Microbiome research and causality

Clinicians and biologists try to find correlations between the gut microbioma and health outcomes. Very often no causal link is found. If one is ill for long time, chances are that medications were used regularly, and if one is obese, chances are that he/she ate unhealthy for long time. These factors will influence the onset of the disease and the gut microbioma composition. Even more, other factors like country of origin and the genetic background will also play a role in the gut microbiome composition and in the chance of developing certain diseases. The main challenge is to find out the right changes in the gut microbiome that actually play a role in the disease. Is then the fact that, in a dataset of thousand of bacteria, some of them show a correlation with the disease real or based on sheer coincidence?

A good example of causal relationship between the gut microbiota composition and the development of a disease is fecal macrobiota transplantation. This strategy was applied for patients with Clostridium difficile infections and the results were good, as this microorganism is able to thrive in people with disturbances in their gut microbioma, but a fecal transplant of a healthy gut microbiome composition will restore the balance and get rid of C.difficile bacteria. Another interesting development in the study of the healthy microbiome shows that the bacterium Akkermansia Muciniphila is abundant in healthy people but often absent or low in human or mice  with obesity. If you feed them with A. muciniphila, a relation between the bacteria and the metabolic health of the host is noted, and a positive effect on health balance and metabolic rate. An ongoing clinical trial with pre-diabetic patients is done right now in order to confirm those positive effects.

Other option to study causal relations between gut microbiome and health can happen in laboratory, using germ free mice, and exposing them to specific bacteria to test the effect on metabolism, digestion or immune system. But we cannot have a decisive answer using these methods, and a clinical trial using an appropriate group of patients is always needed, hopefully resulting in personalized treatments against diseases, taking into account the differences in our microbiome.

Microbiota is defined as everything staying in our gut, small enough to not be seen with naked eye (bacteria, archaea, fungi and viruses) and their habitat. Microbes form our gut play a role in all kind of systems to good liver access, good brain access, good skin access. The microbiota is personalized, everybody has a different microbiome. Monozygotic twins are more similar than average unrelated individuals in terms of microbiome, and this can be because genetics or same time colonization. The microbiome develops through life, so some of our actions will impact later in life (as repeated use of antibiotics for example). We have an enormous number of associations between our microbes and our cells activities, but no casualty (the famous example with recurrent C. difficile patient in intensive care and almost dying being rescued by fecal microbiota transportation in a systematic way, much better than antibiotics).

We got MetaHit project, with over 3 millions genes discovered in the guts of a couple of people, aiming to understand what is it there in our microbiota, but also what is their function, how they are expressed, how they are collaborating and constituting this ecosystem that makes us healthy. There is a symbiosis relationship (Venom is a great movie about symbiosis, by the way) and we feed the microbes that we want to have in our gut. As important hallmark of our discoveries in the last couple of decades, Akkermansia Muciniphila (the gatekeeper of mucus) reinforces our gut barrier and prevents substances like LPS to come into our bloodstream.

In the next posts i will talk about the early life microbiota development.
Have a nice day!
G.

The Microbiome

These days we keep hearing different opinions about this elusive thing called microbiome. What is that and how it can help us? You are in the right place to find out, through my next series of blog posts about it.

Every human microbiome is different and it is continuously changing during the course of one's life. Many factors play a role in the development of the human microbiome. Even early life events, like mode of delivery and gestational age at birth can play a role in seeding and shaping the microbes that colonize the gastro-intestinal tract. Later in life there are also changes in the macrobiome, correlated with the ageing process. Dietary habits impact on the microbiome, and diet related diseases such as obesity and metabolic syndrome will influence it. Effects of the short term dietary changes will be analyzed too.

There are many benefits coming from our microbiome, as microbes digest food components, produce some of the vitamins ( K, B12 ) and stimulate our immune system. Our entire body is colonized by microbes, and those microbes are actually keeping us healthy. They protect against pathogens (microbes that make us ill), by simply taking up the space, preventing colonization by other microbes. A system without microbes is very vulnerable to infectious microorganisms (we are talking here about newborns and germ-free pets). Having a healthy microbiome will stimulate our immune system, as a healthy immune system needs to be exposed to different microbes and compounds and find out what is harmless and what can cause a disease, other way it cannot maturate. If the immune system is not mature, it can turn its attention to non-pathogenic substances, attacking them. Turning against food particles, it can cause allergies. Turning against own body, it can cause auto-immune diseases like multiple sclerosis or diabetes type 1. Working in the right way, the immune system will be on symbiosis with the macrobiota, a mutual helping alliance that helps the immune system to figure out which microbes and particles are trustworthy and which are not. The microbiota also produces some substances that can influence our metabolism, our feeling of hunger and our weight gain or weight loss. The digestion of fiber by our microbes leads to secondary products that our body can use as an energy source (they increase the energy yield from our food, so we need to eat less). The microbiome can produce vitamins that we absorb and use (vitamin B complex and vitamin K).

At the moment we wash our hands a lot, sometime using soap that kill 99.99% of bacteria, we eat meat that was previously treated with potent antibiotics or we use antibiotics directly, and in doing this, we kill the pathogens, but we also kill a part of our "friendly" microbes. We strongly suggest to check the products you use to see if they contain any antibiotics, as excessive and unnecessary use of it, especially at young age, can lead to obesity risk, diabetes type 2 and auto-immune diseases. There are many other diseases linked to the macrobiome disruption. There is a hygiene hypothesis  stating that lack of early childhood exposure to all kind of microbes, infectious agents and parasites will suppres the natural development of our immune system.

Next post: Microbiome study

One year plan "Pathway to excellence"

As a result of achieving the brilliant and extraordinary body fat percentage of 30% and 85 kg, i decided that it is time to make a change. I become proactive and i made a plan for one year, to became a better version of me.

What i decided to do:

1. Training
-one yoga session daily, with yoga postures (asanas), breathing techniques (pranayama) and meditation
-high intensity training - meaning the one promoted by this website, 3 times per week, mainly for building strenght and stamina
-medium intensity training - which could be running, freerunning or parkour, martial arts (mainly Wing Chun)

2. Energy boosting - a clever use of supplements and exercise
-fasting - 24 hours once per week
-supplements - plants and herbs, aromatic oils, magnesium, omega 3/6 rich food, ginseng and bee pollen, cocoa, tea
-memory enhancing techniques - as i write a book about them, i found them useful to master it, for various reason (easy to learn, easy to remember stuff, easy remind lost memories - anamnesia)

3.Life enhancing strategies
-writing every day - books and blogs, poetry and text
-alkaline diet - 70%, plant based diet 70%, no chemicals, additives, sweeteners and such, minimum of sugar and last. I am also exploring the ketosis process (ketosis is sometimes referred to as the body's "fat burning" mode, using fats instead of sugars, on low card diet)
-proper hydration - 200ml every 2 hours.

This is what i got until now, i will review it every end of the month, so my first review is at the end of this month, as i am in the day 23 of my plan.

Random statistics about better health and keeping journals

• The ones who kept gratitude journals scored better on measures of mental health and general well-being than those who kept only routine notes about their days.
• Patients with asymptomatic heart failure who kept gratitude journals experienced better mood, better sleep, less fatigue and less inflammation. 
• Couples who recorded their feelings of appreciation for their partner's actions boosted happiness, romance and satisfaction in their relationships.

What I want to say? Buy a journal. Write at least few minutes every day. Simply list three or five things you are grateful for it. Enjoy a long, happy life.