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The Gut Microbiome

Have you heard of the gut microbiome?

The microbiome refers to the trillions of bacteria, fungi and other microorganisms living in our gut.1,2 Lately, it’s made newspaper headlines and now celebrities are endorsing microbiome tests to inform personalised dietary advice.


It sounds like science fiction, but recent animal experiments have found the bacteria in our gut could influence our behaviour, with an intact microbiome being associated with more social behaviour in mice and shoaling of zebrafish.3,4 It sounds logical that bacteria would want us to spend more time together to aid their spread… and evidence suggests our microbiota could be influencing far more than how sociable we feel!


Changes to our microbiota are potentially associated with mental health conditions.5 For example, bacteria producing certain fatty acids have been linked to improved wellbeing and quality of life.6 Adverse changes to the microbiota could also be associated with the development of neurological conditions, from Alzheimer’s and Parkinson’s disease to migraines.7,8 Beyond neurological connections, changes in our gut microbiota have also been linked with obesity, type 2 diabetes, hepatic steatosis and inflammatory bowel disease, with evidence that the microorganisms in our gut could be influencing our immune pathways, lipid and glucose metabolism.9 


Supporting the gut microbiota


Discovering all these potential links between our microbiota and whole person health, has perhaps made you wonder about the potential impact of antibiotics? Well, evidence suggests there is an association between antibiotic use and colon cancer risk,10, 11 but further research is needed. Perhaps this could inspire an advanced generalist review of antibiotic prescribing in your practice?  You can read more on this in a WiseGP GEM about antibiotics and colon cancer…


So apart from avoiding antibiotics wherever possible, what else can we do to support our microbiota? You may be wondering whether probiotics could help? Well, a recent systematic review found existing evidence to be inconclusive!12 We do know a Mediterranean diet high in fibre, particularly from vegetables is likely to help our gut health.2 Some sources also advocate fermented foods, such as sauerkraut or kimchi.13 Studies are currently exploring the potential benefits of faecal transplants, for instance, in people with Parkinson’s disease.14 Research to uncover the complex interactions between our microbiota and health could help to inform the future treatments of a range of linked conditions.

Considering the gut microbiota in everyday consultations…

So, how would you respond if a 25-year-old patient with irritable bowel syndrome (IBS) presented to you for advice about a video on TikTok recommending home microbiome test-kits and “DIY” faecal transplants for bowel problems?


There are various approaches you could take. What would be your WiseGP instinct?

  • You could highlight the lack of strong evidence to inform this approach in IBS and warn about the potential risks.

  • You might offer to explore the evidence behind these suggestions to inform a follow-up call. However, would you have the time to dedicate to a literature search?

  • You could speak with your colleagues. Following recent rises in consultations about suspected ADHD and weight-loss injections, you may have taken a practice-led approach to managing trending problems. Sharing learning across your team can save time and ensure consistent advice is offered, with information shared on practice social media or via set text messages to support consultations.

  • You could explore with the patient what led them to consider experimental treatments. Have their symptoms changed, do they have red flags, or could their presentation suggest underlying anxiety you could support them to manage? Your exploration of their presentation could inform an explanation of their symptoms, as part of the 3E’s approach discussed in the newsletter linked to this blog, "Have you heard of it?".


Looking beyond the biomedical evidence…


If we look beyond biomedical evidence for IBS management, social sciences literature provides some valuable insights. For example, on exploring patient perspectives of IBS treatments, I came across a qualitative study considering how people with IBS seek and appraise different treatments.16 The study discussed how patients could get trapped in a cycle of hope and despair, while desperately searching for a cure. One suggestion was that GPs could work with patients with IBS to help them to develop acceptance and coping strategies to escape these vicious cycles.


So beyond discussing the evidence surrounding microbiome testing and faecal transplants, would the most effective approach be to explore a patients’ illness perceptions and treatment aims, with a goal of supporting them to move from seeking a cure, to developing coping strategies? In the WiseGP newsletter, “Have I missed something?”, we discuss how using the concept of creative capacity could help patients to draw on their own resources to co-develop personalised management plans. Perhaps this is something you could test in your everyday practice?


So, should we be considering the microbiota as part of whole person care?


Perhaps… Like many areas of medicine, the evidence is rapidly progressing, so where new revelations are likely to be on the horizon, having the skills to respond to new information and guide patients towards productive discussions will prove invaluable.


Hippocrates once said, “All disease begins in the gut”. I wonder how true that will prove to be?


Dr Annabelle Machin

WiseGP Fellow


1.       Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823-1836. doi: 10.1042/BCJ20160510

2.       Frankel M, Warren M. Are you thinking clearly? London: Hachette UK, 2022.

3.       Crumeyrolle-Arias M, Jaglin M, Bruneau A et al. Absence of the gut microbiota enhances anxiety-like behavior and neuroendocrine response to acute stress in rats. Psychoneuroendocrinology. 2014;42:207-217.

4.       Sherwin E, Bordenstein SR, Quinn JL, Dinan TG, Cryan JF. Microbiota and the social brain. Science. 2019;366(6465). doi:10.1126/science.aar2016

5.       Shoubridge AP, Choo JM, Martin AM et al. The gut microbiome and mental health: advances in research and emerging priorities. Mol Psychiatry. 2022;27:1908–1919.

6.       Valles-Colomer M, Falony G, Darzi Y et al. The neuroactive potential of the human gut microbiota in quality of life and depression. Nat Microbiol. 2019;4: 623–632.

7.       Villavicencio-Tejo F, Olesen MA, Navarro L et al. Gut-Brain Axis Deregulation and Its Possible Contribution to Neurodegenerative Disorders. Neurotox Res. 2023;42(1):4. doi: 10.1007/s12640-023-00681-0. PMID: 38103074

8.       Risbud A, Abouzari M, Dialilian HR. Gut-Brain Connection, Myth or Reality? Singapore: World Scientific, 2021.

9.       de Vos WM, Tilg H, Van Hul M et al. Gut microbiome and health: mechanistic insights. Gut. 2022;71(5):1020-1032. doi: 10.1136/gutjnl-2021-326789

10.    Zhang J, Haines C, Watson AJM, et al. Oral antibiotic use and risk of colorectal cancer in the United Kingdom, 1989–2012: a matched case–control study.Gut. 2019;68:1971-1978. doi: 10.1136/gutjnl-2019-318593

11.    McDowell, R., Perrott, S., Murchie, P. et al. Oral antibiotic use and early-onset colorectal cancer: findings from a case-control study using a national clinical database. Br J Cancer. 2022;126:957–967.

12.    Madabushi JS, Khurana P, Gupta N, Gupta M. Gut Biome and Mental Health: Do Probiotics Work? Cureus. 2023;15(6):e40293. doi: 10.7759/cureus.40293

13.    Leeuwendaal NK, Stanton C, O’Toole PW, Beresford TP. Fermented foods, health and the gut microbiome. Nutrients. 2022; 14(7):1527. Doi:10.3390/nu14071527

14.    Vendrik KE, Chernova VO, Kuijper EJ, Terveer EM, van Hilten JJ, Contarino MF; FMT4PD study group. Safety and feasibility of faecal microbiota transplantation for patients with Parkinson's disease: a protocol for a self-controlled interventional donor-FMT pilot study. BMJ Open. 2023;13(10):e071766. doi: 10.1136/bmjopen-2023-071766

15.    Reeve J. Medical Generalism, Now! Reclaiming the Knowledge Work of Modern Practice. Boca Raton:CRC Press; 2023.

16.    Harvey JM, Sibelli A, Chalder T, Everitt H, Moss-Morris R, Bishop FL. Desperately seeking a cure: Treatment seeking and appraisal in irritable bowel syndrome. Br J Health Psychol. 2018;23:561-579.


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