The Gut Microbiome in Health and in Disease

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The Gut Microbiome in Health and in Disease

Your body is full of billions of bacteria, viruses and fungi. They are collectively referred to as the microbiome. While some bacteria are associated with disease, others are actually extremely essential for your immune system, your heart, your weight, and many other aspects of your health. This post serves as a guide to the intestinal microbiome and discusses why it is so important to your health.

The knowledge of the Gut / microbiome is evolving at an increasing rate, and more and more scientists are becoming aware of the profound connections between our gut and our mental health and our overall well-being. We all know that the type of bacteria in our gut influences or affects a very significant part of who we are. As well as extracting energy from our food, the gut account for most of our immune system and generates more than two dozen hormones that affect everything from our appetite to our mood..

For instance, buried in our intestines, deep inside its tissue, is a very thin layer of brain. It’s called the enteric system and it is made up of the same cells, neurons, which are found in the brain. There are over 100 million neurons in the gut, as many as you would find in the brain of a cat. So, the saying the gut is our second brain can be interpreted literally in fact.

Your gut can decide how much energy your body absorbs from the food you eat; it can regulate the signs of hunger; it can help you decide which food you want; and it can determine how much your blood sugar spikes in reaction to a meal. Your microbiome can make you fat, make you feel unhappy, or make you healthy and happy, depending on your eating habits.

The microbiome takes the bits of food that our body can digest and turns them into a wide range of hormones and chemicals. These, it seems, can control our mood, as well as our appetite and general health.

Changing your biome may also reduce anxiety and lessen depression.

Most people's conventional thinking in terms of weight loss and health can thus go into the trash, as new research on bacteria points out.

We like to think that we are in charge of the decisions we make, from what we decide to eat to where we go on vacation, but we neglect the fact that our microbes certainly have the opportunity, the motivation and the tools to manipulate us. Microbes have the ability to manipulate actions and mood by altering the neural signals in the vagus nerve, modifying taste receptors, generating toxins to make us feel bad, and releasing chemical incentives to make us feel good.' They also produce hunger hormones and neurotransmitters that they can use to influence our cravings and behavior.

Changing the microbes in your gut may also change your cravings.

Microbes are influencing our immune system. The 'good ones' are especially important when it comes to teaching our immune system how to behave. Lack of good bacteria leads to overactive immune systems and an increased risk of allergies and other health issues .

Each food decision you make ('Do I have that slice of cake or that handful of almonds?') determines the fate of the countless trillions who live in your colon. It's quite a responsibility.

Evolution of the microbiome

Just as we have destroyed the rainforests and consigned countless animal species to oblivion, so we have decimated the populations that exist within us. Many of the most common illnesses of our time have been overlooked as psychosomatic simply because doctors have not had the right tools to properly investigate them. We have never been able to look at the intestinal connection.

The microbes living in the colon are primarily bacteria, but there are also some fungi, viruses and small, primitive animals called protozoa. Together they form a beautifully complicated eco-system.

Unfortunately, like animals in the wild, many species in our gut are in decline and have been for decades. It’s partly because we eat such a narrow range of foods, which means our gut bacteria also have to live on a restricted diet. Of the 250,000 known edible plant species, we use less than 200. Seventy-five per cent of the world’s food comes from just 12 plants and five animal species. It’s one reason why I am going to encourage you to branch out a bit and try things like fermented foods, which you may never have considered before. Another reason for the decline is the widespread use of antibiotics, not only to treat us but also to help the animals we eat put on weight. Routine use of antibiotics in animals as a growth promoter is now banned in Europe but is still common practice in other parts of the world, including the US. Finally, there are emulsifiers. These are chemicals that are added to processed foods to extend their shelf life. They’ve been shown to reduce microbial richness and may directly contribute to colitis and diabetes.

We’ve cleaned up our world to such an extent that our immune systems, with nothing better to do, have gone on the rampage leading to allergies and auto-immune diseases.

Brief summary

Digestion is a complex process that is regulated and controlled by your second brain, the one that runs the full length of your intestines. When you have a meal, fluids are the first thing pass through your stomach and get absorbed It's great if you've been drinking water, tea or coffee (rich in antioxidants), but it's awful if what you've been drinking is sugar-laden. Then you'll get a lot of sugar spikes, a lot of calories, and you'll feel hungry soon after.

Like sugary drinks, easily digestible carbs, such as bread, potatoes and rice, are quickly broken down and absorbed Being 'easily digestible' sounds good, but if you don't need the energy right away (because you're doing a lot of exercise), you'll also generate a blood sugar spike, accompanied by a drop. Foods that are rich in protein, fat or fiber (eggs, meat, vegetables, whole grains) are absorbed much more slowly and will keep you fuller for longer. Eating plenty of fiber, particularly if you get it from vegetables and grains, is very important to feed the 'healthy' bacteria that live in your large intestine.

Changing the bacterial mixture in your intestine will reduce the number of coughs and colds you get as well as the effect of a variety of allergenic and autoimmune diseases.

Gut Diet

This consisting mainly of a summary of the book "The clever Gut diet" from Michael Mosley

Quotes on:

What to avoid:

-On sugar: Sugar contains no essential ingredients. None. It’s just calories. Other foods may have traces of vitamins, minerals, fiber… something. Sugar does not. One study found that drinking a single sugar-sweetened drink per day increased the risk of becoming obese by around 60 per cent. Because of its effect on your weight and on your insulin levels, consuming lots of sugar puts you at increased risk of type 2 diabetes. This can lead to dementia and amputation. Being a diabetic also cuts 10 years off your life, despite medication.

-Don’t drink your calories: Unlike those in food, the calories we consume in the form of drinks don’t fill us up, and some of the worst offenders are the treats which people fondly imagine are healthy. In particular we’ve been sold the idea that fruit juice and smoothies are good for us because they come from a natural source and contain vitamins. The truth is, unless they are freshly made, they are not a great source of nutrients. What they are good at – the main reason they are so popular – is delivering a very rapid sugar hit to your brain. You drink the juice, it goes down the hatch, swiftly through your stomach and into your small intestine where the sugar is extracted and absorbed into your bloodstream and transported to your brain. Your brain releases the ‘feel good’ hormone, dopamine, and you get that familiar sugar kick. The surplus energy from all that sugar has to go somewhere, and unless you burn it off quickly by doing lots of exercise, it will be stored as fat, either in your liver or around your gut.

-Avoid artificial sweeteners: ‘well, in that case I’ll have one of those drinks with zero-calorie sweeteners that I’ve seen advertised everywhere.’ Sadly, the evidence is mounting that drinking these can lead to inflammation in the gut and an increased risk of obesity. They are most likely even a lot worse than common sugar. In one experiment, mice were given water, sugary water or water laced with saccharin to drink. Unlike those that drank water or sugary water, the mice that got the saccharin soon developed glucose intolerance, a step on the way to diabetes.

-On Gluten and gut disease: When you eat gluten your immune system will not only attack gliaden molecules, but also the lining of your gut. The result is inflammation. This can lead to pain, diarrhea, bloating and fatigue. Or, like 50 per cent of people with gluten intolerance will have no gut symptoms at all – you may just go along for many years feeling a bit tired and run down. In a recent Italian study, researchers tested 392 patients who were complaining of gluten-related problems. They found that 26 out of the 392 (6.6 per cent) had undiagnosed coeliac disease and two (0.5 per cent) had a wheat allergy. The rest were put on a gluten-free diet and followed for two years. Those who were free of symptoms after six months – 27 people (6.9 per cent) – were considered to have NCGS. So, it turned out that 14 per cent of this group, who thought they had a gluten problem, either had coeliac disease or NCGS. But, and this for me was a surprise, most of our volunteers reported far more flatulence and bloating during the weeks we were slipping gluten-loaded pasta into their diet, and this stopped as soon as we took it out. Once we had revealed the results, many, including former sceptics, decided to continue on a gluten-free diet.

Foods that you have to avoid on a gluten-free diet include anything with wheat, rye, barley or spelt. That means bread, pasta, cereals, cake, biscuits, etc. You’ll also need to lay off the beer and read labels very carefully as many processed foods have gluten in them. Frankly, eliminating these foodstuffs is likely to help you lose weight and make you feel better anyway. But be aware that a lot of foods labelled gluten-free are stuffed full of sugar and other junk to make them more palatable. You should also be aware that bread and breakfast cereals are often fortified with iron and a range of vitamins, so if you cut them out you may want to take a multivitamin to replace them.

Diseases of the small bowel are common and often hard to diagnose. Coeliac disease affects 1 per cent of the population and is often not picked up until middle age. Studies suggest it is now four times more common than it was 50 years ago. Gluten intolerance is also on the rise. There is no reliable test and the only way to find out if you have it is by going on an exclusion diet. Irritable bowel syndrome affects one in five people. It is best treated by a change in diet.

-On giving birth and taking care of a baby: Thanks to a large study done by researchers from the Harvard T.H. Chan School of Public Health, we know that babies who are born by Caesarean section are far more likely to become obese children and overweight adults. Newborns delivered by c-section, the study found, tend to lack strains of gut bacteria found in healthy children and adults. Instead, their guts harbor harmful microbes that are common in hospitals.

Breastfeeding is certainly going to give a baby’s biome a good start and may well contribute to the fact that breast-fed babies are half as likely to develop eczema or asthma as a baby who is exclusively bottle-fed. Your microbiome is formed in the first couple of years of life and heavily influenced by how you were born. Breast milk contains a healthy mix of proteins, fats and sugars. It also contains compounds that a baby can’t digest, but which encourage the growth of ‘good’ bacteria. Oddly enough, breast milk contains substances whose only purpose is to feed good bacteria. By the time we are three years old, our biome will be largely settled, though it can still change in response to infection, antibiotic treatment and changes in diet.

Best practices:

-On what to drink and fruits: When thirsty stick to tea, coffee, herbal tea and water. Although I am not a fan of fruit juice or smoothies, eating fruit is ok, particularly apples and pears, which are less sweet. One of the big differences between eating an apple and drinking it in the form of apple juice is that an apple has far more nutrients and a lot more fiber, so it will hang around inside your stomach for a lot longer and you won’t get such a big sugar rush. The undigested bits of the apple will also pass through your small intestine and down into your large intestine, where they will help feed your ‘good’ bacteria.

-On what to eat: In contrast to sugary laden foods or simple carbs, foods that are rich in protein, fat or fiber, on the other hand, take much longer to be processed and absorbed, thus not leading to a big spike of blood glycemic levels.

-Linger over your meal, so to give your hunger hormones time to kick in. The main hormone that makes you hungry is ghrelin. It is secreted by your stomach when it’s empty and travels to a part of the brain called the hypothalamus. There it creates that familiar urge to eat. When you go on a diet your ghrelin levels tend to rise, which makes sticking to it that much harder.

-You can naturally boost your levels of PYY, which make you feel full faster, by eating protein, which is why I tend to eat eggs or fish for breakfast (their high protein content keeps me pleasantly full and hunger-free for far longer than if I take in exactly the same number of calories in the form of cereal or toast). You can also boost your PYY by eating more slowly. It takes time for the food you eat to pass through your stomach, reach your small intestine and then activate those PYY cells. If you wolf down your meal, you will eat considerably more than if you eat in a more leisurely manner.

-On fiber: As well as lowering inflammation, butyrate helps to maintain your gut lining, the barrier that keeps bacteria and other toxins from escaping into your blood. If this barrier starts to break down, you get a condition known as ‘leaky gut syndrome’ which can lead to all sorts of distressing problems, including IBS. One way to counter this is to boost your butyrate levels by eating food with lots of fiber in it. The undigested bits of fiber will reach your colon and give your ‘good’ bacteria plenty to chew on. Well fed, these ‘good’ bacteria will provide you with lots of lovely butyrates.

-Avoid antibiotics if you can, because a course of broad-spectrum antibiotics can ‘take weeks, months or even years for your gut microbial community to bounce back from – if at all.

-Open a window. We spend 90 per cent of our lives living indoors. Studies show that opening a window increases the diversity of microbes in your house and therefore, presumably, in you.

-Eat more plants. That doesn’t necessarily mean giving up meat, nor does it mean simply eating a lot more carrots. It means eating as wide a range of different plants as possible. But it also means eating lots of different bits of the plant, not just the tasty bits. ‘Consume the entire asparagus, not just the tip. Consume the trunk of the broccoli, not just the crown.’

-Get your hands dirty. Preferably by gardening. This connects you with the trillions of bacteria that live in the soil and is a good way of getting in some exercise.

-On fasting: Hippocrates was a great believer in the power of the body to heal itself. To help the body on its way he often prescribed vinegar and fasting. He described fasting as ‘the physician within’ and claimed that ‘to eat when you are sick is to feed your sickness’. As for vinegar, he recommended its use for a wide range of things, from cleaning wounds to sorting out a persistent cough. You can boost your own levels of Akkermansia, which are very beneficial bacteria, by eating more polyphenol-rich foods and also by fasting. Since Akkermansia, unlike most of the bacteria they have to compete with, are not dependent on the food you put in your mouth (they live, as I mentioned before, on the mucus in your gut wall), they will thrive when you cut down your calories. I recommend intermittent fasting as part of any regime to boost your gut health.

-On Candida and Lactobacillus: Lactobacillus destroys pathogens like Candida by spraying or injecting them with hydrogen peroxide, the stuff that people use to bleach their hair. If your Lactobacillus are weakened by a course of antibiotics that you have taken to treat something else, this can give Candida a chance to take over in your gut. Once it does it is hard to dislodge. Some strains of Lactobacillus are important for mental health; at least those who take it in the form of a probiotic (a capsule containing live bacteria) report that it improves anxiety and mood. Some, such as Lactobacillus and Bifidobacterium, produce substances like butyrate that damp down inflammation. They also protect your gut from attack by unfriendly microbes and help reinforce the walls of your gut, preventing leaky gut syndrome.

-On blood sugar levels: They found, to everyone’s surprise, that eating exactly the same foods had very different and often unexpected impacts on people’s blood sugar levels. Some volunteers’ blood sugar levels soared in response to rice, while for others it had very little impact. Is chocolate bad for your blood sugar levels? Yes, for some, but not for others.

-Flavonoids are made by plants to protect themselves against parasites and harsh weather. You’ll find them in blueberries, cherries, blackberries, plums, grapes, tomatoes and green tea. They are powerful antioxidants – and they also encourage your body to burn fat.

-Whether scrambled, boiled, poached or in an omelette, eggs are a superb source of protein, rich in vitamins and minerals.

-On alcohol: What the researchers found is that when the volunteers were drinking the red wine, and to a lesser extent when they drank de-alcoholised wine, there were significant drops in blood pressure, in C-reactive protein (CRP – a measure of inflammation) and in their triglyceride levels (the amount of fat circulating in the blood). In addition, there was a marked change in their gut bacteria, with a particular increase in Bacteroidetes, the type of bacteria associated with slimness. They also noticed a significant increase in Bifidobacteria, which are associated with lowering cholesterol. When it comes to booze, red wine seems to trump white wine, while spirits offer no obvious health benefits. As for beer, which is also known as ‘liquid toast’, I tend to avoid it because of its high carbohydrate content. If you are trying to lose weight or if you have sulphur-reducing bacteria in your gut, then beer is definitely a no-no. Some alcohol gets absorbed by your muscles, and thus removed from your system, but fat and alcohol simply don’t mix.

-On fat: The evidence that full-fat is better for you than low-fat (even when it doesn’t have sugar in it) is compelling. Eating full-fat dairy, particularly yoghurt, is likely to lead to less obesity and a lower risk of diseases such as type 2 diabetes

-On fermented foods: One of the reasons why fermented foods are so good for the gut is that, gram for gram, they contain a huge number of different microbes. The microbes in fermented foods are also far more likely than most other bacteria to make it safely down into your colon because they are extremely resistant to acid, having been reared in an acidic environment. You might worry about the impact on your gut of eating foods which are acidic, like sauerkraut and kimchi, but all the evidence shows that they are good for you. Do, however, start slowly if you haven’t eaten these sorts of food before.

The thing with homemade fermented products is you cant be sure which strains are growing in them. And there's only a handful of strains that have been clinically proven to be valuable - at least as of yet.

-Another good thing about yoghurt is that the fermenting process breaks down lactose so it contains much less than milk. Even if you are lactose-intolerant you should be able to eat yoghurt. In fact, eating it can alleviate symptoms.

-On Apple Cider Vinegar (ACV): Enhances the body’s ability to degrade virus envelopes and decrease the fungi replication in combination with various essential oils. In one experiment, we asked volunteers to eat another bagel, but this time they had to knock back a shot of dilute apple cider vinegar just before doing so. This reduced the amount of sugar going in to our volunteers’ blood by almost 50 per cent.

Other important info:

-A study shows that if you are able to maintain weight loss for a while (and it may mean up to a year), your body will finally ‘accept’ this new weight as normal.

- I was recently involved in a study in which we sent off a number of shop-bought fermented foods, such as sauerkraut and kimchi, to a university to be tested. Sixty per cent of the samples we sent grew nothing.

-‘What we find,’ he said, ‘in elite athletes is that after an intense exercise session you can have temporary damage to the gut, which creates a window of opportunity for pathogens, “bad” bacteria, to take hold. If you are training hard, day after day, you get these spikes of increased vulnerability.’ Which could explain why elite athletes are often ill before a big event. When world champion runner Paula Radcliffe went for Olympic gold in Athens, she was thwarted by a bout of severe diarrhea during the race. To minimize the risk of this happening, Graeme recommends taking a multi-strain probiotic if you are doing heavy training. Graeme also recommends taking vitamin D supplements, particularly during the winter months, because low levels of vitamin D are bad for the biome.

- In an experiment, for 10 days Tom ate nothing but the food he could buy from his local McDonald’s. This included lots of Big Macs, chicken nuggets and fries, all washed down with Coke. Before, during and after, samples of Tom’s poo were sent off to be analyzed. Understandably, Tom did not feel great on this diet, and his gut biome had an even worse time. After a few days he had lost around 1,400 species, roughly 40 per cent of his total. Weeks after returning to his normal diet his biome still hadn’t recovered.

Once we get science to the level that we can quickly map a persons DNA and Microbiome and then tailor specific lifestyle and nutrition recommendations based on that, some very interesting things might happen with regards to diseases.

Good book. I knew this stuff 10 years ago

Yes, we are symbiotic with our gut bacteria for energy and digestion and to defend against other bacteria and viruses. Bacteria are processing food... our body is using the bacteria energy transfer “B vitamins” to keep it going because we die without food and bacteria are on the food anyway, so without a friendly group of bacteria defending against the mutation rates of bacteria, we’d die in a day. People keep finding statistics for how these diseases are connected but not how they are connected. Average doctor is 17yrs out of date and this stuff isn't even know by the best researchers yet. They are just putting together the bacteria cause of these and realizing the intestine requires balances between the bacteria and fungi etc. I wanted the actual research grade data but it's just too hard to convince these doctors they don't know what they think they know when it comes to the pre-pathology of most diseases even when you put the research papers in front of them, they are like well we have to see more research and consensus in the medical community before I can believe that. They have been burned by bad research before!!! But they don't have a clue when it comes to this bacteria stuff, try to convince someone they have a pathogenic bacteria that gives people diabetes or autism and they freak out.

Vinegar is good, multiple entroviruses and encapsulated virus families are susceptible to degradation of the encapsulated membranes so the immune cells can do their job by acetic acid. Not to mention it prevents the little cat parasites from going through their egg larvae stage by again degrading the membrane while it tries to feed in the gut off of all the excess food in the intestines... hint, never eat more than 200cals within 2 hours of eating...Personally, I think taking the small tablespoons of vinegar with food ... every time you eat is a good idea, it helps decrease the desire for food and helps with digestion and helps give you more energy too. Not a bad combination if you can get past the gag reflex.

I have a near photographic memory for all this stuff... that’s why I was able to synthesize the entire model of the biochemical energy pathways of the body and trace down the major chemicals involved (necessary nutrients), nobody does that much research just to solve a health issue.

Then again, I failed to get it right and got lucky that the same molecule I was using for a hypothetical “virus” was awesome at treating bacteria and fungi biofilms by temporarily disrupting them in a way that prevents them from causing toxin production (usually a problem called Thrash symptoms, happen when cleansing bad bacteria and nasty fungi), anytime they feel threatened they dump a ton of toxins.

Substance 13 (research project) is the only molecule I’ve ever seen reduce the infection of cells in HIV research. It gums up the viral infection stages by blocking the virus from doing something and also blocks bacteria dna synthesis, might block the signals in viral synthesis too but I haven’t seen the exact method it does that infection blocking... I just know it attaches on to enough dna signaling fragments to block them from messing with normal cells — then normal cells call over enzymes to remove substance 13 but virus infected and bacteria can’t call over enzymes to clear out substance 13. This break from coordinating bacteria and fungi and viruses gives the body a chance to remove what it doesn’t like. For the HIV patients, you’d need to know the length of time necessary to disable the virus and make sure it cannot hide in the bone marrows (immune stem cells).

People have been eating dirt for millennia, only modern humans avoid all dirt exposure and are now paying the price... These bacteria, on roots, are the protective bacteria that act as the root's immune system and prevent the other/dangerous bacteria from creating super colonies that form biofilms that would prevent the nutrients from getting to the roots. In humans, these bacteria prevent gram-negative bacteria from creating imbalanced gut flora or dominating the ecosystem of the intestine which would allow them to firm biofilms when the right super colonies form, these bacteria are also how the gut flora prevent e-coli and cholera from devastating the host and explain why some people don't get sick from exposures to them!

Anyway, yeah, mostly biofilms that cause anxiety, aggression, delusions, schizophrenia, diabetes, etc. I have a whole article on that. All these people have digestive, colon cancers, cardiovascular disease, diabetes, and all the other diseases that result from messed up gut bacteria health. People are just now catching on..

Become a vegan! The enzymes that are produced for breaking down foreign proteins can do their job without having to constantly deal with the foreign proteins coming into the digestive tract. That being said, eating foreign proteins is one way to cause your body to have to produce more of those enzymes but it shouldn’t be used for that purpose all the time! So cycle diets or avoid eating the meat all the time to allow your body to “digest tumors”, cancer cells, etc.

Fuck soy! Even the soy lecithin used in chocolates. Soybeans kill the worms that eat their leaves with an enzyme that disrupts the cell wall of the worms, e.g. likely does worse things to groups of bacteria in the intestines. I'm pretty damn certain I finished figuring out the second stage of the health reset cleanse; next step is building out a network of people to test my cleanse with, rebuild their health, and see if I can really cure Crohn's, celiac, diabetes, autism, fibromyalgia, food allergies, multiple sclerosis, Gray's, Parkinson's, Alzheimer's, schizophrenia, bipolar, PANDAS, mental depression, etc.

The interesting aspects of this all is if I'm right, and I'm always right, then the biofilms distort the development of the normal behaviors by disrupting the elimination of the hormones and other toxins during the development process and exaggerate the influence of viruses.

Blah, it’s problematic to discuss in limited detail without the science to explain the systemic problems that build up and what supports them... I know of people who eat so much protein it would like cause problems but they don’t have any issues, likely because their body is repairing itself and needs that much protein to do its continuous job of repairing Lyme disease damage. The problem is that several levels of knowledge have to be understood before the problem can be understood, and then the “why” has to be understood or the problem will just show back up in another form until the person removes the cause of the health issues that caused the downward cascade to begin...

You can point to the moon all you want but a lot of people will only ever see your finger outstretched and high... they will even gesture the same way as you do, speaking of a moon, but to them it’s a finger salute called the moon.