Thursday, April 11, 2024

How Do Humans Benefit From The Gut Microbiome

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So What Is Microbiota

What is the Gut Microbiome? How does it affect your health?

The gut microbiota definition refers to the microorganisms found in a specific environment by type. This includes bacteria, fungi, viruses, protozoa, and archaea, and the diversity of the microbiota will vary from person to person.

Different bacteria have specific names determined by a branch of science called taxonomy, where biology experts are tasked with allocating a name and a rank in the tree of life.

For example, the probiotic L. rhamnosus is actually a species of Lactobacillus, a genus that belongs to the Firmicutes phylum, which is a member of the Kingdom of Bacteria .

Different bacteria live on different parts of the body, prefer different foods, and perform different functions. There is an oral microbiota of the mouth, a microbiota of the skin that has many subcategories , and a gut microbiota – among many others of course.

FACT Microbiota plural is often microbiota, but if referencing different types or a collection, the term microbiotas may be used.

Gut Microbiome And Diseases

External factors and host factors can induce dysbiosis in gut microbiome. Dysbiosis is likely to impair the normal functioning of gut microbiota in maintaining host wellness, and potentially induce selective-enumeration of certain microbiota member including pathobionts, leading to dysregulated production of microbial-derived products or metabolites which might be harmful to the host, causing diverse range of diseases on local, systemic or remote organ , with some of the notable diseases, along with their respective microbiome-based therapy being discussed as below.

TABLE 3. Gut microbiome-associated human diseases and their respective dysbiotic features.

Manipulating The Gut Microbiota Through Diet

Changes to the gut microbiota can occur within days of changing diet remarkable differences were found after African Americans and rural Africans switched diets for only two weeks.66 Increased abundance of known butyrate producing bacteria in the African Americans consuming a rural African diet caused butyrate production to increase 2.5 times and reduced synthesis of secondary bile acid.66 Another study comparing extreme shifts between plant and animal protein based diets showed these changes after only five days.67 But healthy microbiota are resilient to temporal changes by dietary interventions, meaning that homeostatic reactions restore the original community composition, as recently shown in the case of bread 68

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Health Intervention By Manipulating Microbiota

In recent years, the identification of prebiotics , probiotics and synbiotics has aroused strong research and commercial interests. However, no studies have been conducted to address clinical beneficiary from probiotics intervention . Consequently, a main focus for probiotics research is to validate the benefit and the mechanisms for physiological effects via clinical trials.

With regards to probiotics, Lactobacillus and Bifidobacterium are most commonly used for investigations . Lactobacillus has been considered an option for preventing antibiotic-associated diarrhea in children . For example, Lactobacillus casei were reported to inhibit growth of Helicobacter pylori . In addition, co-colonization of Lactobacillus rhamnosus GG and Bifidobacterium lactis Bb12 promoted innate immune responses to human rotavirus . Other Lactobacillus strains were used as potential treatment options for non-alcoholic fatty liver disease , type 2 diabetes , and urinary tract and HIV infections . Although Lactobacillus species have been used in dairy food production safely for a long time , species resolution sometimes matter because certain Lactobacillus strains are tolerant in a low pH circumstance , and others are associated with diseases . Therefore, it is crucial to investigate what specific genes or factors can make the difference among these members in the Lactobacillus bacteria.

We’re All Walking Ecosystems

4.1 The Gut Microbiome and its Impact on the Brain ...

Like the fish in a coral reef or the animals in a rainforest, these trillions of bacteria that naturally live in our intestines collectively form a community made up of hundreds of species.

They continually communicate with each other, compete for food, and seek out niches to colonize, making it both a cooperative and a competitive community, says Reimer. The microbiota is also affected by the things we do, such as taking antibiotic drugs or eating a high-fat, low-fibre diet, which can disrupt the balance in the microbial community.

Researchers increasingly see such disruptions or dysbiosis as a factor in everything from asthma, autism and allergies to obesity, diabetes, arthritis, heart disease and cancer, says Reimer. She adds they even play a role in mental health conditions such as anxiety and depression.

How can bugs in your intestine that you cant even see with your naked eye possibly affect your brain? Its really fascinating that things we once thought of as completely separate our brain and our gut microbiota are actually linked by a gut/brain superhighway, says Reimer.

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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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What Is Intermittent Fasting

Intermittent fasting refers to abstinence from food and drinks for a specific period of hours or days. It encompasses various regimens, including alternate-day fasting, several days of fasting, or daily fasting that restricts eating to a certain number of hours per day.1

The most common fasting periods are fifteen to eighteen hours, which allows for six to nine hours of eating time where all needed calories would be consumed. When you are fasting for more than one day, that does not mean that you break the fast with two days worth of calories. Alternate-day fasting is not recommended as a long-term regimen. Most individuals will practice one day of fasting a month or even every few months, with no food consumption for one full day followed by a well-rounded day of normal meals and snacks. Intermittent fasting is not a calorie-restrictive diet instead, it allows you to include all needed calories and macronutrients within a shorter period of time.

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Lactobacillus And Whole Body Health

Specific probiotic species and strains can help manage, treat, and protect from a range of diseases and infections.

In the world of microbes, there is a strict hierarchy. Lactobacillus is a genus of bacteria, within which there are many species, and within these species, there are specific strains of bacteria.

There are many different species of Lactobacillus, several of which have particular probiotic functions. These microbes act directly to protect you from disease or manage it, and also contribute to overall balance in the gut microbiome, which is essential too.

The Atlas Microbiome Test checks probiotic bacteria levels too

For example, L. plantarum is thought to help with the prevention and management of irritable bowel syndrome and inflammatory bowel disease . Others help treat acute diarrhoea and even prevent infections like Helico pylori and Clostridium difficile.

Barrier Functions Of The Microbiome

What is the human 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

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Other Ways To Change Gut Bacteria

There may be other ways to change your gut microbiome and treat things tied to its balance. For example, fecal transplants change your gut bacteria to treat things like C. diff and ulcerative colitis. A device called deep transcranial magnetic stimulation uses a coil put on the scalp to stimulate the brain and change gut bacteria. It shows promise for treating obesity.

9) Jose Luis Pelaez Inc. / Thinkstock

11) AntonioGuillem / Thinkstock

12) olgakr / Thinkstock, skyjo / Thinkstock, MartinFredy / Thinkstock

UConn Today: How Bactera Keep Us Healthy.

Integrative Medicine: A Clinicians Journal: Part 1: The Human Gut Microbiome in Health and Disease.

ACP Microbe Institute: Microbe Magic, The Good Bacteria.

Academy of Nutrition and Dietetics: Prebiotics and Probiotics: Creating a Healthier You.

Crohns & Colitis Foundation: Gut Microbiome Points To Cures and Treatment for IBD.

International Foundation for Functional Gastrointestinal Disorders: Gut Bacteria and IBS.

Cleveland Clinic: How Gut Bacteria May Help Curb Your Heart Disease.

University of California, Los Angeles: Changing Gut Bacteria Through Diet Affects Brain Function, UCLA Study Shows.

Journal of Neuroscience: Gut Microbes and the Brain: Paradigm Shift in Neuroscience.

Endocrine Society: Magnetic Brain Stimulation Causes Weight Loss By Making Gut Bacteria Healthier.

Mayo Clinic: What Are Probiotics?

The Gut Health Cookbook

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One study found that vitamin D supplementation significantly reduced levels of Gammaproteobacteria, including the most common opportunistic pathogens, while also increasing the bacterial richness of the gut microbiota. And, in case we need another reason to keep our vitamin D levels in a healthy range, here it is: research shows vitamin D deficiency may contribute to metabolic syndrome via the gut! Vitamin D deficiency has been shown to aggravate imbalances in the microflora, including by decreasing the production of defensins . These imbalances lead to fatty liver disease, elevated blood sugar, and other signature features of metabolic syndrome. See also Paleo for Weight Loss and The Paleo Diet for Cardiovascular Disease.

Finally, the link between vitamin D and the gut microbiome may actually be a two-way street. While vitamin D can impact the health and composition of the gut microbiota, certain bacteria in the gut may also influence vitamin D levels in the blood by regulating vitamin D metabolism. In humans, higher levels of Coprococcus and Bifidobacterium, for instance, appear to promote higher vitamin D levels, though more studies are needed to determine cause and effect.

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Effects Of Vitamins On The Microbiome

The human gut microbiota contains bacteria that are beneficial to the host, and bacteria with pathogenic potential, termed pathobionts . An important role of beneficial bacteria is the metabolic production of SCFAs by cross-feeding . Fiber-degrading bacteria include Ruminococcus callidus, Ruminococcus albus, Blautia obeum and Prevotella spp. which produce solubilized oligosaccharides and polysaccharides that act as substrates for butyrate-producing species such as Faecalibacterium prausnitzii, Eubacterium rectale, Roseburia spp, Eubacterium hallii and Anaerostipes spp . Butyrate has multiple effects on the host including maintenance of gut barrier function by stimulating the production of mucin, antimicrobial peptides, and tight-junction proteins and reducing colonic oxidative stress . These effects on gut barrier function are important for health as changes in the mucosal barrier have been described in IBD .

A picture of the Gram-stained cells of Faecalibacterium prausnitzii growing in a colony inside agar seen as a big ball at the left lower corner, chains of cells grow away from this colony . A typical single cell has the size of 35 µm in length and 1 µm in diameter. The bar represents 10 µm

Lactobacillus For Gut Health

Do probiotics alter gut microbiome composition ...

These microbes are able to stick to the cells and mucous of the intestinal lining, which explains why they are members of our gut microbiome. It is from here that they do their good work.

This genus of microbes fulfill several beneficial health-promoting functions for us, the hosts. That’s why they are probiotic. They also promote the growth of other beneficial bacteria in our microbiome, which makes them pretty upstanding members of the ecosystem.

The production of lactate and acetate from carbohydrates is an important factor in the pH of the gut. They help to keep the acidity of the gut balanced in a way that encourages beneficial and commensal species while deterring invaders that could make you sick.

Acetate is the most abundant SCFA in the large intestine and is produced by both Bifidobacteria and Lactobacilli. Acetate feeds butyrate-producing bacteria, a process called cross-feeding. Butyrate, another example of a SCFA, is essential for the maintenance of the colon lining and it prevents inflammation.

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What Is The Gut Microbiome

Bacteria, viruses, fungi and other microscopic living things are referred to as microorganisms, or microbes, for short.

Trillions of these microbes exist mainly inside your intestines and on your skin.

Most of the microbes in your intestines are found in a pocket of your large intestine called the cecum, and they are referred to as the gut microbiome.

Although many different types of microbes live inside you, bacteria are the most studied.

In fact, there are more bacterial cells in your body than human cells. There are roughly 40 trillion bacterial cells in your body and only 30 trillion human cells. That means you are more bacteria than human .

Whats more, there are up to 1,000 species of bacteria in the human gut microbiome, and each of them plays a different role in your body. Most of them are extremely important for your health, while others may cause disease .

Altogether, these microbes may weigh as much as 25 pounds , which is roughly the weight of your brain. Together, they function as an extra organ in your body and play a huge role in your health.


The gut microbiome refers to all of the microbes in your intestines, which act as another organ thats crucial for your health.

How Can The Indoor Microbiome Affect My Health

Human beings encounter microorganisms every day, and those microorganisms can have neutral, adverse, or beneficial effects depending on the person, their health, the microorganism, and many other variables. For example, some microorganisms or their products are linked to allergies or asthma, but exposure to some microorganisms early in life may also protect against asthma and recurrent wheeze in children. Much remains unknown about the direct and indirect connections between humans and the indoor microbiome. Many ongoing research projects aim to understand the interactions between microbiomes, the indoor environment and human health.

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Microorganisms In The Human Body

Microorganisms inhabit various sites of the human body, including the skin, nose, mouth and the gut. In particular the human gut is home to an enormous number of microorganisms, approximately 100 trillion bacteria cells, outnumbering human cells by an estimated 10 fold.1 The microorganisms present in the gut are mainly bacteria and belong to more than 1,000 species, 90% of which belong to Firmicutes and Bacteroidetes.2,3 Each person has a distinct and highly variable composition of gut microbes, although a core set of microorganisms are common to all individuals.2,4 The composition of the gut microorganisms is called the gut ‘microbiota’, whereas the totality of the genes of the microbiota is called the ‘microbiome’. The genes of the gut microbiome outnumber the genes of the human body by approximately 150-fold.1

The Gut Microbiome: How Does It Affect Our Health

The microbiome: How gut bacteria regulate your health | Science with Sam

We can carry up to 2 kg of microbes in our gut. Within the tens of trillions of micro-organisms that live there are at least 1,000 species of bacteria consisting of over 3 million genes. What is more, two thirds of the gut microbiome the population of microbes in the intestine is unique to each individual. But do you know how your gut microbiota could be influencing your health?

Most of us are aware that the bacteria in our gut play an important role in digestion. When the stomach and small intestine are unable to digest certain foods we eat, gut microbes jump in to offer a helping hand, ensuring we get the nutrients we need.

In addition, gut bacteria are known to aid the production of certain vitamins such as vitamins B and K and play a major role in immune function.

But increasingly, researchers are working to find out more about how gut bacteria particularly the bacteria that is unique to us individually influence our health and risk of disease.

Perhaps most studied is how gut microbiota affects an individuals risk of obesity and other metabolic conditions. In November 2014, for example, Medical News Today reported on a study claiming our genetic makeup shapes what type of bacteria reside in our gut, which may affect our weight.

In this Spotlight, we take a look at obesity and some of the other perhaps surprising health conditions that may be driven by our gut microbiota.

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Preemptive Strike: Type 2 Diabetes In Its Early Stage

Type 2 diabetes is nearing epic proportions in the world and is closely linked to the rising epidemic of obesity. Ten percent of the US adult population has T2D, and another 30% are prediabetic. Prediabetes is a health condition where a persons blood sugar levels are elevated, but not sufficiently high enough to warrant a T2D diagnosis. This happens because both prediabetic and T2D individuals usually suffer from insulin resistance, where the body no longer responds to the hormones signals to move glucose out of the bloodstream and into cells. Almost 70% of the prediabetic population will become diabetic in their lifetime.

The iHMPs third model system, the Integrated Personal -Omics Project , led by Michael Snyder, Ph.D., Stanford University, and George Weinstock, Ph.D., Jackson Laboratory for Genomic Medicine, was formed to answer fundamental questions such as: what causes the progression of prediabetes to T2D? What stressors during the prediabetes state increase the risk of such a shift?

The IPOP study recruited 106 healthy and prediabetic individuals, who were studied over a period of four years. Their gut and nasal microbiomes, as well as biological factors of both host and microbiome were followed over those four years.

To start with, researchers found that healthy participants had different gut microbiome makeup than those with prediabetic symptoms, thereby already setting up these prediabetic patients with a possibly diminished or unhealthy microbiome.

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