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What Is Microbiota And Microbiome

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Effects Of Food And Drugs On The Gut Microbiota

What is the human microbiome?

Specific foods and dietary patterns can all influence the abundance of different types of bacteria in the gut, which in turn can affect health .

Examples of foods, nutrients, and dietary patterns that influence human health linked to their effect on the gut microbiota

High-intensity sweeteners are commonly used as sugar alternatives, being many times sweeter than sugar with minimal calories. Despite being generally recognised as safe by regulatory agencies, some animal studies have shown that these sugar substitutes may have negative effects on the gut microbiota.46 Sucralose, aspartame, and saccharin have been shown to disrupt the balance and diversity of gut microbiota.46 Rats given sucralose for 12 weeks had significantly higher proportions of Bacteroides, Clostridia, and total aerobic bacteria in their guts and a significantly higher faecal pH than those without sucralose.47 Mice given sucralose for six months had an increase in the expression in the gut of bacterial pro-inflammatory genes and disrupted faecal metabolites.48

Other areas of concern include the side effects of popular restrictive diets on gut health. These include some strict vegan diets, raw food or clean eating diets, gluten-free diets, and low FODMAP diets used to treat irritable bowel syndrome.

Box 2 summarises our current knowledge on the interactions between gut microbiota, nutrition, and human health.

Understanding The Human Microbiome And Gut Microbiota Is Critical

Advances in knowledge about the human microbiome may open the possibility of additional microbiota-based drug therapies for challenging diseases. Large governmental research initiatives including the Human Microbiome Project in the U.S. and the MetaHIT Project in Europe accelerated research on the human microbiome. Scientists are quickly learning the details of how microbial populations interact and the roles they play in health and disease.

Part of the Rebiotix MRT drug platform is to constantly contribute to the growing body of evidence that the microbiome, particularly in the gut, has an important role to play in fighting disease. Our goal is to incorporate scientific research into our clinical programs to help further understand the impact of dysbiosis and microbiome restoration in patient populations with unmet medical needs.

Skin Conditions And The Microbiome

Your microbiome can change in ways that arenât helpful. This imbalance is called dysbiosis. Itâs not clear why this happens. But itâs linked to certain health conditions, including:

Researchers are also looking into how the skin microbiome affects conditions such as vitiligo, albinism, dandruff, toenail infections, and warts.

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Microbiome Medicine: Scientists Harness The Bodys Bugs To Treat Asthma Ms And More

Plenty of probiotic yogurts, pickles and kombuchas claim to boost our digestive health with armies of microbes, but some scientists have more ambitious therapeutic plans for the bugs that colonize us. They hope to leverage these microbes as living therapeutics for a range of health conditions, including ulcerative colitis, multiple sclerosis, eczema, and asthma.

Members Of The Microbiome

What is the Difference Between Microbiome and Microbiota ...

Table 2 Microbiome/microbiota etymology

Microbiome studies sometimes focus on the behavior of a specific group of microbiota , generally in relation to or justified by a clear hypothesis. Despite more and more terms like bacteriome, archaeome, mycobiome, or virome have started to appear in the scientific literature, and these terms do not refer to biomes organisms, and physical environment often reflecting a certain climate and soil) as the microbiome itself. Consequently, it would be better to use the original terms . In contrast to the microbiota, which can be studied separately, the microbiome is always composed by all members, which interact with each other, live in the same habitat, and form their ecological niche together. The well-established term virome is derived from virus and genome and is used to describe viral shotgun metagenomes consisting of a collection of nucleic acids associated with a particular ecosystem or holobiont . However, also here viral metagenomes can be suggested as semantically and scientifically better terms.

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The Role Of Probiotics

If microbiota are so vital to our health, how can we ensure that we have enough or the right types? You may be familiar with probiotics or perhaps already using them. These are either foods that naturally contain microbiota, or supplement pills that contain live active bacteriaadvertised to promote digestive health. Probiotic supplement sales exceeded $35 billion in 2015, with a projected increase to $65 billion by 2024. Whether you believe the health claims or think they are yet another snake oil scam, they make up a multi-billion dollar industry that is evolving in tandem with quickly emerging research.

Because probiotics fall under the category of supplements and not food, they are not regulated by the Food and Drug Administration in the U.S. This means that unless the supplement company voluntarily discloses information on quality, such as carrying the USP seal that provides standards for quality and purity, a probiotic pill may not contain the amounts listed on the label or even guarantee that the bacteria are alive and active at the time of use.

Microbiota Diversity And Health

Lower bacterial diversity has been reproducibly observed in people with inflammatory bowel disease,31 psoriatic arthritis,32 type 1 diabetes,33 atopic eczema,34 coeliac disease,35 obesity,36 type 2 diabetes,37 and arterial stiffness,38 than in healthy controls. In Crohns disease smokers have even lower gut microbiome diversity.39 The association between reduced diversity and disease indicates that a species-rich gut ecosystem is more robust against environmental influences, as functionally related microbes in an intact ecosystem can compensate for the function of other missing species. Consequently, diversity seems to be a generally good indicator of a healthy gut.4041 But recent interventional studies indicate that major increases in dietary fibre can temporarily reduce diversity, as the microbes that digest fibre become specifically enriched, leading to a change in composition and, through competitive interactions, reduced diversity.22

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What Is Niehs Doing

NIEHS studies the microbiome to gain a better understanding of its complex relationships with the environment, and how these interactions may contribute to human health and disease. This knowledge could help us revolutionize the way new chemicals are tested for toxicity, and design prevention and treatment strategies for diseases that have environmental causes.

NIEHS-supported research related to the microbiome includes the environmental factors described below.

Chronic stress NIEHS researchers found chronic stress disturbs the gut microbiome in mice, triggering an immune response and promoting the development of colitis, a chronic digestive disease characterized by inflammation of the inner lining of the colon.4

Artificial sweeteners A NIEHSfunded study found sucralose, a widelyused artificial sweetener, changes the gut microbiome in mice and may increase the risk of developing chronic inflammation.5 In a separate study, they found that acesulfamepotassium, another artificial sweetener, induced weight gain in male, but not female, mice.6

Diet NIEHS researchers showed a highfat diet shaped the gut microbiome of mice in a way that predisposed them to gain weight and develop obesity.7

Caesarean delivery NIEHSfunded research indicates the way a newborn enters the world, by C-section or natural birth, and what is eaten, formula or breast milk, during the first six weeks of life may affect the type of microbes in the gut microbiome.8

Personalised Nutrition And Future Directions

Human Gut Microbiota | Human Microbiota | Human Microbiome |

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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The Human Microbiome And Covid

  • Shinya Yamamoto,

    Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Resources, Supervision, Visualization, Writing original draft

    Affiliation Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan

  • Makoto Saito,

    Roles Methodology, Supervision, Writing review & editing

    Affiliation Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan

  • Azumi Tamura,

    Roles Data curation, Formal analysis, Investigation, Visualization, Writing review & editing

    Affiliation Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan

  • Diki Prawisuda,

    Roles Writing review & editing

    Affiliation Division of Infectious Diseases, Advanced Clinical Research Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan

So What Is The Human Microbiota

Human microbiota is a complex system made up of trillions of cellular organisms, or microbes, that include bacteria, viruses, fungi, yeast and protozoa. The system is designed to aid in humans nutrition, immune and endocrine systems, even our central nervous system. This explains the human microbiotas implication in health of the digestive tract, immunity, brain functioning and its impact on human behavior. Its believed that trouble can begin when the microbiotas balance in the gut gets out of whack, an imbalance known as occasional dysbiosis. Theres growing consensus that antibiotics can cause dysbiosis. Other factors suspected of contributing to occasional dysbiosis include dietary components and even stress.

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What Is A Biome

Animals, plants, and even oceans and soils have their own individual biomes made up of specific inhabitants.

Our bodies are not just ours, they are home to a vast collection of microorganisms. Ask most people to define microbiome, and a handful might say that it refers to a bacterial ecosystem that lives in a specific place. They may even mention the gut.

For scientists, a biome is an ecosystem made up of flora and fauna. They use the word micro to indicate that this ecosystem is invisible to the human eye. It is made up of mostly bacteria, but also viruses, archaea, and fungi, which all play a role in maintaining the environment’s stability.

The human microbiome encompasses trillions of microbes that can be separated into subsections dependent on their location. When we say gut microbiome, we mean the microorganisms that reside in your colon.

But the microbiome isnt just a feature of human beings – animals, plants, soils, and oceans have their own ones too. And no matter how you look at it, the gut microbiome plays a major role in human health.

Home to trillions of microbial cells, it is an essential part of our biology that supports many physiological functions, helps maintain the integrity of our gut lining, and protects us from disease and illness.

What Is The Gut Microbiome And How Does It Affect Your Health

Difference Between Microbiome and Microbiota

Home » Food and Nutrients » What is the Gut Microbiome and How Does it Affect Your Health?

By Harriet Smith, BSc , RD

The gut microbiome has become a hot topic as it is thought to play an important role in good health and disease prevention.

Its made up of trillions of live microbes living within the human intestine known as the gut microbiota.

Here we will explore what the gut microbiome is, how it is related to our health, and how we can best support it.


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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 .

What Is A Microbiota

Microbiota is an ecological community of commensal, symbiotic and pathogenic microorganisms. The term was introduced by Lederberg and McCray, who emphasized the importance of microorganisms inhabiting the human body in terms of health and disease. Generally, a microbiota includes bacteria, archaea, protists, fungi, and viruses. These microorganisms can be crucial for immunologic, hormonal and metabolic homeostasis of their host.

Figure 2: Human Skin Microbiota

Furthermore, molecular methods which rely on the analysis of 16S rRNA genes, 18S rRNA genes, or other marker genes and genomic regions of biological samples involve in defining the microbiota of a particular organism or a part of the organism. Here, molecular biology techniques including amplification and sequencing of DNA and other taxonomic assignments are helpful to identify the type of microorganisms in the microbiota.

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From Functional Predictions To The Phenotype

Fig. 5

Methods for assessing microbial functioning. Complex microbiome studies cover various areas, starting from the level of complete microbial cells , followed by the DNA , RNA , protein , and metabolites . In that order, the focus of the studies shifts from the microbial potential over the metabolic potential towards microbial functioning

Gut Microbiota And Health

What is Your Microbiome/Microbiota? Explained Simply.

The human microbiome is composed of trillions of microorganisms living inside and outside the human body. Often used interchangeably, the terms microbiome and microbiota are, in fact, distinctive. The microbiome defines the collection of the genomes that the microbiota possess. The microbiota are now considered an essential organ and have been associated with overall health and chronic disease.,, Bacteria, fungi, protozoa, yeast, and viruses comprise up to 90% of the human cellular population. These organisms, until recently, were the unrecognized organ system responsible for most of our immunity. The microbiota rely on us, and in turn, we rely on them, representing a truly symbiotic relationship. An imbalance of healthy and derogatory bacteria can lead to uncontrolled processes resulting in the development of chronic conditions, including cancer.,, Results of recent investigations have suggested that specific hormones, particularly estrogen, and the gut microbiome might act synergistically in the development of obesity, type 2 diabetes mellitus , and cancer.,

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Barrier Functions Of The Microbiome

The gut microbiome acts as a barrier against harmful microbes by means of competition for nutrients and ecological binding site occupancies , and production of antimicrobial substances . Numerous antimicrobial compounds, such as defensins, cathelicidins and C-type lectins, are produced by cells in the GI tract . The presence of commensal bacteria or their structural components, as well as the presence of products of bacterial metabolism, has the capacity to induce the expression and activation of these antimicrobial substances, contributing to host protection against invading pathogens and preventing the overgrowth of the commensals themselves. Induction can be mediated through various signalling pathways.

Gram-positive anaerobic faecal isolates were shown to have a greater inhibitory effect on the growth of enteric pathogens in vitro than Gram-negative anaerobic isolates . The competitive activity between commensal microbes has been shown to vary between individuals, as well as from different time points in the same individuals, highlighting the interindividual variations of the gut microbiome and its dynamic fluctuations over time .

H. Neuman, O. Koren, in, 2016

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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