The Gut Microbiome and Health: A Comprehensive Overview

The human body is a living landscape teeming with microscopic life forms, collectively known as the microbiome. These tiny inhabitants, including bacteria, viruses, and fungi, are crucial for our health. They assist in digestion, regulate our immune system, produce vital vitamins [1] and can even impact our mood. [2]

The food we eat transforms your gut microbiome, influencing the structure and behaviour of your gastrointestinal tract, immune cells, and beyond. Laboratory testing can identify the unique composition of your microbiome to personalise nutrition recommendations.

The microbiome is a dynamic entity, constantly changing in response to our diet, environment, lifestyle, and medication use; we can mould our microbiome and influence our health. Understanding the microbiome and its profound impact on our well-being is a fascinating journey into the microscopic world within us.

An Introduction to the Microbiome

We're at least as much bacterial as we are human if you look at cell and gene counts. Bacteria, while only a fraction of our body weight, may even outnumber our human cells by 1.3 fold [3] and our human genes 100 to 1. [4]They're vital for our immunity, digestion, and disease protection, and they start colonising us from birth.

The largest bacterial population in our bodies is in the colon. The types of bacteria that predominate change dramatically over the first 1000 days of our life, influenced by our gestation term, birthing method, early feeding and weaning patterns, and our dietary habits after weaning.

For instance, the Bacteroides species comprise up to a quarter of the bacteria in our gut due to their ability to adapt quickly to environmental, dietary and immune system variability [5].

Bacteroides are more than just passive inhabitants. They're mutualists, benefiting us and benefiting from us. For instance, certain Bacteroides strains can digest various complex carbohydrates and fibres in early weaning as the diet expands beyond milk consumption [6]. Several genes have been identified in this species that allow them to sense signals in their environment and adjust their metabolism, structure and behaviour in response [5].

This flexibility is advantageous given the changes in food and nutrition sources we consume in the first few years of life and across the seasons. As mutualists, they can do more than utilise different nutrient sources for their energy use: they even pre-digest complex sugars that other bacteria in our gut cannot digest alone, making it easier for them to get enough energy as dietary sources change. Like many other beneficial bacteria, Bacteroides can also change antigens on their surface to evade our immune response, making them valuable allies.

The gut microbiome's equilibrium and metabolites are fundamental to our health and well-being. Shifts in the balance of this ecosystem are linked to obesity [7], diabetes [8], cardiovascular disease [9], and even neurological conditions [10]. This is because the gut microbiome can produce a variety of bioactive compounds that can enter the bloodstream and influence the function of distant organs. In the following sections, we will delve deeper into the fascinating world of the gut microbiome, exploring its connection with diet, its impact on metabolic health, and its potential as a target for therapeutic interventions. We will also introduce laboratory stool testing as a tool for assessing gut health and the role of nutrition in maintaining a healthy microbiome.

The Gut Microbiome in Obesity and Metabolic Disease

The Gut Microbiome and Inflammatory Bowel Disease

Enteric Infections and Malnutrition

The Role of Nutrition in Maintaining the Microbiome

Probiotics vs Prebiotics: A Brief Introduction

Laboratory Stool Testing and the Microbiome

Plenty remains to be discovered about the microbiome, how it affects our health, and how we can optimise it through diet, lifestyle and therapeutic products. Yet even now, there are many simple, safe and exciting applications to help hone and improve our gut health.

A professional nutritional therapy practitioner like Adam Greer can help you customise and prioritise dietary changes that are most suitable for optimising your gut microbiome. If you're interested in learning about your unique microbiome, book a free discovery call to find out how nutritional therapy can help you. You can also read about nutritional therapy, which goes far beyond the microbiome to personalise your diet and lifestyle recommendations.

References 1. Rowland I, Gibson G, Heinken A, Scott K, Swann J, Thiele I, et al. Gut microbiota functions: metabolism of nutrients and other food components. European Journal of Nutrition. 2017 Apr 9;57(1):1–24. 2. Skowron K, Budzyńska A, Wiktorczyk-Kapischke N, Chomacka K, Grudlewska-Buda K, Wilk M, et al. The Role of Psychobiotics in Supporting the Treatment of Disturbances in the Functioning of the Nervous System—A Systematic Review. International Journal of Molecular Sciences. 2022 Jan 1;23(14):7820. 3. Sender R, Fuchs S, Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLOS Biology. 2016 Aug 19;14(8):e1002533. 4. Gilbert JA, Blaser MJ, Caporaso JG, Jansson JK, Lynch SV, Knight R. Current understanding of the human microbiome. Nature Medicine. 2018 Apr;24(4):392–400. 5. Wexler HM. Bacteroides: the Good, the Bad, and the Nitty-Gritty. Clinical Microbiology Reviews. 2007 Oct 1;20(4):593–621. 6. Zafar H, Saier MH. Gut Bacteroides species in health and disease. Gut Microbes. 2021 Jan 1;13(1):1–20. 7. Davies Naomi K, O’Sullivan JM, Plank LD, Murphy R. Altered gut microbiome after bariatric surgery and its association with metabolic benefits: A systematic review. Surgery for Obesity and Related Diseases. 2019 Apr;15(4):656–65. 8. Letchumanan G, Abdullah N, Marlini M, Baharom N, Lawley B, Omar MR, et al. Gut Microbiota Composition in Prediabetes and Newly Diagnosed Type 2 Diabetes: A Systematic Review of Observational Studies. Frontiers in Cellular and Infection Microbiology. 2022 Aug 15;12(943427). 9. Sanchez-Gimenez R, Ahmed-Khodja W, Molina Y, Peiró OM, Bonet G, Carrasquer A, et al. Gut Microbiota-Derived Metabolites and Cardiovascular Disease Risk: A Systematic Review of Prospective Cohort Studies. Nutrients. 2022 Jun 27;14(13):2654. 10. Hung CC, Chang CC, Huang CW, Nouchi R, Cheng CH. Gut microbiota in patients with Alzheimer’s disease spectrum: a systematic review and meta-analysis. Aging. 2022 Jan 14;14(1):477–96. 11. Roshanravan N, Bastani S, Tutunchi H, Kafil B, Nikpayam O, Mesri Alamdari N, et al. A comprehensive systematic review of the effectiveness of Akkermansia muciniphila, a member of the gut microbiome, for the management of obesity and associated metabolic disorders. Archives of Physiology and Biochemistry. 2021 Jan 15;129(3):1–11. 12. Abuqwider JN, Mauriello G, Altamimi M. Akkermansia muciniphila, a New Generation of Beneficial Microbiota in Modulating Obesity: A Systematic Review. Microorganisms. 2021 May 20;9(5):1098. 13. Pittayanon R, Lau JT, Leontiadis GI, Tse F, Yuan Y, Surette M, et al. Differences in Gut Microbiota in Patients With vs Without Inflammatory Bowel Diseases: A Systematic Review. Gastroenterology. 2020 Mar;158(4):930-946.e1. 14. Nadalian B, Yadegar A, Houri H, Olfatifar M, Shahrokh S, Asadzadeh Aghdaei H, et al. Prevalence of the pathobiont adherent‐invasive Escherichia coli and inflammatory bowel disease: a systematic review and meta‐analysis. Journal of Gastroenterology and Hepatology. 2020 Sep 28;36(4):852–63. 15. Aldars-García L, Chaparro M, Gisbert JP. Systematic Review: The Gut Microbiome and Its Potential Clinical Application in Inflammatory Bowel Disease. Microorganisms. 2021 Apr 30;9(5):977. 16. Abdel-Rahman LIH, Morgan XC. Searching for a Consensus Among Inflammatory Bowel Disease Studies: A Systematic Meta-Analysis. Inflammatory Bowel Diseases. 2022 Sep 16;29(1):125–39. 17. Zhang M, Sun K, Wu Y, Yang Y, Tso P, Wu Z. Interactions between Intestinal Microbiota and Host Immune Response in Inflammatory Bowel Disease. Frontiers in Immunology. 2017 Aug 14;8(942). 18. Iddrisu I, Monteagudo-Mera A, Poveda C, Pyle S, Shahzad M, Andrews S, et al. Malnutrition and Gut Microbiota in Children. Nutrients. 2021 Aug 1;13(8):2727. 19. Tickell KD, Atlas HE, Walson JL. Environmental enteric dysfunction: a review of potential mechanisms, consequences and management strategies. BMC Medicine. 2019 Nov 25;17(1). 20. Haberman Y, Iqbal NT, Ghandikota S, Mallawaarachchi I, Tzipi Braun null, Dexheimer PJ, et al. Mucosal Genomics Implicate Lymphocyte Activation and Lipid Metabolism in Refractory Environmental Enteric Dysfunction. Gastroenterology. 2021 May 1;160(6):2055–71.e0. 21. Bhattacharjee A, Burr AHP, Overacre-Delgoffe AE, Tometich JT, Yang D, Huckestein BR, et al. Environmental enteric dysfunction induces regulatory T cells that inhibit local CD4+ T cell responses and impair oral vaccine efficacy. Immunity. 2021 Aug 10 [cited 2023 Jun 7];54(8):1745-1757.e7. 22. Oliver A, Chase AB, Weihe C, Orchanian SB, Riedel SF, Hendrickson CL, et al. High-Fiber, Whole-Food Dietary Intervention Alters the Human Gut Microbiome but Not Fecal Short-Chain Fatty Acids. Jansson JK, editor. mSystems. 2021 Apr 27;6(2). 23. Cândido TLN, da Silva LE, Tavares JF, Conti ACM, Rizzardo RAG, Gonçalves Alfenas R de C. Effects of dietary fat quality on metabolic endotoxaemia: a systematic review. British Journal of Nutrition. 2020 May 8;124(7):654–67.