Factors that affect your inner gut microbial forest (II)

Building on our previous exploration of how diet, medication, and lifestyle choices intricately shape the gut microbiota, part two of our series delves deeper into this fascinating ecosystem. We will examine the profound effects of exercise on gut health, uncover the complex relationship between dietary habits and gut-related diseases, explore the influence of genetics on microbiota composition, and discuss emerging therapeutic applications. 

Exercise and Its Influence on Gut Microbiota

Physical exercise has been identified as a key determinant in shaping gut microbiota. Studies reveal that individuals engaging in regular physical activity exhibit a more diverse microbial population in their intestines, which is linked to improved gut health and enhanced immune function. This diversity is not just in terms of species but also in their functional roles, contributing positively to the host's health. For instance, professional athletes like rugby players have demonstrated a more diverse gut microbiota compared to non-athletes.

This increased microbial diversity is associated with the promotion of an anti-inflammatory state within the gut. Physical activity fosters the production of short-chain fatty acids (SCFAs) by gut microbes, which have anti-inflammatory effects. This is particularly beneficial in managing conditions related to gut inflammation, showcasing the therapeutic potential of exercise in maintaining a healthy gut microbiota and mitigating disease risks linked to microbial dysbiosis.

Additionally, the influence of exercise on gut microbiota extends across different age groups. In children, physical activity is associated with a healthier and more diverse gut microbiota, emphasising the importance of exercise from a young age for gut health and disease prevention.

Regular physical activity is also associated with lower levels of systemic inflammation, contributing to a balanced gut microbiota and prevention of gut-related disorders. Furthermore, exercise leads to changes in the relative abundance of specific beneficial bacterial species, underscoring the multifaceted impact of physical activity on gut microbiota and overall well-being.

Dietary Habits, Gut Microbiota, and Disease

Dietary habits profoundly influence the composition and function of the gut microbiome. A Balanced diet plays a crucial role in maintaining overall health and can significantly impact the risk of various diseases. For instance, the Western diet, characterised by low intake of microbiota-accessible carbohydrates (MACs), has been associated with changes in microbiota composition and functionality, potentially leading to inflammation and immune dysregulation.

Given the profound impact of diet on gut health, various dietary habits have been examined for their influence on the gut microbiota. High-fat diets, for example, have been associated with a decrease in intestinal bacterial diversity, negatively impacting gut health and overall well-being. On the other hand, the intake of non-digestible carbohydrates, particularly dietary fiber, has been shown to play a crucial role in shaping the gut microbiome and influencing health outcomes.

A specific example of the impact of diet on the gut microbiome is the influence of the Western diet, which is low in microbiota-accessible carbohydrates (MACs). Research has shown that this diet can lead to alterations in microbiota composition and functionality, potentially resulting in inflammation and immune dysregulation. This underscores the importance of a balanced diet rich in MACs for promoting a healthy gut microbiome and overall well-being.

Long-term dietary habits also have a significant impact on gut microbial diversity. Traditional populations, for example, showcase different gut microbiomes compared to those in modern societies. The shift in human eating habits over time, particularly during the industrial era, has not necessarily contributed to a more resilient gut microbiome. This emphasizes the need for dietary interventions to alleviate health problems associated with microbiota dysbiosis.

Host Genetics and Its Impact on Gut Microbiota

Host genetics play a significant role in determining the composition of the gut microbiota. Research has shown that specific genetic loci can significantly influence the microbiome, highlighting the complex interplay between host genetics and the gut microbial ecosystem [10,13].

Several studies have highlighted the complex relationship between host genetics and the gut microbiome. For instance, a genome-wide association study identified 31 loci affecting the microbiome at a genome-wide significant threshold, providing insights into the genetic factors influencing the gut microbiome [10,13]. Such findings not only provide a deeper understanding of the role of genetics in shaping the microbiome but also emphasize the potential for leveraging this knowledge to develop personalized interventions targeting the gut microbiome.

Moreover, the interplay between host genetics and gut microbiota has been implicated in the pathogenesis of various diseases. For instance, compelling evidence suggests that the gut microbiome may play a causal role in conditions like ulcerative colitis and rheumatoid arthritis. This highlights the intricate relationship between host genetics, gut microbiota composition, and human health and underscores the need for a deeper understanding of this relationship.

Therapeutic Implications of Gut Microbiota

The composition of the gut microbiota has significant therapeutic implications. Understanding the influence of diet, medication, lifestyle, and genetics on the gut microbiome can guide the development of targeted interventions to optimize gut health [1,2,3,4].

Physical exercise, for instance, has been shown to increase intestinal microbial diversity, promoting an anti-inflammatory state. Recognizing this, healthcare professionals could leverage exercise as a therapeutic intervention to positively influence the gut microbiota. This approach could be particularly beneficial in managing conditions such as inflammatory bowel disease and obesity, which are associated with gut dysbiosis.

Dietary interventions also represent a promising approach to managing gut health. Given that the Western diet, low in microbiota-accessible carbohydrates (MACs), has been linked to altered microbiota composition and functionality, leading to inflammation and immune dysregulation, dietary strategies that promote a balanced intake of MACs could be beneficial. Such strategies could help mitigate the risk of obesity and inflammatory bowel disease, conditions linked to gut microbiota alterations.


In our previous comprehensive exploration of the gut microbiota, spanning two insightful articles, we have unraveled how diet, medication, lifestyle choices, and genetics intertwine to shape this vital ecosystem within us. From the profound impacts of our daily habits on microbial diversity to the potential of targeted dietary and lifestyle interventions, these discussions have highlighted the critical role of gut microbiota in our overall health and well-being. The conclusion underscores the importance of understanding these complex interactions for developing personalised approaches in healthcare. Integrating insights from both parts of our series makes it evident that a holistic view of gut health, informed by individual characteristics and habits, is key to preventing and managing diseases linked to microbial imbalance. This journey through the world of gut microbiota enlightens us about the intricate connections within our bodies and opens up new avenues for health optimisation and disease prevention. 

  1. Falony G,Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, et al. Population-level analysis of gut microbiome variation. Science. 2016; 352(6285):560-4. doi: 10.1126/science.aad2503.
  2. Rothschild D, WeissbrodO, Barkan E, Kurilshikov A, Korem T, Zeevi D, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018; 555(7695):210-5. doi: 10.1038/nature25973
  3. Rothschild D, WeissbrodO, Barkan E, Kurilshikov A, Korem T, Zeevi D, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. 2018; 555(7695):210-5. doi: 10.1038/nature25973.
  4. Sonnenburg ED, Sonnenburg JL.Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab. 2014; 20(5):779-86. doi: 10.1016/j.cmet.2014.07.003.
  5. David LA, Maurice CF, Carmody RN, GootenbergDB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2013; 505:559-63. doi: 10.1038/nature12820.
  6. GenoniA, Christophersen CT, Lo J, Coghlan M, Boyce MC, Bird AR, et al. Long-term Paleolithic diet is associated with lower resistant starch intake, different gut microbiota composition and increased serum TMAO concentrations. Eur J Nutr. 2019. doi: 10.1007/s00394-019-02036-y.
  7. Tuck CJ, Staudacher HM.The keto diet and the gut: cause for concern? Lancet Gastroenterol Hepatol. 2019; 4(12):908-9. doi: 10.1016/S2468-1253(19)30353-X.
  8. TilgH, Kaser A. Gut microbiome, obesity, and metabolic dysfunction. J Clin Invest. 2011; 121(6):2126-32. doi: 10.1172/JCI58109.
  9. Ruiz-Ojeda FJ, Plaza-Díaz J, Sáez-Lara MJ, Gil A.Effects of sweeteners on the gut microbiota: a review of experimental studies and clinical trials. Adv Nutr. 2019; 10 (Suppl 1):S31-S48. doi: 10.1093/advances/nmy037.
  10. MokkalaK, Houttu N, Cansev T, Laitinen K. Interactions of dietary fat with the gut microbiota: evaluation of mechanisms and metabolic consequences. Clin Nutr. 2020; 39(4):994-1018. Doi: 10.1016/j.clnu.2019.05.003.
  11. Carmody RN, Bisanz JE, Bowen BP, Maurice CF, LyalinaS, Louie KB, et al. Cooking shapes the structure and function of the gut microbiome. Nature Microbiology. 2019. doi: 10.1038/s41564-019-0569-5.
  12. Forslund K, Hildebrand F, Nielsen T, FalonyG, Le Chatelier E, Sunagawa S, et al. Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota. Nature. 2015; 528(7581):262-6. doi: 10.1038/nature15766.
  13. CodellaR, Luzi L, Terruzzi I. Exercise has the guts: how physical activity may positively modulate gut microbiota in chronic and immune-based diseases. Dig Liver Dis. 2018; 50(4):331-41. doi: 10.1016/j.dld.2017.11.016.

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