The GI microbiome is (arguably) the most important of the human microbial communities. It is also the most studied. Thirty years ago, analysis of the GI microbiome involved taking stool samples and culturing (i.e. growing) the bacteria found within and categorising them by the bacterial family (or genus) they belonged to. Different families were considered good (probiotic), others bad (pathogenic) and those in the middle were called commensals. Fast forward to today and microbiome analysis is no longer conducted using culture techniques at the genus level (e.g. bifidobacterium) - or even the species level (e.g. Bifidobacterium animalis) - but at the much more precise individual bacterial strain level (e.g. Bifidobacterium animalis subsp. lactis CECT 8145; otherwise known as BPL-1). This is because two strains of the same species can, and do, have unique effects on their human host, hence the beneficial effects of probiotics are ‘strain-specific’ i.e. one strain may be beneficial in diagnosis-x whereas another strain from the same species may be beneficial in diagnosis-y, but not in diagnosis-x. The analysis does not stop at just understanding which probiotic strains may be present (or absent) in a particular individual; now it is possible to conduct functional analyses of microbial communities to understand how these microorganisms work together. After all, the presence or absence of a particular probiotic strain might not be of primary importance; but rather the cocktail of microbial metabolites (the study of which is known as metabolomics) or proteins (the study of which is known as proteomics) produced which is important. Understanding the complex systems-level interactions seen in the GI microbiome is only possible with advanced bioinformatics and machine learning technology: the result being that microbiome research is an odd mix of microbiologists, geneticists, clinicians, data scientists and AI techies.


Manipulation of the GI microbiome as a route to protecting or enhancing GI health has traditionally been the primary focus of probiotic research. There is an astonishing number of clinical trials and scientific papers on the microbiome and its effect on gastroenteritis, irritable bowel syndrome and antibiotic associated diarrhoea, to name but a few. However, in recent years, the role of the microbiome on organ systems beyond the GI tract has shifted the centre of gravity for research. Now you are as likely to read a scientific publication about the GI microbiome impacting disorders of the skin, the immune system or even psychiatric disorders. The GI microbiome can also exert interesting indirect effects. One of the really exciting developments in microbiome research in recent years has been understanding how medications might be affected by the organisms in our GI tract. A number of biotech companies exist solely on this basis – to understand how GI microbiome patterns can affect commonly-prescribed medications: a field known as pharmacomicrobiomics. In some high-cost pharmaceutical treatments – such as the so-called ‘biologics’ for inflammatory bowel disease and some cancers – understanding which patients will respond to which treatments can have enormous cost implications for payers. In this instance, understanding how microbiome modulation can turn non-responders into responders offers huge financial incentives.


21 | ADMISI - The Ghost In The Machine | Q2 Edition


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