Tag: gut-brain axis

Restarting probiotic foods

So I am restarting probiotic foods. I suppose I had a bad start when I went all in and started consuming everything at once – yougurt, kefir, sourdough, yeast supplements, probiotic capsules. I was also fermenting apples, vegetables, plantains, trying to make my own chickpea tempeh. Home fermentation could go wrong at some point, also I think the supplements were a bad choice. Maybe taking saccharomyces boulardii for a week could improve gut microbiome, but taking the capsules everyday for several months I think for me led to SIBO (small intestinal bacterial overgrowth, in this case there was also yeast).

I think at first when I started eating goat yougurt and drinking homemade kefir, I felt better. I remember there were several days when I was helping put up posters for a missing person – the man was my close friend’s co-worker. He was last seen at a bar on a Friday night but never made it home. I didn’t personally know the guy, but since I was putting up the posters and was part of a Facebook search group, I’ve learned a lot of details about his girl friend, his parents. A week later his body was found in lake Ontario and it really got to me. I know that this tragic ending of a search for a missing person would be painful for anyone in the search group, but with depression I think such event further triggers a cascade of negative thoughts about your own life. I didn’t know the guy, I didn’t know his parents, nor his girl-friend. It was their loss, this was not about me, but anxiety and depression always find a way to relate events to your own personal issues. I remember feeling overwhelmed with anxiety and physical pain, as if it was me who let something bad happened and now I would be punished for it. I couldn’t let go of the fear of punishment for things that were happening in the world. There was a sense that I had to fix them. Maybe when I was younger I would imagine that I have these feelings because I am a morally better person, but now I know that no, feelings of guilt and fear of punishment is depression showing through.

That weekend coincidentally was also when my first batch of goat kefir was ready. The day when I tried the first cup of kefir, I had continued sense of guilt and fear. I felt guilty for trying to feel well when such tragic things were going on in the world. I have already been through a lot of cognitive behavioural therapy by that point, so logically I understood that I was not obliged to feel unwell or be responsible for the world,  but the feeling was still there. This was more than a year ago, but I do remember feeling more calm the next day after starting goat kefir and letting go of some of the guilt. It wasn’t a complete relief, but I remember  no longer feeling overwhelmed and on the verge of tears.

Studies on probiotics and mental health are inconclusive. “A recent article in Annals of General Psychiatry reviewed the currently available medical literature on using probiotics to treat anxiety and depression. The doctors identified 10 studies that were well done (in other words blinded and placebo-controlled), and looked at each study in depth. All of these studies had relatively small numbers of patients, ranging as from as few as 42 to as many as 124. The results of these studies were mixed; some suggested that there may be mild benefits of taking probiotics if you have anxiety or depression while other studies showed no benefit. Overall, the authors concluded “the clinical effects of probiotics on mental health have yet to be studied comprehensively.” 

Can probiotics help treat depression and anxiety?

Probably just adding kefir to your diet will not cure mental issues, but I do enjoy drinking it, the sour yet creamy taste. It is also a source of calcium and protein. A glass of kefir has less sugar than a glass of milk since the bacteria and yeast from kefir grains break down the milk sugar lactose and convert it into lactic acid. “The only sugar naturally present is milk is lactose (is a sugar composed of galactose and glucose subunits). Most microorganisms lack the enzyme lactase which is required to break lactose into its two component sugars, namely, glucose and galactose. Lactic acid bacteria which do have lactase readily break down lactose and use glucose as an energy source. Lactic acid bacteria, therefore, have a competitive advantage in milk; that is, they are able to out grow other bacteria which are unable to obtain glucose from lactose. Further, some lactic acid bacteria are able to convert galactose to glucose.” Therefore when we drink kefir, the bacteria had already used up glucose and galactose for energy and therefore we don’t get glucose from the drink. When humans drink milk, it contains the sugar lactose. We have a protein named lactase that is produced in our small intestine. Lactose is then broken down by lactase into galactose and glucose, which is then absorbed into bloodstream. Therefore drinking non-fermented milk raises blood sugar more than kefir.

Is it safe to make kefir at home?

The good news is that fermentation of warm milk by lactic acid bacteria reduces milk pH to less than 4.0 and in turn makes the environment unlivable for pathogenic bacteria. Most organisms grow best at pH near physiological pH of 6.8, and not in acidic environments. I assume it would be great though for microbes from Yellowstone National Park acidic pools. these pools are usually of temperature ranging from 65 to 90 degrees Celsius and contain high sulfur contents, either as hydrogen sulfide (H2S(g)) emitted as a volcanic gas, or as elemental sulfur crystals. Who lives there – thermoacidophiles, a unique group of bacteria that are a combination of acidophiles and thermophiles. Thermoacidophiles are characterized by their exclusive ability to live in both highly acidic environments and also high temperatures. The typical conditions these thermoacidophiles live under include pH at around 2 with temperatures ranging from 80 to 90 degrees Celsius.

I am not sure if thermoacidophiles  are likely to contaminate homemade kefir, but I do sterilize my jars by pouring boiling water over them. Then I let the jar cool, place the kefir grains in, pour in milk, and cover with a coffee filter. I ferment my kefir at room temperature for 24 hours. Kefir is a versatile food as it can be drank on its own, used for smoothies, used to make tvorog (quark), syrniki (fried quark pancakes), and oladyi (fritters). Easy breakfast recipe – in the evening combine kefir, sorghum flour, ground oatmeal, egg, salt, and avocado oil in a bowl and let it stand overnight in the fridge. In the morning preheat a frying pan and then use the dough for fritters. Consume with honey and yougurt on top.

Who inhabits kefir?

The kefir grains initiating the fermentation consist of a symbiotic culture of lactic acid bacteria and yeasts embedded in a matrix of proteins, lipids, and polysaccharides. The matrix is formed by microbial activity, with color ranging from white to creamy yellow. Grains can include lactic acid bacteria, acetic acid bacteria, and yeasts. During fermentation, changes in the composition of ingredients occur. Lactose, the sugar present in milk, is broken down mostly to lactic acid (25%) by the lactic acid bacteria, which results in acidification of the product. Propionibacteria further break down some of the lactic acid into propionic acid. Other substances that contribute to the flavor of kefir are pyruvic acid, acetic acid, diacetyl and acetoin (both of which contribute a “buttery” flavor), citric acid, acetaldehyde, and amino acids resulting from protein breakdown. The slow-acting yeasts, late in the fermentation process, break lactose down into ethanol and carbon dioxide. Usually ethanol concentrations are 0.2–0.3%, so kefir is not much of an alcoholic beverage.

Probiotic bacteria found in kefir products include: Lactobacillus acidophilus, Bifidobacterium bifidum, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactococcus lactis, and Leuconostoc species. Lactobacilli in kefir may exist in concentrations varying from approximately 1 million to 1 billion colony-forming units per milliliter, and are the bacteria responsible for the synthesis of the polysaccharide kefiran. In addition to bacteria, kefir often contains strains of yeast that can metabolize lactose, such as Kluyveromyces marxianus, Kluyveromyces lactis, and Saccharomyces fragilis, as well as strains of yeast that do not metabolize lactose, including Saccharomyces cerevisiae, Torulaspora delbrueckii, and Kazachstania unispora.

Kefir is made by adding kefir grains to milk typically at a proportion of 2-5% grains-to-milk. The mixture is then placed in a corrosion-resistant container, such as a glass jar, and stored preferably in the dark to prevent degradation of light-sensitive vitamins.

Planks, gut health, and mental health

I’ve had many conflicts with my father, but one thing I’ve always agreed with him on is that there is no mental health without physical exercise. Especially for those with emotional instability like me, I find that exercise is a necessity. It’s definitely not easy to do it with an autoimmune disease since sometimes after I get home from work – I feel lethargic, or I feel arm pain, or I feel isolated and a need to go on Facebook and see that people are alive. Well this is where logical thinking comes in – in the end choosing to exercise has the best payoff even though it’s not immediate. Lying down on the sofa and turning on Netflix has an immediate pay off, but if this is what I will do daily after work, after a while I will be worse off.

Currently I am trying to exercise two to three times a day. I do about 10-12 minutes before leaving for work in the morning, I include stretching, planks, downward dog, inversion poses, etc. Recently there have been some articles about positive impact of even very short intervals of exercise. I would like to believe that these statements are true as I am not able to force myself to wake up another twenty minutes earlier and engage in a 30 minute work out before work or breakfast. I do believe that some exercise is better than no exercise. I work in a boring office, so my hours are pretty standard. During lunch I walk around listening to a podcast and currently I signed up at a yoga studio located in the office building downstairs, which offers lunch classes. In the evening I try to do another 20-30 minutes of exercise. Is this exercise plan difficult? Yes, but once you do it several days in a row, I feel that there is some kind of adjustment and you get used to the schedule. Also I find it easier when I know that my exercise interval is only 12 or 20 minutes, I am not trying to push myself into an hour jog. In fact I don’t jog at all. I mentioned this before – one psychiatrist with whom I had a consultation stated that the best way to combat inflammation is exercise and that I should only do the type of exercise that I like, otherwise I will not stick with the routine for long. Therefore no jogging for me, I am doing planks and yoga poses.

“The latest research shows that a single 10-minute bout of very light (30% of VO2 Max) physical activity can increase the connectivity between brain regions linked to memory formation and storage.

This potentially groundbreaking study on the cognitive benefits of short periods of mild exertion activity (such as gentle yoga, tai chi, slow dancing, or playing bocce) was conducted by researchers at the University of California, Irvine (UCI) and the University of Tsukuba in Japan.“

Ten minutes of mild exercise may improve brain connectivity and enhance memory

From the abstract of the actual paper: ” A single 10-min bout of very light-intensity exercise (30%V˙O2peak) results in rapid enhancement in pattern separation and an increase in functional connectivity between hippocampal DG/CA3 and cortical regions (i.e., parahippocampal, angular, and fusiform gyri). Importantly, the magnitude of the enhanced functional connectivity predicted the extent of memory improvement at an individual subject level. These results suggest that brief, very light exercise rapidly enhances hippocampal memory function, possibly by increasing DG/CA3−neocortical functional connectivity.“

Rapid stimulation of human dentate gyrus function with acute mild exercise

I now have some evidence to support my belief that my 10 minute work-outs are useful. Sometimes at work I do yoga poses in the staircase, or run up ten flights of stairs. There are many ways to exercise for free, it’s not necessary to purchase a monthly gym membership or pay $20 for a yoga class.

Some studies also indicate that exercise positively modifies gut bacteria. This change in turn can reduce inflammation and depression.

“Recent studies suggest that exercise can enhance the number of beneficial microbial species, enrich the microflora diversity, and improve the development of commensal bacteria.

Collectively, the available data strongly support that, in addition to other well-known internal and external factors, exercise appears to be an environmental factor that can determine changes in the qualitative and quantitative gut microbial composition with possible benefits for the host. In fact, stable and enriched microflora diversity is indispensable to the homeostasis and normal gut physiology contributing also to suitable signaling along the brain-gut axis and to the healthy status of the individual. Exercise is able to enrich the microflora diversity; to improve the Bacteroidetes-Firmicutes ratio which could potentially contribute to reducing weight, obesity-associated pathologies, and gastrointestinal disorders; to stimulate the proliferation of bacteria which can modulate mucosal immunity and improve barrier functions, resulting in reduction in the incidence of obesity and metabolic diseases; and to stimulate bacteria capable of producing substances that protect against gastrointestinal disorders and colon cancer (such as, SCFAs). “

Exercise Modifies the Gut Microbiota with Positive Health Effects

From ScienceDaily – “Two studies — one in mice and the other in human subjects — offer the first definitive evidence that exercise alone can change the composition of microbes in the gut. The studies were designed to isolate exercise-induced changes from other factors — such as diet or antibiotic use — that might alter the intestinal microbiota.”

Exercise changes gut microbial composition independent of diet, team reports

I think it’s very crucial to our mental health to exercise daily in any way – on a yoga mat at house, running up the stairs at work, going out for a jog, dancing, playing ping-pong, jogging with your dog, anything really that replaces sitting.

Are you sure your depression is in your brain?

I’m not. Actually I’m pretty sure that’s not where my depression started. I am quite positive that the encephalitis  – brain inflammation – had developed after several years of chronic gut inflammation. What if my irritable bowel/gastritis was stopped right after it started? What if I had known about celiac disease and stopped eating gluten not two, but ten years ago? My assumption is that I would not have developed brain inflammation then, I would not experience seeing the old women asking me to help them die, I would not feel the walls of my room closing in on me. There would be no primal fear, no encephalitis. Whatever has happened to me, happened, no point to dwell on the past, but I am writing for others, for whom such terrifying experiences may be prevented. It’s important to ask the question – are you sure your depression is only in your brain?

meds

Above is my combination of the psychiatric meds that I was given by my first psychiatrist. She never questioned the origins of my depression – to her it was all a chemical imbalance in my brain, therefore she combined SSRIs, antipsychotics, benzodiazapines, and she failed at treating me. She started treating me in November 2015 and in May 2016 I bought hibachi grills and drove away into a forest with the two grills and a bag of charcoal, police had to track me. In June I could no longer work and became unemployed. Clearly I did not improve in the six months that I was her patient.

I did not improve because I don’t just have some serotonin imbalance, I have autoimmune encephalitis – brain inflammation. I also was diagnosed previously with irritable bowel syndrome (IBS) and chronic gastritis – gut inflammation. Did one lead to another? I believe so. I believe my depression started in the gut and there is research to support this theory.

“Recently, studies have emerged focusing on variations in the microbiome and the effect on various CNS disorders, including, but not limited to anxiety, depressive disorders, schizophrenia, and autism.2,8,9 Therapeutic interventions to treat dysbiosis, or disturbance in the gut, and mitigate its effects on the GBA (gut-brain axis) are only recently coming to the forefront as more is known about this unique relationship. As a result, research has been done on the use of probiotics in treatment of anxiety and depression both as standalone therapy and as adjunct to commonly prescribed medications.”

“When the human microbiome is challenged with changes in diet, stress, or antibiotics, the physiology of the normal microbiome undergoes change. A dysbiotic state leads to increased intestinal permeability and allows contents such as bacterial metabolites and molecules as well as bacteria themselves to leak through the submucosa and into the systemic circulation, a phenomenon aptly named leaky gut syndrome. … Increased intestinal permeability leads to detrimental effects on the host immune system, which have been demonstrated in diseases such as inflammatory bowel disease (IBD), diabetes, asthma, and psychiatric disorders including depression, anxiety, and autism.2,4,10,34,35“

“Depressive disorders are characterized by both neuroplastic, organizational changes, and neurochemical dysfunction.42 Illness is thought to begin when there is deregulation of these systems and can largely be attributed to cytokine release secondary to an exaggerated systemic response to stressors.39,41 Endotoxin infusions to healthy subjects with no history of depressive disorders triggered cytokine release and subsequent emergence of classical depressive symptoms. The study established a direct correlation between increased levels of IL-6 and TNF-a with symptoms of depression and anxiety,43 indicating that pro-inflammatory cytokines play a role in the development of anxiety and depression. These effects correlated with a state of chronic inflammation and altered immune cells in the peripheral blood. However, TNF-a administered to healthy subjects resulted in no depressive symptoms,38 suggesting that toxin induced inflammation caused the mood disturbance.”

Gut microbiota’s effect on mental health: The gut-brain axis

There has also been found a link between IBS and depression and recent studies are indicating that probiotics may help with both issues.

“For the new research, scientists from McMaster University in Canada recruited 44 adults with IBS as well as mild to moderate anxiety or depression. They were followed for 10 weeks; half took a daily dose of the probiotic Bifidobacterium longum, and half took a placebo. The probiotics were manufactured and provided by Nestle, which also funded the study. (Nestle was not involved in collection, analysis or interpretation of study data.)

After six weeks, twice as many people who took the probiotic had decreased depression scores compared to those who took the placebo: 64% versus 32%. Results were similar after 10 weeks, as well. When people in the study were given functional MRI scans, the researchers found that improved depression scores were associated with changes in activity of several brain areas involved in mood regulation.”

How Probiotics May Help Depression

If you are suffering from treatment resistant depression – you are not improving with the SSRIs/SNRIs/TCAs/MAOIs/NASSAs/etc., it’s important to ask yourself whether you are also suffering from any other conditions. If I had previously known all the information about the gut-brain axis, inflammation, and autoimmune diseases, it would be more evident to me that the cause of my psychiatric issues was likely gut inflammation. My severe depression started in 2015 but other health problems were starting long before that. I experienced dry and peeling skin since I was 11 years old and after the age of 12 I developed severe acne. When I was 17 I started having strong abdominal pain in the evenings. Sometimes the pain was so severe that I found it difficult to sit up. I also remember difficulties with falling asleep because as I lay down I would feel my stomach grumble and I could not relax. Later on more symptoms were added such as facial swelling, gastric pain, rapid weight gain, and brain fog. Then the depression and psychosis came. A coincidence ? Just a chemical imbalance unrelated to the other health issues? Clearly not and these symptoms were all related. They developed together as I continued to have a diet, unknowingly, that was terrible for me – pasta, bread, pizza, cheesecakes, and the symptoms declined together as I changed my diet, got treated with steroids, and started consuming fermented foods.

Now that I am equipped with all of this information I hope that I will continue to improve. I no longer have a feeling that it will only get worse and worse. I hope this will be useful to you as well and I hope I can help you feel happier again. There is more and more research now on other possible treatments for depression in addition to existing antidepressants, so I am optimistic that something will work for you, there are many things to try, don’t give up!

Probiotics, biome restoration, could it helps with psychiatric issues?

Of course I am hoping that it could. As I have written in my previous posts, I went through a lot of conventional psychiatric treatments with no success. Mirtazapine, Olanzapine, Wellbutrin, Latuda, Cymbalta, Sertraline… you name an antidepressant or an antipsychotic, and I probably tried it. Also benzodiazapines – Lorazepam and Clonazepam. Dangerous little pills, doctors themselves say that you should not be taking benzos for longer than two weeks. Later on, after being diagnosed with Hashimoto’s Encephalitis, I was treated with IV Solu-Medrol and oral prednisone – glucocorticoids for suppressing the immune system. This was in December and I think I am better now, but I cannot say that I have no unwanted or obsessive thoughts. Since the treatment, and selecting that I eat very carefully, my physical symptoms did reduce, these thoughts are the main thing that tortures me. I could not stay on prednisone as it can itself cause psychosis and I experienced violent mood swings, migraines, and severe insomnia. For this reason I continue to look for ways to improve my brain. Or is it my stomach? I am more inclined to think that my main brain is in my stomach, given how sensitive my mood is to ingredients that I eat.

I have experimented a lot with probiotics, but did not find benefits from capsules. Maybe they don’t contain enough organisms or not many of them end up alive in the gut? My gastroenterologist recommended Align brand,  but the capsules contain casein from cow’s milk. I did try it for a while, but did not notice any improvements. After feeling somewhat better since receiving the steroid treatment, I decided to let go of the strict AIP diet and to introduce some foods. I had a craving for black tea with milk and yogurt, so I thought that maybe dairy is what I need. In fact I found it quite difficult to get enough calcium on AIP diet, probably I was lacking some. AIP followers do advise that you can obtain calcium from fish bones and kale, but you would really need to eat large amounts of very salty canned salmon or a whole salad bowl of steamed kale. I found it to be not feasible in practice. Also I have not tried goat milk before so there was no evidence that I would have an adverse reaction to it. I did not find that I do after consuming it. I have been adding goat milk to black tea and I actually found that this way the tea was smoother and felt less acidic, drinking black tea on its own often caused me gastric pain. I have started buying goat and sheep yogurt, turns out it’s now available in plain form at many stores in Toronto. In general, since adding the milk and the yogurt, I have experienced less frequent gastric problems. I have only experienced gastric pain when I ate a lot of bacon (maybe that was too much saturated fat at once?), and when I took naproxen. Gastric/stomach discomfort is a common side effect of naproxen, but unfortunately taking it during my period is unavoidable for me.

I have found several studies indicating positive benefits of goat milk, which also adds a benefit for me when drinking it, even if only a placebo effect.

Anxiety behavior is reduced, and physical growth is improved in the progeny of rat dams that consumed lipids from goat milk

Anti-inflammatory and anti-allergic properties of donkey’s and goat’s milk

I have been reading on the idea that human gut biome depletion could be causing many diseases, included neuropsychiatric ones. With the invention of clean water, sewage systems, hygiene practices, the rate of infections has been greatly reduced in developed countries, but it also led to lower diversity of bacteria and parasites in our intestines. The theory states that we evolved to co-live with these organisms and part of the rise in the number of autoimmune diseases in developed world could be caused by this gut biome depletion. In terms of restoring the biome, fermented milk and vegetable products are advised. There is also an experimental helminthic therapy, but I will post about that later. Kefir is said to be a fermented product that contains a great diversity of bacteria, more than yogurt.

What’s the difference between yogurt and kefir?

About three weeks ago I purchased live kefir grains on Kijiji for $5 and this was a great investment. Making kefir is even easier than buying kefir, it really doesn’t require much action. Place kefir grains into a clean glass jar. Pour milk over the grains, leave one inch at the top. Cover the jar with a coffee filter and tighten with an elastic. Leave it at room temperature for 24 hours and there you go, you’ve got kefir. Then you strain out the grains and drink the resulting liquid, repeat the process.

“The evidence for probiotics alleviating depressive symptoms is compelling but additional double-blind randomized control trials in clinical populations are warranted to further assess efficacy.”

The effects of probiotics on depressive symptoms in humans: a systematic review

How do I feel after three weeks? I think I am calmer. I am hoping this is more than a temporary placebo effect and that there are actually material changes. A few days ago I had a sudden desire to pick up my violin again, which I haven’t touched in years. At the most acute stages of encephalitis I could not stand hearing any music, it all would cause me a feeling of unbearable nostalgia and grief. Since the steroids treatment I have gotten back to creating playlists for workouts and now I even wanted to play music again. That feels like waking up from the dead. I vividly remember a day in the fall of 2015. At that point I had already quit my PhD and I was trying to apply for jobs, sitting in Starbucks. I tried to focus on sending out my resume, but I became overwhelmed with a feeling of grief. It was as if all sounds coming out from the speakers in the corner were trying to cause me pain on purpose, they were reminding me of someone who died, each note was screaming at me. I couldn’t stand it, I packed my laptop and left home. That was when I started to think that I really wanted to die.

I am at Starbucks now again, two and a half years later. I am typing this on my laptop and music is playing from the speakers, as usual. Right now I don’t have a sudden urge to run out, the sounds are not unbearable. I think my brain is healing, knowing that healing is possible gives me a lot of hope.