Monday, December 4, 2023

How Is The Microbiome Of The Gut Determined

Must read

Is Mental Health A Gut Feeling How Your Microbiome May Or May Not Affect Your Mental Health

Mike Fisher

Only recently, the idea that your gut could be shaping your mental health was considered far-fetched, more science fiction than actual science.

Now, UCalgary researchers are at the vanguard of worldwide research into whats known as the gut-brain axis and how it may affect the way you think and feel, hoping their work will hold clues to causes of illness and perhaps novel new treatments.

As we gain a better understanding of how microbes in the gut play a role in our health, researchers are examining whether this information could also yield new therapies for psychiatric illness.

So, can our microbiome, which is the genetic material of the trillions of microbes that live in and on our body, influence our mental health?

Id say that really is the million-dollar question, says Dr. Valerie Taylor, MD, PhD, a professor and head of the Department of Psychiatry in UCalgarys Cumming School of Medicine, and a member of the schools Mathison Centre for Mental Health Research & Education and the Hotchkiss Brain Institute.

“Were doing research but the jury is still out on whether we can actually leverage what seems to be a gut-brain connection into the next generation of therapies. There is reason to be excited and to pursue this work and that’s what fuels us the possibility.

Microbial therapies hold the promise of leveraging the gut-brain axis in ways that could shape cognition, behaviour and emotion.

Microbiota Diversity And Health

Lower bacterial diversity has been reproducibly observed in people with inflammatory bowel disease, psoriatic arthritis, type 1 diabetes, atopic eczema, coeliac disease, obesity, type 2 diabetes, and arterial stiffness, than in healthy controls. In Crohns disease smokers have even lower gut microbiome diversity. 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. 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.

It Affects Gut Health

The microbiome can also affect gut health and may play a role in intestinal diseases like irritable bowel syndrome and inflammatory bowel disease (



A healthy gut microbiome controls gut health by communicating with the intestinal cells, digesting certain foods and preventing disease-causing bacteria from sticking to the intestinal walls.

Personalized Medicine: The Future Of Health

If you heard the recent 100th episode of The Wellness Mama Podcast, you know that I strongly feel that there is not a single perfect diet that works for everyone or a supplement that will fix all your problems. We all need sleep and community and sunshine, but the rest is very personalized based upon each individuals needs.

What works wonderfully for one person may make someone else feel worse. I feel great when I take a lot of magnesium. Some people experience low blood pressure from taking it. I dont feel good if I eat a lot of carbs. Some people feel amazing on a relatively high carb diet.

At the end of the day, we each have to figure out the foods, supplements, and lifestyle factors that are best for us.

But how?

Thankfully, today we dont have to wait on a doctor to get insight into our health. There are now services with on-call doctors that are only a text or a call away.

Even without a doctor, we can do testing like 23 and Me, which shows our genes. This is helpful, but most of us arent geneticists and dont know what the results mean. . I know I have MAO-A and an MTHFR mutation, and thanks to research Im able to make some dietary changes based on this, but the research is still new. It also only shows half of the picture.

Other Metal Nanomaterials And The Gut Microbiome


Toxicity of nano-Ag to the gut microbiome has also been assessed in nonmammalian models. A study with Japanese quail found that waterborne exposure to nano-Ag increased lactic acidâproducing bacteria in the gut microbiome. In addition, a study with zebrafish found that dietary exposure to both nano-Cu and nano-Ag impacted the diversity of the gut microbiome. Nano-Cu exposure induced the most significant changes, causing complete suppression of common gut bacterial species , whereas nano-Ag exposure induced only minor changes in bacterial diversity. A study with Drosophila melanogaster reported a significant reduction in the diversity of the gut microbiota of larvae exposed to nano-Ag, specifically an increase in Lactobacillus brevis and Acetobacter compared to control groups . Surprisingly, nano-Cu-treated experimental groups did not show the same changes in bacterial diversity as seen in the nano-Ag treatment groups, which indicates that the sensitivity to the nanomaterials may be host species-specific.

What Is The Human Microbiome

In many ways the best way to define the microbiome is to begin with the simple question, What are we? If youd answer human to this question, youre partially correct But in fact, only 10% of the cells in our body are human!

Research has determined that we share our life with around 100 trillion organisms which comprise something called our microbiome. For every one of our cells, there are 10 microbial cells living on or inside our body, helping us to perform life-sustaining functions that we couldnt perform without their help.

Our dependence on the microbiome within us has led many experts to observe that we are truly more of a super-organism than simply human.

Gut Microbiome Analysis Of Gf

The gut microbiome of GF-transplanted male mice was analyzed by ZymoBIOMICS® Targeted Sequencing Service for Microbiome Analysis . The ZymoBIOMICS®-96 MagBead DNA Kit was used to extract DNA, using an automated platform. Bacterial 16S ribosomal RNA gene-targeted sequencing was performed by using the Quick-16S NGS Library Prep Kit . The bacterial 16S primers amplified the V3V4 region of the 16S rRNA gene. The sequencing library was prepared by using an innovative process in which PCR reactions were performed in RT-PCR machines to control cycles and, therefore, limit PCR chimera formation. The final PCR products were quantified by qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned with the Select-a-Size DNA Clean & Concentrator and then quantified with TapeStation® and Qubit® . The final library was sequenced on Illumina® MiSeq with a v3 Reagent Kit . The sequencing was performed with a 10% PhiX spike-in.

The Role Of The Gm In Infectious Disease And The Covid

The COVID-19 global pandemic caused by coronavirus SARS-CoV-2 represents one of the most recent and acute examples of health inequities. Although all populations are susceptible, Black and Latino populations in the United States are exhibiting higher infection and mortality rates compared to their White and Asian counterparts . These disparities are likely due to a combination of factors including limited opportunities to engage in isolating behaviors to reduce exposure; increased probability of underlying comorbidities such as obesity, cardiovascular disease, and diabetes; and reduced access to health care .

The Composition And Stability Of The Adult Gut Microbiota

The specific microbial diversity present in healthy adult subjects plays an important role in maintaining immune homeostasis. This links with the fact that microbiota alterations are related to gut-related diseases . Due to the important role of the microbiota in health, studies using next-generation sequencing methodologies are aimed at identifying and characterizing microbial diversity and functionality. While different projects have attempted to identify and describe the microbial composition in healthy subjects, this has been really difficult due to the high variation between individuals, the studied samples, and also, the methodology applied for that purpose. Furthermore, the composition that is typically measured is that which can be isolated from fecal samples, and this does not truly reflect the full diversity of the GI tract. This disconnects between fecal sample analysis, and the true composition of the different niches in the GI tract will need to be bridged if we are to better understand the role of the gut microbiota in human biology. Until we have technologies to bridge this gap, fecal samples and limited biopsy samples will still be used as proxies for the large intestinal microbiota. So as we enter the second decade of research into the gut microbiota, we are still faced with the reality that the descriptions that we provide of the composition and the functions may be misleading, but are currently our best guesses.

Future Areas Of Research

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 .

The Hunt For A Healthy Microbiome

What does a healthy forest look like? A seemingly thriving, verdant wilderness can conceal signs of pollution, disease or invasive species. Only an ecologist can spot problems that could jeopardize the long-term well-being of the entire ecosystem.

Microbiome researchers grapple with the same problem. Disruptions to the community of microbes living in the human gut can contribute to the risk and severity of a host of medical conditions. Accordingly, many scientists have become accomplished bacterial naturalists, labouring to catalogue the startling diversity of these commensal communities. Some 5001,000 bacterial species reside in each persons intestinal tract, alongside an undetermined number of viruses, fungi and other microbes.

Rapid advances in DNA sequencing technology have accelerated the identification of these bacteria, allowing researchers to create field guides to the species in the human gut. Were starting to get a feeling of who the players are, says Jeroen Raes, a bioinformatician at VIB, a life-sciences institute in Ghent, Belgium. But there is still considerable dark matter.

Diet is also a powerful external influence, even if the precise mechanisms by which it exerts its effects remain unclear. One study in 2018 found that immigrants to the United States from Thailand experienced a striking westernization of their gut flora a transformation that could be, at least in part, attributed to adopting a US diet.

Disease Risk Reduction Claims

A disease risk reduction claim is any statement linking the consumption of a food or constituent of food with a reduction in risk of developing a diet-related disease or condition. Regulatory agencies in the United States, Canada, and Europe authorize disease risk reduction claims that are supported by significant scientific agreement . In Canada, premarket review and approval of claims about diseases or health conditions not listed in Schedule A to the Food and Drugs Act are voluntary .

To date, disease risk reduction claims have been authorized for fiber-containing foods and reduced risk of some types of cancer as well as foods that contain fiber from certain foods and reduced risk of coronary heart disease . In 2009, Canada approved nonspecies-specific claims for probiotics in foods with a restricted list of species , but none relate to the gut microbiome. In the United States, guidance was issued on the types of studies from which the FDA can draw conclusions for evaluating health claims , but neither the FDA or Canada has approved any microbiome-specific claims for foods containing prebiotics. The EU-issued draft guidance specifically related to gut and immune function and the characterization of claims referencing a beneficial physiological effect and disease reduction .

Microbiome 101: Understanding Gut Microbiota

Special Issue: The Gut Microbiome

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.

Effects Of Antibiotic Use

Altering the numbers of gut bacteria, for example by taking broad-spectrum antibiotics, may affect the host’s health and ability to digest food. Antibiotics can cause antibiotic-associated diarrhea by irritating the bowel directly, changing the levels of microbiota, or allowing pathogenic bacteria to grow. Another harmful effect of antibiotics is the increase in numbers of antibiotic-resistant bacteria found after their use, which, when they invade the host, cause illnesses that are difficult to treat with antibiotics.

Changing the numbers and species of gut microbiota can reduce the body’s ability to ferment carbohydrates and metabolize bile acids and may cause diarrhea. Carbohydrates that are not broken down may absorb too much water and cause runny stools, or lack of SCFAs produced by gut microbiota could cause diarrhea.

A reduction in levels of native bacterial species also disrupts their ability to inhibit the growth of harmful species such as C. difficile and Salmonella kedougou, and these species can get out of hand, though their overgrowth may be incidental and not be the true cause of diarrhea. Emerging treatment protocols for C. difficile infections involve fecal microbiota transplantation of donor feces . Initial reports of treatment describe success rates of 90%, with few side effects. Efficacy is speculated to result from restoring bacterial balances of bacteroides and firmicutes classes of bacteria.

New Research Suggests Genetics Shape Gut Microbiome

The gut microbiome is made up of trillions of different types of bacteria, fungi, viruses and other species, most of which reside inside the cecum, a pocket within the large intestine. Although the individual species are microscopic, as a whole, they can weigh up to five pounds. The gut microbiome is so important to human health that it is often considered to be its own separate organ. The gut microbiome works to protect your overall health in many different ways.  Recently, new research has discovered more about how genetics shape gut microbiome function, providing additional insight into the importance of maintaining a healthy balance of gut microbes.

The Gut Microbiota And Obesity

The gut microbiota seems to play a role in the development and progression of obesity. Most studies of overweight and obese people show a dysbiosis characterised by a lower diversity.31-39 Germ-free mice that receive faecal microbes from obese humans gain more weight than mice that receive microbes from healthy weight humans. A large study of UK twins found that the genus Christensenella was rare in overweight people and when given to germ free mice prevented weight gain. This microbe and others such as Akkermansia correlate with lower visceral fat deposits. Although much of the confirmatory evidence comes from mouse models, long term weight gain in humans correlates with low microbiota diversity, and this association is exacerbated by low dietary fibre intake.

Gut microbiota dysbiosis probably promotes diet induced obesity and metabolic complications by a variety of mechanisms including immune dysregulation, altered energy regulation, altered gut hormone regulation, and proinflammatory mechanisms .

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.

State Of The Evidence

In 2012, the International Life Sciences Institute North American Microbiome Committee commissioned a review on the question what constitutes a healthy human gut microbiome that came to the following conclusions: 1) a healthy microbiome cannot be defined by a single idealized community composition, 2) a healthy microbiome is more resistant and resilient to disruption, 3) certain microbial distributions may increase susceptibility to infection and disease, and 4) it is unknown if dysbiosis, an imbalance in the types of microorganisms present in a given microbiota, is a cause or consequence of disease. For this article, we revisited the central question and evaluated whether the state of the evidence has changed substantially in the past 6 y.

The Microbiome And Intestinal Homoeostasis

The intestinal mucosa is highly adapted to be able to tolerate a large population of microorganisms and dietary antigens whilst preserving nutrient uptake and raising an effective immune response to pathogenic infection or commensal intrusion into the underlying host tissue . For the most part, the microbiota maintains symbiosis with the gut environment forming a mutually beneficial relationship with the host. The gut provides a nutrient-rich habitat for the microbiota whilst the microbiota stimulates the hosts immune system, aids digestion, and provides otherwise unobtainable metabolites. In a normal healthy gut, the microbiota is diverse with an abundance of beneficial bacteria that help to maintain gut homoeostasis, promoting protective intestinal immune responses at the mucosal surface, and limiting excessive mucosal inflammation .

What Types Of Studies Can Address These Gaps

Because of the dynamics of the human gut microbiome, static genetic sampling misses important short-term and long-term microbiome-related changes to host health. Future studies need to be conducted in larger human populations to address interindividual variability and use repeated measures within individuals to help overcome intraindividual variability.

Leveraging The Gm To Address Health Inequities

Gut microbiome composition in WELL and ILL. Rarefaction ...

The growing evidence that the GM is a link between social environments and diseases characterized by marked disparities points to new levers that could be harnessed to help ameliorate their effects. However, key gaps remain to be addressed before the GM can be used to guide interventions. For example, current studies describe either the relationship between the social dynamics of SES/race/gender identity and the GM, or the relationship between the GM and health. We are aware of no study that simultaneously and empirically assesses SES/race/gender identity, the GM, and health outcomes to determine what facets of health inequities are mediated by the GM and the relative importance of the GM versus other potential mediating pathways. Additionally, no GM study has quantitatively examined the relative importance of inequities ranging from the personal to the global scale and the extent to which they interact with each other.

The Human Microbiome: How It Works + A Diet For Gut Health

January 7, 2016

Most people think of bacteria within the body as a cause of getting sick or developing certain diseases, but did you know that at all times there are actually billions of beneficial bacteria present within all of us? In fact, bacteria make up our microbiome, an integral internal ecosystem that benefits our gut health and the immune system.

Recently, the scientific community has really come to embrace the important role that bacteria have in fostering a strong immune system and keeping us healthy. Not only are all bacteria not detrimental to our health, but some are actually crucial for boosting immunity, keeping our digestive systems running smoothly, our hormone levels balanced and our brains working properly.

So what is the microbiome, why is it so important and how can we protect it? Lets find out.

Update: My Viome Test Results Explained

Viomes lead medical researcher, Dr. Helen Messier, was kind enough to shoot the following video explaining my test results and breaks down the app recommendations based on my own gut bacteria. She also explains how the food recommendations work and how to use Viome most effectively.

This article was medically reviewed by Dr. Scott Soerries, MD, Family Physician and Medical Director of SteadyMD. As always, this is not personal medical advice and we recommend that you talk with your doctor.

Are you as excited about this new technology as I am? Ever tried any at-home tests like this before? Weigh in below!

How To Test Gut Microbiome At Home

Now for why Im so excited about testing poop!

Until recently, most gut testing cost thousands of dollars and had to be ordered through a doctor. Testing also provided an incomplete picture of gut health and used the old 16S method of sequencing.

The 16S method analyzes the bacteria in the gut, but as I showed above, this is an incomplete picture. To fully analyze the bacteria, viruses, bacteriophages, archaea, fungi, yeast, parasites, and other organisms, a more complete testing is needed.

Why Is The Microbiome Function Important

The gut microbiome is responsible for a host of functions necessary for good health and optimal wellness. Obsiouvsly, perhaps, the gut microbiome is responsible for good digestive system health, playing a vital role in intestinal diseases such as irritable bowel syndrome and inflammatory bowel disease . A properly functioning gut microbiome works to maintain good gut health and mitigate the chance that disease-causing bacteria sets in and takes hold.

Additionally, the wrong balance of healthy and unhealthy microbes has also been demonstrated to increase the risk of weight gain. Conversely, probiotics that support healthy microbes in the gut can help you to control your weight.

While it may not seem related, a healthy gut microbiome can also help to prevent blocked arteries that lead to heart disease. A robust microbiome may also support healthy blood sugar levels, helping to prevent the onset of diabetes.

Lastly, the gut microbiome organ can affect brain health, as it delivers chemicals and communicates with the nerves that run to the brain. Numerous recent studies have demonstrated a connection between the health of the gut microbiome and the risk of developing mental health conditions such as depression and anxiety. This bidirectional communication between the gut and the central nervous system is aptly known as the gut-brain axis.

Carbon Nanomaterials And The Gut Microbiome

Carbon nanomaterials are an emerging class of nanomaterials consisting primarily of cylindrical single-walled and multiwalled nanotubes and spherical fullerenes. Although currently not as widely produced as metal and metal oxide nanomaterials, their unique properties, coupled with their overtly low toxicity, has made them a major player in the nanomaterial industry . Although detection and quantification of these materials are difficult, recent models predict their environmental release and partitioning into surficial sediments , where they may be potentially bioavailable to aquatic organisms.

Although this is a relatively new area of research, there is some evidence indicating that dietary exposure to carbon nanomaterials may induce changes in microbial groups involved in lipid synthesis and metabolism, and additional research is necessary to explore this possibility.

More articles

Popular Articles