There are hundreds-of-trillions of microbes that live in/on your body - in the gut, on the skin, around your organs, and even in the blood. There are both friendly and unfriendly microbiome. We have ignored the microbiome for far too long, and the latest research is demonstrating how critical it is to our health and longevity. They say “there are over 1000 species of bacteria, and around ten times as many bacterial cells in your body as there are human cells.” Your microbiome is unique and can not be compared to that of your family or friends because your lifestyle, diet, exposure to toxins, exposure to antibiotics and behaviours all impact the diversity of your microbiome.
There is 100 times more bacterial DNA (between 2 million and 20 million genes) in your body than human DNA (~20,000 genes) - you are less than 1% human. The current medical system doesn't consider the microbiome, and pharmaceutical drugs cannot prevent or cure disease, drugs only treat the symptoms and trying to manage the issue. 90% of your health is determined by your social, behavioural, and environmental factors and only 10% of your health is determined by medical intervention. You have more control over your health than you think.
“My mom always said life was like a box of chocolates. You never know what you're gonna get.” ~ Forest Gump
Your genes are not to blame for your health, or your body fat mass, this is 100% dictated by your environment. Where you live, what you eat, what you drink, your behaviours, how physically active you are, your exposure to toxins, your sleep, your stress management and the community in which you interact play a crucial role in your physical and mental well-being.
Recently, it has been observed that the composition of gut bacteria of a healthy person is different from that of an obese person, or persons with chronic disease. Such observations suggested a possible relationship between the compositional pattern of gut bacteria and the pathology of metabolic disorders. The human gut harbours a vast number of microorganisms which are extremely diverse. Out of these, three phyla, Bacteroidetes (Gram-negative), Firmicutes (Gram-positive) and Actinobacteria (Gram-positive), are most abundant and have been found to play a dominant role in the pathophysiology of metabolic disorders - specifically, obesity. 
The gut harbours the highest density of microorganisms in the body (e.g., about 1.5 kg of bacteria in the human gut). Your digestive system is not 100% efficient, you do not absorb all of the calories that you eat. Only a proportion of the energy in food is extracted by your gut, how much depends on your gut bacteria. It’s not just the type of bacteria in your gut that matters, it’s also the diversity. You want your gut bacteria to be as multicultural as possible and have a certain balance of bacteria.
Some gut bacteria extract more calories from the food you eat than others, bacteria like Firmicutes (Bacillus, Listeria, Staphylococcus, Streptococcus, Enterococcus, and Clostridium) can extract more calories from the food we eat. If you have more Firmicutes in your gut than I do, we can eat exactly the same meal, and you will extract more calories and have a higher chance of being obese .
A study conducted by the National Food Institute collected faeces from 32 children, half of whom were overweight and half of whom weren’t, and implanted the faeces into sterile (bacterial free) mice. The mice who received the poo from the overweight kids gained significantly more weight than the mice who got poo from the slim kids, despite eating the same food and living in the same condition. The researchers measured the “unspent calories” in the mouse poo and found that those who put on the least weight were excreting more calories. 
Studies like this continue to undermine the idea that has dominated the weight loss industry for decades: calories in versus calories out (CICO). According to CICO, the reason we get fat is that we eat more calories than we burn off, and the answer to the rising obesity problem is to eat less and exercise more. Except, of course, it’s not that simple.
Firmicutes - When food was less plentiful Firmicutes are an incredibly useful thing because they extract a greater amount of calories from food. These days having a lot of Firmicutes is not such a good thing, and has been linked to obesity. People who have a high Firmicutes count tend to follow a typical Western diet (i.e. high in fat and sugar) and low in nutrients.
When people are on a calorie restricted diet for extended periods of time they can increase the number of Firmicute bacteria in the gut.
A 2015 study done by the Weizmann Institute recruited 800 volunteers and ran an extensive test on them.  At the beginning of the study researchers took blood and stool samples as well as physical measurements, like height and weight.
The volunteers were fitted with devices that continuously measured their blood sugar levels. For 1-week the volunteers recorded everything they ate and drank, how many hours they slept, and their exercise. The researchers collected over 1.5 million blood sugar measurements.
Researchers found that eating the same foods had very different impacts on people’s blood sugar levels. Some of the volunteers could eat rice and have a very low increase in blood sugar levels, other would eat rice, and their blood sugar would soar. The hormonal response to eating certain foods is not the same for everyone, further debunking the idea of CICO.
The scientists used data from the stool samples (looking at the gut bacteria), along with details like age and gender, to create an algorithm that could predict which foods would cause an individual’s blood sugar levels to spike. Volunteers were given an individual list of “good” (didn’t raise blood sugars levels significantly) and “bad” (raised blood sugar significantly) foods and asked to follow their diet for 2-weeks.
The volunteers were able to keep their blood sugar levels in a healthy range, and the balance of bacteria in the gut began to change, all from the power of food. The volunteers were able to change the balance of bacteria in their gut in a matter of days by eating the “good” foods. It makes sense that the bacteria in your gut will also change in a matter of days when eating “bad” foods. This has nothing to do with the number of calories you are eating and more to do with the types of foods you are feeding the gut microbiome and the type of bacteria you have in your gut.
Foods that are “healthy” for one person, may not be healthy for another person. The latest celebrity diet might work for some, and be disastrous for others. Some people can follow a Keto Diet with great success and others feel and function terribly on a high-fat diet. There is no one diet that works for everyone. If you eat the same food all year round you will only feed certain types of bacteria, and others will die. The diversity of your gut bacteria is critical to your health and this is why a seasonal diet is essential.
Your gut bacteria influence how many calories you absorb, and your gut bacteria dose not treat all calories the same. Eating 100 calories of processed carbohydrates (flour, sugar, bread, pasta, crackers, pastries, milk chocolate, etc..) will not have the same effects as eating 100 calories of healthy carbohydrates like vegetables, or eating 100 calories of steak.
Unlike the fibrous vegetables and the high protein steak, the processed carbs will be swiftly absorbed, making your blood sugar levels soar. Many of the harmful bacteria in the gut thrive on sugar, while the good bacteria go hungry waiting for the real food. In response to the sharp rise in blood sugar, your pancreas will release a high amount of insulin (storage hormone) into the bloodstream to help control the sugar levels. It will turn your body into a fat storage machine unless you learn to manage your blood sugar levels.
The surge of insulin is often followed by a crash in blood sugar levels, which then leaves you tired, low on energy, and very hungry. So, what do you do? Eat more, store more, feed theb bad bacteria, and dontinue the energy roller coaster throughut the day.
Sugar is the favourite food for the "bad bacteria" that live inside your gut. The more you feed them, the faster they multiply. Notice I said sugar and not carbohydrates, as the good bacteria actually survive on healthy carbohydrates like fruits, vegetables and resistance starch. The “good bacteria” in the gut thrive on nutrient-dense real whole foods, and if your diet is low in these foods, the good bacteria will start to disappear. The higher the number of bad bacteria the greater the desire to eat crap food and the more body fat you will store. The species of bacteria in your gut can affect your mood and the food choices you make.
Your gut microbiome controls more than just your appetite. Studies show that the microbiome controls our metabolism hormones, our stress hormones, our immune defence, our circadian rhythms (sleep and wake cycles), our sex hormones, the absorption of nutrients from our food, and the production of vitamins and compounds essential to life. Without them, we would not be alive, and with an imbalance we will get fat and sick.
Taking care of your microbiome is the critical factor to being healthy and lean. Adjusting the diet and eating the right food can help feed the good bacteria, lower inflammation, fixing the integrity of the gut (“leaky gut”) improve health markers, and help the body thrive. A happy gut makes a happy microbiome and lowers body fat without reducing calorie intake.
Personalised nutrition by prediction of glycemic response. Zeevi et al. 2015
New-found link between microbiota and obesity, Chakraborti, CK et al, 2015