Human Microbiome: what it is and how it works.


You may have stumbled upon this word before and if not here it is. I am actually glad somehow you ended up here, reading about it because your Microbiome is very important for your health. I believe everyone ( or at least whoever cares about their health and happiness) should know about it and how it works. There is a ton of research on this topic, as a matter of fact, I once did a paper about it in my fifth year of Medical School. It fascinated me at that time and it fascinates me now.

Male body,man surrounded by microbiome cloud of bacteria, viruses, microbes. 3d rendering. Dense microbe population

The term was coined by Joshua Lederberg in 2001 “microbiome, to signify the ecological community of commensal, symbiotic, and pathogenic microorganisms that literally share our body space”.  Lederberg won the Nobel Prize in Physiology or Medicine for discovering that bacteria can mate and exchange genes (bacterial conjugation). He also did extensive research in artificial intelligence. So, thank you, Dr. Lederberg!

Now, going back to our main question ” What is The Human Microbiome?”. According to The National Center for Biotechnology Information, ” The human microbiota consists of the 10-100 trillion symbiotic microbial cells harbored by each person, primarily bacteria in the gut; the human microbiome consists of the genes these cells harbor. Microbiome projects worldwide have been launched with the goal of understanding the roles that these symbionts play and their impacts on human health. Just as the question, “what is it to be human?”, has troubled humans from the beginning of recorded history, the question, “what is the human microbiome?” has troubled researchers.”.

Ok, let’s ” translate” this. Many of you might think that bacteria are harmful and that if it enters our body we can get sick or develop diseases. But the truth is that inside of our body there is another ” body” made of trillions of bacteria ( good and bad). The problem arises when there is an imbalance between them, more bad than good. The human microbiome is an integral internal ecosystem. We can think of it as another organ, made of trillions of bacteria, that it’s not just located in one location. Today, microbiome science is playing an important role in fields such as psychology, nutrition, and medicine. Studies show that if you do a fecal transplant ( poop transplant) from someone with normal weight to someone that is obese for example, that person will lose weight. Some support this theory and some don’t. ( read more about it). The concept behind fecal transplants is that, if your microbiome is defective, introducing someone else’s healthy gut bacteria through their poop, will repopulate your gastrointestinal tract with the good one that you’re missing. We can conclude from here that obese people are inclined to have a different composition of gut bacteria compared to lean individuals. Certainly, gut health can impact how your body extracts nutrients from your diet and stores fat.

Humans are born sterile and microbial colonization begins immediately at birth. According to The National Center for Biotechnology Information ” Studies have shown that there are distinct differences in the microbiome profiles of newborns born vaginally compared with those born by cesarean”. Cesarean deliveries and limited breastfeeding have been linked to conditions such as allergies, asthma, allergies, celiac disease, obesity, and Type 1 diabetes. As reported by New York Times ” Recent studies have shown that both a vaginal birth and exclusive breastfeeding can significantly affect the kinds and numbers of their gut microbes and the risk of developing various health problems.”. To reverse the effects of a surgical birth on the baby’s microbiome, some women whose babies are delivered by cesarean are soliciting that medical staff transfer microbes from the mother’s vagina to their infants soon after birth.

I always notice moms who try to protect their kids too much so I feel like I need them to know this. Now, I am not a mother yet so I clearly don’t know how it feels but I can talk from my personal experience as a child who was raised in ” dirt” haha. My mom would let my siblings and I play, get our clothes dirty, sleep next to our dog, lay on the grass, basically do whatever we want in nature. On the other hand, my aunt was always more protective of her child; she would make her wear a baby bonnet even in August. I can never forget how often that child got sick and later on I understood the reason behind this. Her immune system never got the chance to develop properly. So dear moms or future moms, let your child get dirty haha.


Dr. Ruebush, the “Why Dirt Is Good” author writes “Children raised in an ultraclean environment, are not being exposed to organisms that help them develop appropriate immune regulatory circuits.” . Dr. Weinstock a leading researcher and the director of gastroenterology and hepatology at Tufts Medical Center in Boston said “Children should be allowed to go barefoot in the dirt, play in the dirt, and not have to wash their hands when they come in to eat,”  He and Dr. Elliott, a gastroenterologist and immunologist at the University of Iowa that he conducted the study with, pointed out that children who grow up on farms and are frequently exposed to worms and other organisms from farm animals are much less likely to develop allergies and autoimmune diseases. He adds by saying “let kids have two dogs and a cat,” which will expose them to intestinal worms that can promote a healthy immune system.




The majority of the microbiome exist in the gut so yes, ” You are what you eat!”. Dr. Mark Lyte conducted a study that shows how the bacteria in your gut can influence your mood. Poor gut health can also contribute to autoimmune diseases and disorders like heart disease, arthritis, dementia, Alzheimer’s, depression, anxiety, ADHD, autism, infertility, and cancer, while our health, happiness, fertility, and longevity are influenced by a healthy gut.


Functions of good bacteria:

  • Produce vitamins;
  • Digest food and unused nutrients;
  • Balances hormones and lowers inflammation;
  • Strengthens immune function;
  • Protects against overgrowth of pathogenic bacteria and yeast;
  • Balances blood sugar;
  • calms stress and emotional response;
  • helps your brain to function at its maximum potential ( some refer to the microbiome as ” the second brain” );
  • behavioral development;


What can damage the microbiome?



How to build a better microbiome?

  • Avoid antibiotics, birth control pills, acid blockers, NSAIDs, antibacterial soap;
  • Increase your intake of natural organic food instead of GMOs.
  • Skip the trans fats/hydrogenated fats ( doughnuts, cookies, crackers, muffins, pies, cakes, fried foods);
  • Avoid refined carbohydrates and refined vegetable oils (canola, soybean, corn);
  • Eat more fresh vegetables like beets, carrots, onions, peas, salad greens, squash, sea vegetables, leafy greens.
  • Avoid pasteurized dairy products and conventional meat, eggs, and poultry;
  • Eat more fresh fruits such as apples, blackberries, blueberries, grapefruit, cherries, oranges, pomegranates.
  • Avoid added sugar ( anhydrous dextrose, confectioner’s powdered sugar, corn syrup, corn syrup solids, dextrose, fructose, high-fructose corn syrup (HFCS), invert sugar, lactose, malt syrup, maltose, maple syrup, molasses, pancake syrup, raw sugar, sucrose, white granulated sugar);
  • Use herbs and spices like turmeric, ginger, basil, oregano, thyme.
  • Drink green tea and organic coffee;
  • Eat probiotic foods: sauerkraut, kefir, yogurt, kombucha, fermented foods like pickles;
  • Take probiotic supplements;
  • Use wild-caught fish instead of farm-raised, pasture raised eggs, grass-fed/pasture raised meat;
  • Healthy fats: coconut oil, organic butter, extra virgin olive oil, nuts, and seeds;
  • Drink red wine!  I am serious. The National Center for Biotechnology Information studied this.
  • Eat dark chocolate.
  • Lower stress by finding methods of relaxation ( walks, yoga, exercise);
  • Exercise more. Jeffrey Woods, a professor of kinesiology and community health at the University of Illinois conducted a study which revealed that a few weeks of exercise can alter the makeup and function of people’s microbiomes. 



‘‘If you transfer the microbiota from one animal to another, you can transfer the behavior’’ – Mark Lyte PhD, MS, MT(ASCP)


There are approximately 22,000 genes in the human gene catalog and 3.3 million non-redundant genes in the human gut microbiome. Without a doubt, the microorganisms present in the human gut are critical for human health. Exactly to what length, how and what areas of human health are influenced by our “friends” is yet to be established.


Fun germ



Haha, with all my love,








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