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What Is Human Gut Microbiome

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The Microbiome Interfaces Faecal And Systemic Metabolism

What is the human microbiome?

At the species level, unclassified Subdoligranulum spp. accounted for 49% of the putative dialogue, and F. prausnitzii, R. inulinivorans, M. smithii, E. rectale, and A. muciniphila together contributed to a further 36%. In contrast, the results at the pathway level were not dominated by a limited number of pathways, with the top six contributing only towards 24% of the observed dialogue.

How To Improve The Gut Microbiome

;Fortunately, you can improve the composition and diversity of your gut microbiome by making changes in your diet.

Consuming a varied and diverse diet is important for maintaining a healthy gut microbiome .

A study comparing the diets and gut microbiomes in people from Europe and rural regions of Africawhere a more diverse and predominantly plant-based diet is consumedfound a significant difference in the gut microbiome. People from Africa had greater diversity of microbes and less harmful bacteria in their guts compared with Europeans .

In particular, you want to focus on consuming high-fiber foods.

The Gut Microbiome Helps Control Blood Sugar

Managing your blood sugar at a normal level is important for your health, particularly for your organs such as your eyes, heart, kidneys, and nerves. Researchers from a 2019 study concluded that it is now well-established that imbalanced gut microbiota is linked to host glycemic control impairment and T2DM development. This means that if theres an imbalance in your microbiome, you may be more likely to have unhealthy blood sugar levels and even be more susceptible to developing type 2 diabetes.

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How Microbiota Benefit The Body

Microbiota stimulate the immune system, break down potentially toxic food compounds, and synthesize certain vitamins and amino acids, including the B vitamins and vitamin K. For example, the key enzymes needed to form vitamin B12 are only found in bacteria, not in plants and animals.

Sugars like table sugar and lactose are quickly absorbed in the upper part of the small intestine, but more complex carbohydrates like starches and fibers are not as easily digested and may travel lower to the large intestine. There, the microbiota help to break down these compounds with their digestive enzymes. The fermentation of indigestible fibers causes the production of short chain fatty acids that can be used by the body as a nutrient source but also play an important role in muscle function and possibly the prevention of chronic diseases, including certain cancers and bowel disorders. Clinical studies have shown that SCFA may be useful in the treatment of ulcerative colitis, Crohns disease, and antibiotic-associated diarrhea.

The microbiota of a healthy person will also provide protection from pathogenic organisms that enter the body such as through drinking or eating contaminated water or food.

Why Is The Human Microbiome So Important

What is the Gut Microbiome

The bacteria and microbes that make up our microbiome have existed for millennia in some cases and have evolved with us to the extent that we are now dependent on them to perform a number of roles from educating our own immune system and fighting infection to the production of enzymes and nutrients critical for our bodies to health and well being.The make up of the microbiota is unique to each of us and the right or wrong mix of these microbes is linked with health and diseases such as:

  • Asthma
  • Obesity

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Unlocking The Gut Microbiome And Its Massive Significance To Our Health

If you want to learn more about whats going on in your gut, the first step is to turn your poo blue. How long it takes for a muffin dyed with blue food colouring to pass through your system is a measure of your gut health: the median is 28.7 hours; longer transit times suggest your gut isnt as healthy as it could be. We are only now beginning to understand the importance of the gut microbiome: could this be the start of a golden age for gut-health science?

The gut microbiome is the most important scientific discovery for human healthcare in recent decades, says James Kinross, a microbiome scientist and surgeon at Imperial College London. We discovered it or rediscovered it in the age of genetic sequencing less than 15 years ago. The only organ which is bigger is the liver. And, for all that the internet may be full of probiotic or wellness companies making big health claims about gut health, We dont really know how it works, he says. At the risk of sounding like the late Donald Rumsfeld, theres what we know, what we think we know, and an awful lot that we dont yet have a clue about.

A very small Italian study using a similar commercial probiotic, Sivomixx, piqued his interest after it suggested acute Covid patients treated with it might be less likely to end up in ICU or to die, and eight times less likely to suffer respiratory failure. Bjarnason is hoping to start a larger study in the next few months.

What Matters: Quality Quantity Or Activity Of Microbes

Over the last decade, pioneering papers have shown that some metabolic disorders, such as obesity and diabetes, are associated with shifts in the microbiota at the phylum level . Since this discovery, not all papers have been able to replicate this finding, which gives rise to the following question: should we focus only on the general composition at the phylum level or should we go deeper ? However, in addition to these considerations, there is another important question: is it more relevant to explore the metabolic capacity of the intestinal microbiota and, eventually, to the metabolites produced than it is to study the microbial composition alone? Indeed, as briefly described in the previous chapter of this perspective, there are numerous metabolites produced by the gut microbiome that can influence our metabolism.

Having said that, the specific examples highlighted above and relating the quantity of bacteria and the activity of the bacteria strongly demonstrate the importance of multiomics approaches and how various genomic and metabolomics approaches complement each other to further dissect the interactions between microbes, host and the overall metabolism.

Actually, there is not yet a full consensus reached on what is the best option and how to proceed to design future personalised medicine, but the field is relatively young and warrants further work.

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How To Restore Your Gut Biome To Good Health

Your gut microbiota is malleable and changes day to day, so can be affected – positively as well as negatively – by everything you consume. This means by improving your gut microbiome, you have the power to change many aspects of your health, including your gut health, immune health and so much more.

Here are some ways you can boost your gut microbiome:

What Is The Gut Microbiome

Introducing The Human Gut Microbiome

Microbes include bacteria, viruses and fungi that exist within our bodies.

There are approximately 100 trillion microbes living in the gastrointestinal tract alone, mostly within the large intestine. These microbes are collectively referred to as the gut microbiome, and can be thought of as a separate, multi-functional organ within the body .

The development of the gut microbiome begins at birth, when a newborn babys GI tract is first exposed to microbes in the vaginal birth canal. However, emerging evidence suggests babies may come into contact with microbes even earlier while in the womb .

As you get older, your gut microbiome continues to grow and develop, and its influenced by factors such as diet, lifestyle, medications and stress .

Many of these gut microbes are beneficial to health, though some can be harmful and promote infection or disease. To prevent ill-health, its important that the gut bacteria maintain a natural balance of good bacteria, such as Lactobacillus and Bifidobacterium, and bad bacteria, like Staphylococcus or Clostridium. .

Summary: The gut microbiome contains a complex community of microbes that live within the gastrointestinal tract. Many of these microbes are beneficial to our health, though some can be harmful and promote infection or disease. Maintaining a natural balance of the good and bad microbes is important for maintaining good health.

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Why Does Our Gut Microbiome Matter

The more diverse our microbiome, the better. A diverse microbiome can help digest our first food and fiber, which is challenging to digest without good bacteria. It is also crucial for preventing disease like obesity, type 2 diabetes, or heart disease.

Along with digesting our food, our gut bacteria regulate the immune system and produce chemicals circulating in our bloodstream. These chemicals can impact all of our organs, including the brain. Much of our immune system concentrates in our gut. Therefore, when our gut bacteria are off-balance or have an overaccumulation of “bad” bacteria, we are at an increased risk of infection, inflammation, and autoimmune diseases.

Gut bacteria can also affect your digestive health. When the microbiome is off-balance, people can suffer from irritable bowel syndrome, inflammatory bowel disease, bloating, abdominal cramping, and weight gain.

Diseases Related To Overnutrition

More than half of the worlds adult population is overweight or obese, and the related conditions of diabetes and cardiovascular disease are now the leading causes of death globally . The rise of these conditions has been particularly rapid in minoritized populations , and it is unclear why individuals and populations vary in susceptibility when faced with similar diets and environments . Factors such as stress and sleep disruption, cesarean births, and early life antibiotics have been implicated .

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How To Help Your Microbiome

Simple daily habits make a difference. What you eat can change the microbes that live in your body. High-fiber foods feed the helpful bacteria in your colon. They also discourage the growth of some harmful ones. Probiotic foods, such as yogurt and pickled vegetables, also deliver helpful bacteria to your gut. Getting enough sleep, easing stress, and exercising may also improve your microbiome.

Future Areas Of Research

Personalised nutrition for the gut microbiome

The microbiome is a living dynamic environment where the relative abundance of species may fluctuate daily, weekly, and monthly depending on diet, medication, exercise, and a host of other environmental exposures. However, scientists are still in the early stages of understanding the microbiomes broad role in health and the extent of problems that can occur from an interruption in the normal interactions between the microbiome and its host.

Some current research topics:

  • How the microbiome and their metabolites influence human health and disease.
  • What factors influence the framework and balance of ones microbiome.
  • The development of probiotics as a functional food and addressing regulatory issues.

Specific areas of interest:

  • Factors that affect the microbiome of pregnant women, infants, and the pediatric population.
  • Manipulating microbes to resist disease and respond better to treatments.
  • Differences in the microbiome between healthy individuals and those with chronic disease such as diabetes, gastrointestinal diseases, obesity, cancers, and cardiovascular disease.
  • Developing diagnostic biomarkers from the microbiome to identify diseases before they develop.
  • Alteration of the microbiome through transplantation of microbes between individuals .

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Dietary Effects On The Gut Microbiome

The quantitative contributions of host genetics, environmental factors and diet to shaping the gut microbiota remain largely unknown. Significant associations between host genotypes and their gut microbiota composition have been reported in both human and mouse studies for a comprehensive recent review). The environment also plays an important role in establishing and modifying the gut microbiota. For example, the close physical contact between humans and companion animals facilitates the acquisition and exchange of microbes. A study of skin, oral and gut microbiomes showed that the microbial communities of cohabiting family members resemble each other and that adults share more microbial taxa with their own dogs than they do with others’ dogs. Having a dog, and the resulting exposure to a diverse microbial community, can be beneficial. Pet ownership in the early, but not later, years of life is associated with a significant decrease in the risk of allergic disease.

Role Of The Gi Microbiota In Health

Owing to its large genomic content and metabolic complement, the gut microbiota provides a range of beneficial properties to the host. Some of the most important roles of these microbes are to help to maintain the integrity of the mucosal barrier, to provide nutrients such as vitamins or to protect against pathogens. In addition, the interaction between commensal microbiota and the mucosal immune system is crucial for proper immune function.

The GI microbiota is also crucial to the de novo synthesis of essential vitamins which the host is incapable of producing . Lactic acid bacteria are key organisms in the production of vitamin B12, which cannot be synthesised by either animals, plants or fungi . Bifidobacteria are main producers of folate, a vitamin involved in vital host metabolic processes including DNA synthesis and repair . Further vitamins, which gut microbiota have been shown to synthesise in humans, include vitamin K, riboflavin, biotin, nicotinic acid, panthotenic acid, pyridoxine and thiamine . Colonic bacteria can also metabolise bile acids that are not reabsorbed for biotransformation to secondary bile acids . All of these factors will influence host health. For example, an alteration of the co-metabolism of bile acids, branched fatty acids, choline, vitamins , purines and phenolic compounds has been associated with the development of metabolic diseases such as obesity and type 2 diabetes .

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Microbiome : Understanding Gut Microbiota

Our gut microbiota is fundamental to the breakdown and absorption of nutrients. Without it, the majority of our food intake would not only be indigestible, but we would not be capable of extracting the critical nutritional compounds needed to function.

Enviromedica » Learn » Microbiome 101: Understanding Gut Microbiota

Duration: 3.3 Minutes

Key Message: As our understanding of our microbiomes impact on our health as both individuals and as a species grows, so does the realization that current bacteria-phobic trends must come to an end.

What Is Relevant To My Patients

Why is the gut microbiome important?

a. Hype or hope? Currently, the science provides proof of concepts and the establishment of correlations and associations. For example, what is known is that the gut microbiota play a casual role in metabolic disease. Most of this evidence is currently based on epidemiological associations and rodent studies. For confidence in recommendations, causality between disease and the gut MB needs to be established. This confidence will transpire through well designed, high-powered perspective studies looking at changes before and after disease states, leading to interventional studies and randomised clinical trials .

b. An understanding of how ecological principles translate to the internal ecosystem provides a comprehensive insight into the role and function of the MB. The imbalance between protective and harmful bacteria has been implicated in many human conditions, including local gastrointestinal and systemic diseases. This understanding has provided support in a paradigm shift away from ‘germs’ as bad.

e. From a dietary perspective, the nourishment of a healthy biome is the combination of prebiotic plant fibres that fertilise and nourish the probiotic bacteria. Basic recommendations are to:

f. Regarding probiotic supplements: when researchers in the area of MB were asked if they take supplementation of probiotics, the majority stated that they instead;focus on food choices high in probiotics .

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Microbiome Definition: Its About The Genes

In other words, when we define microbiome, were referring to the microbes and their genetic material, and how they contribute to the health of the human body. Remember, pathogens will also make up some of your microbiome, not just the beneficial or commensal ones.

Can Diet Affect Ones Microbiota

In addition to family genes, environment, and medication use, diet plays a large role in determining what kinds of microbiota live in the colon. All of these factors create a unique microbiome from person to person. A high-fiber diet in particular affects the type and amount of microbiota in the intestines. Dietary fiber can only be broken down and fermented by enzymes from microbiota living in the colon. Short chain fatty acids are released as a result of fermentation. This lowers the pH of the colon, which in turn determines the type of microbiota present that would survive in this acidic environment. The lower pH limits the growth of some harmful bacteria like Clostridium difficile. Growing research on SCFA explores their wide-ranging effects on health, including stimulating immune cell activity and maintaining normal blood levels of glucose and cholesterol.

Be aware that a high intake of prebiotic foods, especially if introduced suddenly, can increase gas production and bloating. Individuals with gastrointestinal sensitivities such as irritable bowel syndrome should introduce these foods in small amounts to first assess tolerance. With continued use, tolerance may improve with fewer side effects.

If one does not have food sensitivities, it is important to gradually implement a high-fiber diet because a low-fiber diet may not only reduce the amount of beneficial microbiota, but increase the growth of pathogenic bacteria that thrive in a lower acidic environment.

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Personalised Nutrition And Future Directions

Given the variation in the gut microbiota between people, the optimal diet of a person may need to be tailored to their gut microbiota. Zeevi et al.94 obtained a multidimensional microbiota profile in 900 people and monitored food intake, continuous blood glucose levels, and physical activity for one week. The researchers devised a machine learning algorithm to predict personalised glucose responses after meals based on clinical and gut microbiome data and showed that it achieved significantly higher predictions than approaches such as carbohydrate counting or glycaemic index scores. In a follow-up double blinded randomised crossover trial of 26 participants, personalised dietary interventions based on the algorithm successfully normalised blood glucose levels.94

A study on response to bread68 using a randomised crossover trial of one week long dietary interventions showed significant interpersonal variability in the glycaemic response to different bread types. The type of bread that induced the lower glycaemic response in each person could be predicted based solely on microbiome data collected before the intervention.68 Much more research is needed to establish whether these kinds of personalised approaches are feasible, sustainable, and have a positive effect on clinical outcomes.

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