How your microbiome can help you to lose weight

Following scenario:
Two identical twins eat the same meal and to the same amount of exercise for one month. The only difference is that one of them was on a course of antibiotics for the last weeks. Will the body composition be the same?
Absolutely not!

Mice, which own microbiome was depleted by antibiotics received a microbiota transplantation from identical twins. The difference here is one twin is obese while the other one is lean. After just 15 days, the mice who received the obese microbiome showed +10% change in fat mass, while their counterparts stayed slim on the same diet [1].



The obese Microbiome: The microbiome of overweight and obese people is very different from lean and healthy ones [2]. Researchers found that the obesity-associated gut microbiome can harvest more energy from food, which accelerates the weight gain [3].

"Fat people harbor fat microbes"
Helen Pearson

A 32-year old female who suffered from re-occurring infections of the antibiotic-resistant bacterium Clostridium difficile received a microbiota transplantation to cure her infection [4]. Her overweight daughter (BMI of 26.4) was chosen as the stool donor. The transplantation cured her infection but after 16 months the mother, who was lean before, gained 34 pounds!

"The obese are often blamed for their own corpulence. But perhaps, just perhaps, some of the blame should be placed on another type of organism entirely: bacteria.”
Helen Pearson

Should we instead of our genes now blame our microbes if we have problems to lose weight?
Certainly not!
It is not your fault, which set of microbes you received as a kid but the composition of your microbiome is highly flexible. Little changes in the diet can re-introduce and nourish healthy bacteria that support weight loss [5].
The other way is also true. A study from 2006 set obese people on a diet and throughout the diet, their microbial composition shifted towards a more favorable microbiome [2].

Increase in the beneficial microbial group of  bacteroidetes  during a diet course of one year [2].

Increase in the beneficial microbial group of bacteroidetes during a diet course of one year [2].

The Microbiome Diet Plan

The proposed diet here equals to big parts the "Brain Maker 7-Day Meal Plan" from Dr. David Perlmutter - a neurologist with focus on the microbiome - but with slight modifications to make it easier and affordable.

The without further ado:


I usually do Intermittent Fasting and skip breakfast when I restrict calories but when I have breakfast, I want my first meal of the day to be nutritious and rich in fiber and good fats:

Scrambled eggs with onions, mushrooms, and spinach topped with some sriracha sauce. Additionally, a coffee and a self-made Kefir

Scrambled eggs with onions, mushrooms, and spinach topped with some sriracha sauce. Additionally, a coffee and a self-made Kefir

Example #1:
2-3 scrambled eggs with stir-fried onions, mushrooms, and spinach.
-> This breakfast, provides you besides the fats and fiber also a good amount of proteins and keeps you sated during the day!

Example #2:
Greek yogurt with mixed nuts and blueberries.
-> The yogurt contains probiotic cultures and the nuts and blueberries high amounts of polyphenols.


- Kefir
-> Kefir contains a extreme variety of microbial species and many vitamines, including B vitamins, vitamin C and vitamin E  [18]
- Coffee, green or black tea.
-> Caffeine to boost your metabolism and wakes you up, plus more polyphenols to nourish your microbes.

Supplements (optional):
Probiotic capsule before breakfast with a big glass of water.
-> Probiotics are not necessary on a daily base, but re-introducing the good bacteria at the beginning of a diet will certainly benefit you.



For years, I ate a lunch rich in carbs and was surprised and angry how tired lunch always made me. If you want to be productive in the afternoon, I highly recommend to cut down carbs here!


Example #1: (the cheap vegan option)
Lentils with broccoli, carrots, onions, cauliflower, and whatever else you feel like. All nicely cooked in coconut milk spiced with curcuma.
-> Coconut fat is rich in the beneficial lipid lauric acid, which is anti-inflammatory and increased HDL cholesterol [6+7] and also curcuma, which is an ingredient in curry showed strong anti-inflammatory properties [8].

Codfish with baked broccoli and some rice. Home-made kombucha as a drink and full-fat organic yogurt with berries as dessert.   

Codfish with baked broccoli and some rice. Home-made kombucha as a drink and full-fat organic yogurt with berries as dessert.


Example #2: (the other cheap vegan option)
A burrito bowl with leafy greens, avocado, and beans topped with self-made salsa.
-> Studies suggest that avocados support cardiovascular health, weight, and aging [9].

Example #3: (the chicken-salad)
Mixed greens salad with grilled chicken dressed in olive oil and apple cider vinegar.
-> High olive oil consumption showed a reduced risk for heart diseases and an overall risk reduction of "all-cause mortality by 11%. Apple cider vinegar helps to lose body fat and improves the blood lipid profile [10-11].

Example #4: (the fishy option)
Stir-fried vegetables with salmon, cod or any other fish.
-> Omega-3 fatty acids reduce inflammation [12] and there is an indication that Omega-3 protect against brain aging  [13, 14].


Example #5: (the steak)
Grass-fed beef with broccoli, beans, mushrooms, and spinach, sautéed in organic butter.
-> Great meal on slow-carb diet, high on proteins and fiber

Greek yogurt with mixed nuts, seeds or berries.

- Kombucha
-> Kombucha is a fermented tea that has its origin in China. Apart from being very refreshing, it contains diversity of microbes and also B vitamins!
- Coffee, green or black tea, and occasionally a water-diluted table spoon of apple cider vinegar.
-> Caffeine to boost your metabolism and wakes you up, plus polyphenols to nourish your microbes.


Against the notion that eating in the evening makes you fat, I eat the majority of my calories after my workout, 2-3 hours before bed. Depending on your goal, we can include carbs here or you can keep them low if you want to lose more body fat.

In case you want to lose more weight, I recommend any of the lunch options. And if not, here are my favorite filling, and microbiome-nourishing options:

Example #1:
Stir-fried Asian vegetables with chicken, beef or tofu, together with kidney beans and two hardboiled eggs and brown rice on the side.

Example #2:
Whole wheat burrito with corn, beans, tomatoes, onions, leafy greens, and self-made guacamole.
-> The science behind gluten is most controversial, however, the addition of whole grain product was shown to beneficial in studies -  most likely through the extra fiber [15, 16].

A smoothie with berries, bananas, and any other fruits you desire.
-> berries are full of vitamins and polyphenols that feed your microbes, which in turn provide you with healthy metabolites. Fruits like babanas and berries also contain a good amount of fiber that slows down the sugar release [17].




- Nuts

- Oven-baked veggies dressed with olive oil




  1. Ridaura et al., Gut Microbiome from Twins Discordant for Obesity Modulate Metabolism in Mice, Science, 2013
  2. Ley et al., Human gut microbes associated with obesity, Nature 2006
  3. Turnbaugh et al., An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 2006
  4. Alang and Kelly, Weight Gain after fecal microbiota transplantation, Open Forum Infect Dis., 2015
  5. Mekkes et al., The development of probiotic treatment in obesity: a review, Beneficial Microbes, 2014
  6. Huan et al., Anti-bacterial and anti-inflammatory properties of capric acid against Propionibacterium acnes: A comparative study with lauric acid, J Dermatol Sci., 2014
  7. Mensik et al., Effects of dietary fatty acids and carbohydrates on the ratio of serum total to HDL cholesterol and on serum lipids and apolipoproteins: a meta-analysis of 60 controlled trials, Am J Clin Nutr., 2003
  8. Jurenka, Anti-inflammatory Properties of Curcumin, a Major Constituent of Curcuma longa: A Review of
    Preclinical and Clinical Research, Alternative Medicine Review, 2009
  9. Dreher and Davenport, Hass Avocado compostion and potential health effects, Crit Rev Food Sci Nutr., 2013
  10. Kondo et al., Vinegar Intake Reduces Body Weight, Body Fat Mass, and Serum Triglyceride Levels in Obese Japanese Subjects, Biosci. Biotechnol. Biochem, 2009
  11. Schwingshackl and Hoffman, Monounsaturated fatty acids, olive oil and health status: a systematic review and meta-analysis of
    cohort studies,Int J Food Sci Nutr., 2014
  12. Li et al., Effect of Marine-Derived n-3 Polyunsaturated Fatty Acids on C-Reactive Protein, Interleukin 6 and Tumor Necrosis Factor a: A Meta-Analysis, PLoS One., 2014
  13. Perica and Delas, Essential Fatty Acids and Psychiatric Disorders, Nutr Clin Pract., 2011
  14. Denis et al., Omega-3 polyunsaturated fatty acids and brain aging. Curr Opin Clin Nutr Metab Care., 2015
  15. Chanson-Rolle et al., Systematic Review and Meta-Analysis of Human Studies to Support a Quantitative Recommendation for Whole Grain Intake in Relation to Type 2 Diabetes., PLoS One, 2015
  16. Hollaender et al., Whole-grain and blood lipid changes in apparently healthy adults: a systematic review and meta-analysis of randomized controlled studies., Am J Clin Nutr, 2015
  17. Schwartz and Levine, Effects of dietary fiber on intestinal glucose absorption and glucose tolerance in rats, Gastroenterology, 1980
  18. Prado et al., Milk kefir: composition, microbial cultures, biological activities, and related products, Front Microbiology, 2015