamics and how these may be affected by disease, lifestyle and environmental factors (including diet). However, composition does not provide information on microbial function, and considering the gut contains the most metabolically active microbial community in the whole body, it is thus equally as important to be able to answer the question “what are the microorganisms doing”? This is of particular importance with respect to better understanding the impact of dietary interventions such as prebiotics, probiotics and other ‘biotics on health, where health benefits conferred on the host are mediated via the gut microbiota.

Investigating microbial function

Advances in phenotypic analytical technologies (for example, high-throughput sequencing, biochemical analysis, as well as bioinformatics and other multivariate data analysis approaches), have resulted in a stepwise change in our understanding of microbial function. Metabolic phenotyping (also referred to as metabolomics, metabonomics or metabolic profiling) is an exciting field in systems biology that provides information on the multiple metabolic mechanisms taking place in a system, at a given moment in time (see here). This top-down approach enables high-throughput detection and quantification of low molecular weight molecules present in a biological sample at the time of sampling, without a priori knowledge of metabolites present. Hence, it is ideally suited to augment and complement information obtained from microbial profiling approaches such as metataxonomics, to gain deeper insight into microbial function.

Metabolic phenotyping is conducted by applying analytical chemistry technologies (typically, 1H-nuclear magnetic resonance spectroscopy, and/or mass spectrometry often with chromatographic separation techniques such as gas chromatography and liquid chromatography (for prior separation of molecules followed by detection)) to capture a biochemical snapshot of a sample. In human samples (e.g. urine, blood plasma/serum and stool), metabolites detected using metabolic phenotyping are low molecular weight molecules and include intermediate and end by-products of endogenous host metabolic pathways (e.g. TCA cycle, amino acid metabolism), but also exogenous signals arising from diet, drugs and other lifestyle and environmental stimuli, including products of microbe-host co-metabolism, which provide insight into host-gut microbiota interactions. These include short-chain fatty acids (predominantly acetate, butyrate and propionate, which have a key role in host energy metabolism), bile acids (involved in the gut-liver axis), biogenic amines (involved in the gut-brain axis) and vitamins. Metabolic phenotyping, which provides functional assessment of the gut microbiota and captures information on microbial metabolic activity following ‘biotics intervention, can aid in forming hypotheses about microbial activity that may lead to health benefits.

Challenges in determining the functions of microbes

Nevertheless, functional assessment of the microbiota remains analytically challenging. For example, human metabolic phenotypes contain information relating to different forms of optically active isomers, such as lactate and amino acids (where D- forms originate from bacteria). These enantiomers cannot be differentiated using standard metabolic phenotyping experiments, and it would be important particularly in studies identifying potential biomarkers of disease, to understand the origin of these compounds. Hence, we and others have also conducted mechanistic studies using in vitro human gut model systems (e.g. the model developed by Macfarlane et al., 1998, which  has been validated against gut contents from sudden death victims and give a very close analogy to bacterial activities and composition in different areas of the hindgut), Metabolic screening of fermentation samples using metabolic phenotyping approaches provides a unique opportunity to capture dynamic microbial metabolism that is reflective of the gut microbiome in vivo, and removes contributions derived from host physiological processes (see here).

Unravelling the close interplay between microbes and host, using approaches such as metabolic phenotyping, not only provides insight into host-gut interactions, but aids our understanding of the alterations in gut microbiota mediated mechanisms that result in disease, and which demonstrate potential as therapeutic targets. More research in this area will aid in deepening understanding of the role of the gut microbiota in health and disease, and aid in the design of interventions targeting the gut microbiota (for example, the development of functional foods) for therapeutic benefit.