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  and can even impact our mood. 
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  and our human genes 100 to 1. 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 .
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 . 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 .
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 , diabetes , cardiovascular disease , and even neurological conditions . 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
Obesity is associated with more than over-consumption of high-calorie foods. It can lead to metabolic changes linked to diabetes, heart disease and non-alcoholic fatty liver disease. Interestingly, alterations in two important phyla, or groups, of bacteria known as Firmicutes and Bacteroidetes have been observed in people with obesity. Ordinarily, a careful balance of these phyla is maintained, whereas, in obesity and diabetes, the ratio of Firmicutes to Bacteroidetes is increased. This shift also reverses when people lose weight and eat fewer calories. A relative over-abundance of Firmicutes is noteworthy because genes linked to cardiovascular disease and obesity, ordinarily suppressed, are more active in people with increased Firmicutes in their microbiome. Some of the bacteria in this phyla can also improve the efficiency of digestion, making it easier for us to extract more calories from the diet and store the energy in fat cells around the body.
Some people who are obese do not develop diabetes or heart disease and appear fairly metabolically healthy. Gut bacteria, such as Akkermansia Muciniphilia , may play a protective role in maintaining metabolic health in these individuals. After making dietary changes, obese adults with a higher baseline relative abundance of Akkermansia Muciniphilia have more significant improvements in obesity-related parameters such as insulin tolerance, blood triglycerides and body fat distribution .
Dietary interventions for obesity may be more important than the mere reduction of calories to promote weight loss: targeted to reshape the gut microbiota could impact both obesity and metabolic health.
The Gut Microbiome and Inflammatory Bowel Disease
Inflammatory Bowel Disease (IBD), including Crohn's disease and ulcerative colitis, is a chronic condition affecting the gut. Its causes are multifaceted, involving genetics, environment, and immune response. However, the gut microbiome, our internal community of microbes, plays a pivotal role in IBD.
In a healthy gut, these microbes aid digestion, produce vitamins, and protect against harmful bacteria. But in IBD, this microbiome is disrupted, leading to a decrease in beneficial bacteria and an increase in harmful ones .
Certain bacteria, like adherent-invasive E. coli (AIEC), Ruminococcus gnavus, and Fusobacterium are more prevalent in IBD patients, which can adhere to and invade the gut lining, triggering an inflammatory response [14, 15, 16]. Moreover, the balance between the immune system and the gut microbiota is disturbed in IBD, leading to chronic inflammation .
Enteric Infections and Malnutrition
Enteric infections, caused by pathogenic bacteria, viruses, or parasites, are a significant health concern, particularly in low-income countries. These infections, often resulting in diarrhoea, can profoundly impact nutritional status and gut physiology.
Malnutrition, particularly undernutrition, is a common consequence of enteric infections . The relationship between enteric infections and malnutrition is bidirectional. On the one hand, malnourished individuals are more susceptible to infections due to impaired immune function. On the other hand, frequent enteric infections can lead to malnutrition by reducing appetite, impairing nutrient absorption, and increasing nutrient losses.
Enteric infections also affect gut physiology. The gut lining, or the intestinal epithelium, acts as a barrier, preventing the entry of pathogens and toxins into the body. Enteric pathogens can damage this barrier, leading to increased intestinal permeability. As the gut barrier becomes compromised, the potential translocation of bacterial toxins from the gut into the bloodstream can trigger inflammation and further contribute to malnutrition. Moreover, enteric infections can disrupt the broader gut microbiome, exacerbating nutrient malabsorption and inflammation.
Chronic enteric infections can also lead to environmental enteric dysfunction (EED), characterised by gut inflammation, reduced absorptive capacity, and poor response to oral vaccines [19, 20, 21]. EED is particularly problematic to vulnerable populations, such as infants, older and immune-suppressed adults, and during pregnancy.
The Role of Nutrition in Maintaining the Microbiome
Nutrition is a cornerstone in maintaining a healthy microbiome. The food we consume significantly influences the composition and function of our gut microbiota. Consuming a high-fibre diet rich in fruits, vegetables, whole grains, and fermented foods can foster the growth of beneficial bacteria, such as Bifidobacterium and Lactobacillus, increasing the microbiome's diversity and enhancing gut health . Conversely, a diet high in fat and sugar can encourage the growth of harmful bacteria.
The type and quality of food sources may be an essential determinant of how our diet alters the microbiome. For instance, a high-saturated fat diet can increase the relative abundance of Bilophila Wadsworthia, which can disturb the intestinal barrier, impair glucose metabolism and influence fatty liver disease. In contrast, a high-unsaturated fat diet may not significantly alter the gut bacterial profile .
Probiotics vs Prebiotics: A Brief Introduction
Probiotics and prebiotics are increasingly popular tools for managing gut microbiota. Probiotics are beneficial live microorganisms that can inhibit the growth of pathogens, produce use metabolites that act both within and beyond the intestines, and modify the activity of the immune system. In comparison, prebiotics are non-digestible food ingredients that stimulate the growth and activity of beneficial gut bacteria.
The field of probiotics and prebiotics is expanding, with new developments like synbiotics, postbiotics, microbial consortia, and genetically modified organisms. Personalised nutrition and precision medicine are beginning to influence the application of probiotics and prebiotics, with growing interest in the modulation of microbial signatures of health and disease. These advancements are driving innovation in quality assurance techniques for probiotics and prebiotics.
Laboratory Stool Testing and the Microbiome
Laboratory stool testing has been a medical diagnostic tool in various circumstances for many years. It can identify specific pathogens, like Helicobacter pylori and Clostridium difficile, detect blood that might indicate risk for colorectal cancer, and inflammatory markers, such as Calprotectin, that are often raised in people with IBD. Beyond diagnosis of diseases, stool tests are now available, which offer a more comprehensive analysis of the microbiome. In addition to detecting pathogens and disease-related biomarkers, these tests can provide a detailed snapshot of the beneficial bacteria and some of the metabolites they produce. Nutritional therapists can use these tests to get a broader insight into a person's gut health and offer highly-focused and personalised recommendations to optimise the gut 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.
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