Gut Metatranscriptome & Microbiome Analysis
Im super excited about a new kind of testing that allows us to have a deeper picture of what is happening inside the gut. Weve all heard the studies about the importance of the gut and how it impacts every single aspect of our lives, and now we can actually get a glimpse of what is happening inside the gut and know how to impact our own gut environment.
Five Ways To Keep Your Gut Microbiome In Equilibrium
WASHINGTON Have you heard about the gut microbiome recently? More and more people are talking about the microbiome, which is another word for trillions of microscopic organisms that we all have in our bodies, according to Dr. Munzer Sundos, founder of Nupeutics Health and a nutrition and functional ingredients specialist.
Dr. Sundos said the gut microbiome is the home base for the bacteria in your digestive tract. These are the bacteria and organisms in your gut that help break down food into nutrients.
Keeping your gut microbiome in equilibrium is very important for your health. Dr. Sundos recommended five things people can do now to help keep their gut microbiome healthy.
Eat a Healthy Diet
Dr. Sundos said the diet has a significant impact on gut health and the balance of good and bad bacteria. He recommends reducing the number of processed, high-sugar and high-fat foods. Instead, aim for a diet that includes a lot of plant-based foods, lean proteins and fiber.
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Avoid Taking Unnecessary Medications
You might have heard about this one before too. Dr. Sundos said the gut can still lack beneficial bacteria even six months after antibiotic use. Other medications like NSAIDs, antacids, birth control, steroids and hormone replaces can also harm your guts good bacteria, according to Dr. Sundos.
Eat Probiotics and Prebiotics-Rich Food
Prebiotics: bananas, garlic, onions and leafy greens
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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The Microbiome Endocrine Organ
Scientists have now identified the gut microbiome as an organ all of it’s own – and not only that but it’s an endocrine organ, and considered the master regulator of our hormones!;
In fact there is a secondary microbiome within our gut microbiome that is especially pronounced in women called the estrobolome which governs the levels of estrogen, the primary female reproductive health hormone, in our body.;
Imbalance in the estrobolome causing estrogen dominance can lead to all kinds of women’s hormonal challenges from PMS, to PCOS, infertility, mood swings and bloating,;as well as may lead to a higher risk of breast cancer;and ovarian cancer.;
The new research coming out about how vital our gut health and a healthy microbiome is for women’s health and hormone balancing is vitally important because disruptions to our microbiome from synthetic hormones, chemicals, and artificial foods can cause systemic health challenges that can be hard to identify.
Improve Your Gut Microbiome Today For The 4rs
There are a number of factors that contribute to the health of your gut microbiome, including your environment, the amount of exercise and sleep you get, and of course, stress. But the number one factor that determines what microbes live in your gut is your diet.
In Functional Medicine, there is a very successful protocol called the 4Rs, which stands for Remove, Replace, Reinoculate, and Repair. There are many resources for learning more about the 4 Rs. I like Raphael Kellman, M.D.s book, The Microbiome Diet: The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss.
The beautiful thing about the 4Rs protocol is that it doesnt have to be followed in order. Once you remove the processed foods and toxins from your diet, you can start doing all of the remaining 3 steps together. Unless you suffer from a serious digestive disorder or other condition, you can follow the 4Rs on your own. Or, find a practitioner who can tailor the protocol to your specific needs.
Here are my suggestions for following the 4Rs and improving your gut microbiome starting today:
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Studying The Gut Microbiota
Twin studies have shown that, although there is a heritable component to gut microbiota, environmental factors related to diet, drugs, and anthropometric measures are larger determinants of microbiota composition.45
Gut microbes are key to many aspects of human health including immune,6 metabolic5 and neurobehavioural traits .78 Different levels of evidence support the role of gut microbiota in human health, from animal models910 and human studies.4111213
Schematic representation of the role of the gut microbiota in health and disease giving some examples of inputs and outputs. CVD=cardiovascular disease; IPA=indolepropionic acid; LPS=lipopolysaccharide; SCFA=short chain fatty acids; TMAO=trimethylamine N-oxide
Animal models can help identify gut microbes and mechanisms, though the degree to which findings translate to humans is unknown. In humans, observational studies can show cross-sectional associations between microbes and health traits but are limited by the inability to measure causal relations. The strongest level of evidence is obtained from interventional clinical studiesin particular, randomised controlled trials.
The composition of gut microbiota is commonly quantified using DNA based methods, such as next generation sequencing of 16S ribosomal RNA genes or whole genome shotgun sequencing, which also allow inference of microbiota functions.1415 Metabolic products of the microbiota are now measurable in stool and serum using metabolomic methods.16
Working Out Where Your Microbiome Has Gone Awry
Testing for gut health is one of the more controversial areas of Functional Medicine. Even within our own discipline we have internal wrangling and clinical debates, all professionals do not agree and different labs offer different tests – each claiming relevance, accuracy and clinical utility. I have written about this before, so I won’t go over old ground, but the microbiome can be sequenced using full, complicated ‘gut analysis’ testing or it can be tested using Functional Medicine diagnostics which are looking for and at very specific things.
The latter is typically referred to as a comprehensive stool analysis – and depending upon which test is used, this provides a relatively good idea of the presence of certain strains of bacteria within the gut. It’s not full sequencing by any means, but it’s clinically relevant sequencing – i.e. we examine what we know to be good, we check for what we know to be bad, and we assess the digestion and relative functioning of everything else.
We do believe that we know there needs to be a certain level of diversity and quantity of bacteria in the gut in order to classify it as ‘healthy’. We also know that probiotic supplementation has shown positive effects in trials and clinical studies.
And yet, I have seen clients who thrive even though they have a lower quantity, lower diversity microbiome. I have also seen probiotics do nothing and even aggravate patients’ symptoms, regardless of the classification of probiotic used.
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How The Gut Microbiome Affects Autoimmunity
Intestinal permeability is a condition that allows bacteria and toxins to “leak” through the intestinal wall into our circulatory system. Leaky gut can exacerbate when our microbiota is out of sync and can cause inflammation and infection in other body areas. In response, our immune system can become overactive and attack our healthy tissues. Such is the case for people with Hashimoto’s, the leading cause of hypothyroidism in the United States. In Hashimoto’s, your immune system mistakenly attacks healthy thyroid tissue, causing inflammation and the thyroid’s possible failure.
How To Rejuvenate The Microbiome For Optimum Health
Now you can see why it is important to maintain and support the healthy bacteria in order to have a body that is functioning at its full potential. ;There are simple methods you can incorporate into your everyday life to help maintain the proper balance of the microbiome including:
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How To Improve Gut Health Naturally With Less Sugar
Sugar is everywhere, even when you cant taste it. Sadly, refined sugar can upset the balance in your gut and your metabolism.
If youre wondering how to get rid of bad bacteria in the gut, less sugar can help. Soft drinks, processed foods, takeaways, and restaurant food can contain high levels of sugar because it helps balance flavour and cover up poor quality ingredients. But dont get these sugars confused with complex carbs that your gut bacteria need to thrive and survive.
How Can Probiotics Help
They can make your immune system stronger. They may boost gastrointestinal health, too, especially if you have something like irritable bowel syndrome. Some probiotics also may help ease allergy symptoms and help with lactose intolerance. But because our gut microbiomes are unique, if and how they work can be different for everyone.;And some experts feel more research is needed.
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Limit Your Alcohol Intake
Drinking too much may negatively affect your microbiome, too. Repeated alcohol use is linked to gastritis, an irritation of the gut in which it becomes inflamed. Such inflammation can lead to heartburn, chronic discomfort, ulcers and bacterial infections.
Drinking too much is also associated with intestinal inflammation, which is a sign of an unhealthy gut. Research suggests that this kind of inflammation alters the microbiotaincluding how well it worksand can throw it off balance.
What Makes A Healthy Microbiome
Thats a very good question and sadly, it is not taught in medical schools. Put simply, its all about the balance between the different organisms in your gut. Theres also a number of keystone species that have a large impact on the overall ecosystem, even when present in very small quantities.
At Biomesight, we use ranges for several key microbes, established by one of the leading researchers in this field, Dr. Jason Hawrelak. These ranges include probiotics, commensals, and what we call pathobionts. We give you a score that indicates how well balanced and diverse your microbiome is.
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Microbiome Diversity Is Probably Not Achievable By Swallowing A Whole Range Of Supplements
While taking a probiotic may be like planting a seed, taking a prebiotic is like nurturing it by giving it the nourishment it needs. But again, this approach comes up against the same limitations as taking a probiotic alone.
Verdict: “Prebiotics do not increase the diversity of the microbiome,” says Whelan. “They will increase specific bacteria, but they won’t increase the number of different types of bacteria.”
Mixing it up
So microbiome diversity is probably not achievable by swallowing a whole range of supplements. But there are ways to improve diversity by focusing on the foods you eat.
“Have a look at the people around you,” says Whelan. “You’ll find some people will have the same lunch every day. And in the evening, three or four different main dishes, and they will eat that for a whole year bar going out occasionally.”
Even if your habitual diet is balanced, with plenty of fruit, vegetables, whole grains and so on, having a predictable routine is not likely to do much good for a diverse microbiome.
Eating the same few meals all the time may not be the best for beneficial gut microbes – scientists say variety is key
“Dietary diversity is about challenging the concept of constantly eating the same thing,” says Whelan. “For example, if you have fish regularly, make sure it isn’t always salmon. Make sure you have wholegrains regularly, but not just wholegrain bread.”
Whelan agrees that some people may be taking fermentation too far.
How To Restore Your Gut Microbiome
Deborah Freudenmann BHSc
The human microbiome is a collection of trillions of microorganisms which populate your intestines. Your microbiome is essentially its very own complex ecosystem. Although the microbiome consists of a diverse range of microorganisms , it is primarily populated with bacteria which are located in your gut.
Your microbiome is a complex ecological community, which communicates, cross feeds, combines, evolves with you and your environment. The symbiotic relationship between your body and your gut is important to understand. You depend on your gut microbiome and your gut microbiome depends on you. One cannot thrive without the other. The micro-organisms living in our gut perform a wide range of useful and health promoting activities, however they can also be responsible for the development of different diseases.
In the modern world, your human microbiome is often exposed to harmful factors. Poor dietary and lifestyle habits as well as increased stress levels decrease the diversity and effectiveness of your microbiomes functions. All of these factors lead to an increased chance of developing various chronic conditions.
For maintaining your long-term health, prioritisation of your microbiomes health is necessary.
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The Genetic Analysis Map Dysbiosis Test
In an article published in 2015 in Alimentary Pharmacology and Therapeutics, a team of European researchers introduced a new algorithmic test that uses DNA probes to identify and characterize dysbiosis in fecal samples to recognize the genetic profiles of specific bacterial species.4 This study is of particular interest because of the different nature of dysbiosis in gut conditions IBS is a functional condition while Crohns disease and ulcerative colitis are organic inflammatory diseases, yet both show gut dysbiosis.
Casen et al. established a profile of normobiosis through the sampling of fecal matter from 668 adults aged 17-76, 69% of whom were women. This group comprised 297 healthy volunteers who were the controls, 236 patients with IBS, including all sub-types, and 135 with IBD, including both Crohns disease and ulcerative colitis. They then designed special DNA probes to recognize typical bacterial imbalances associated with dysbiosis in IBS and IBD, as identified by previous studies. After computer and laboratory testing, the researchers settled on a final panel of 54 probes covering species in these dominant intestinal bacteria taxonomies: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, Tenericutes, and Verrucomicrobia.
How Is The Gut Microbiome Related To Mental Health
There is a strong relationship between having mental health problems and having gastrointestinal symptoms like heartburn, indigestion, acid reflux, bloating, pain, constipation, and/or diarrhea.1
Research in animals has shown that changes in the gut microbiome and inflammation in the gut can affect the brain and cause symptoms that look like Parkinsons disease, autism, anxiety and depression.
Having anxiety and depression can cause changes in the gut microbiome because of what happens in the body when it has a stress response.2
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Your Gut Microbiome Regulates Your Hormones
If your hormones are like a symphony, then your gut microbiome is the conductor. Your gut microbiome regulates your hormones carefully. When your gut microbiome is healthy, it does its job well. But when it is unhealthy, it throws your hormones out of tune and can cause all sorts of problems.
Women are especially impacted when hormones are thrown off balance. Common hormone disorders in women include:
- Endocrine disruption from toxins
Your gut microbiome plays an important role in most of these conditions. The various roles of the gut microbiome within in the endocrine system include:
- Synthesizing and secreting most hormones
- Regulating the expression of these hormones
- Inhibiting the production of certain hormones in other organs of the body
- Enhancing production of hormones throughout the body
This means your gut microbiome isnt just producing hormones, its also telling the other glands in the body how much or how little of each hormone they should be creating and releasing.
What are some of the specific hormones controlled by the gut microbiome?
Glyphosate & Hormonal Havoc
Glyphosate is the #1 most common herbicide and crop desiccant used today.
It’s the active ingredient in Monsanto’s Roundup and is now present in 75% of our food supply and has been tested to be present in 93% of American’s urine.
It’s not only in GMO crops, but sprayed on most crops, as well as in public parks, apartment complexes, lawns, all non-organic grains, water supply, and finds it’s way into our guts, urine, bodies, and babies.
It kills enzymes and microorganisms thus destroying the microbiome in our guts, causing disruption of our nutrient digestion, immune system, wellbeing, and mood.
Glyphosate has also been shown to kill embroyonic, umbilical and placental cells, causing challenges to fertility, and adversely effecting development of a baby during the critical primal period.;
Did you know that even eating 100% organic doesnt protect you from the negative effects of glyphosates and GMOs?
Even if we eat organic, we’re being exposed to it by living in the modern world through our environment, and cross contamination of organic foods by this pervasive weed killer.
It’s important that we take conscious proactive action to reduce glyphosate and chemicals in our food supply and our environment through supporting organic farmers and companies.;
The best way to nourish a healthy gut microbiome is to eat a diverse array of phytonutrient and fiber-rich organic whole foods, and to reduce the amount of inflammation triggering processed and chemical-laden foods.;
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