The word microbiome was coined by Joshua Lederberg in 2001. He signified the ecological community of commensal, symbiotic and pathogenic organisms that share our body space.
Although technically the human microbiome was defined as the complete genome (an organism’s complete set of DNA including the genes) of all microorganisms in and on the human body, the term is now usually used synonymously to refer to the community of all microorganisms in this habitat.
Yes indeed! The human microbiome consists of 10-100 trillion symbiotic microbial cells, primarily bacteria in the gut. Compared cell-wise, the microbes living on and in the human body outnumber the human cells by a factor of 1.3:1 with a total mass of about 1-3% of the body they inhibit (for a 60-kg person that would be 0.6 -1.8 kg).
The human body is a complex ecosystem which has long been thought to be able to exist as its own physiological island. BUT WE WERE SO WRONG!
Without the trillions of microbes we share our body with, we would struggle to break down essential nutrients, to receive signals from the body concerning our state of hunger or satiety, or to keep our immune system in check!
Interestingly, our microbiome is what makes us so special: if we compare the human gene catalogue with our microbiome, our human genetic diversity pales in comparison. In the gut alone, where the majority of our microbiota are located, 3.3 million genes are reported to exist, compared to 22,000 genes present in the human genome. Human individuals are 99.9% identical to each other in terms of their own genome, whereas the microbiome of each individual can be 80-90% different from one another.
Picture: Gaby D’Allesandro / American Museum of Natural History
These microbes inhabit all parts of our body that are exposed to the environment, such as the skin, mouth, vagina, urogenital tract, airways or gut.
As a matter of fact, new-born life begins sterile, picking up its mother’s commensal bacteria during birth and breastfeeding, and continues to be exposed through contact with parents, grandparents, siblings, pets and the environment itself, which is crowded with bacteria.
During the first year of life, the microbiome matures to an adult status, making it one of the most complex ecosystems in the world. During this time and further down the road, the nutrition plays a major role, determining the nature of the microbiome. Formula-fed and breast-fed infants showed significant differences in their gut microbiota, again changing substantially with every introduction of a new diet, while the microbial diversity increases with time.
Our immune system is engaged in a constant, highly-sensitive balancing act between states of aggression and tolerance. Our immune system can only manage this balancing act with the help of microbiota. The microbiota teach the immune system which cells to fight and which cells to leave alone.
A common commensal microorganism called Bacteroides fragilis was found to boost regulatory T cells, and thus stop the pro-inflammatory T cells from becoming too aggressive. These findings show that bacteria are necessary in helping our immune system not to react against cells that do not actually harm our body. If these bacteria are missing, our body overreacts on all kinds of cellular material we pick up resulting in allergies and asthma.
Normally, when people think of bacteria in the body, they think of pathogens. That's why research focused on these harmful bacteria for a long time and ignored the “good bugs”.
The reason, argues biologist Sarkis K. Mazmanian of the California Institute of Technology, is our skewed view of the world. “Our narcissism held us back; we tended to think we had all the functions required for our health,” he says. “But just because microbes are foreign, just because we acquire them throughout life, doesn’t mean they’re any less a fundamental part of us.”
Another reason is the lack of modern technology. Although the first studies on the microbiome emerged as early as the 1680s with Antonie von Leewenhoek, who found striking differences between his own fecal and oral microbiota, the methods used in the past weren't adequate to fully investigate the microbiome. Now the existence of modern (molecular) techniques allows the isolation of ALL bacteria, even the hard-to-grow anaerobic ones, and the ability to understand what these microbes are good for!
The biggest threat to our microbiome was and still is the widespread use of antibiotics. Although antibiotics have saved many lives, they are too-often used without precaution or as prophylaxis. Antibiotics do not distinguish between the good and the bad bugs! By the age of 15, most children in the U.S. have had multiple rounds of antibiotic treatment for a single ailment – otitis media, or the common ear infection.
In other words, you can protect your microbiome by avoiding the use of antibiotics and other non-selective antimicrobials and by playing in the dirt a little more often.
This question can be answered with YES from two different perspectives.
- The food we eat influences our gut microbiome by favouring those bacteria that are either better or worse in their ability to use energy from food. The consumption of high-fat products reduces the total volume of the intestinal microbiome volume and induces the growth of bacteria that support a fast fat deposition. When colonizing sterile mice with the gut microbiome of obese mice, a tendency towards faster fat deposition was observed compared to mice which were transplanted with the microbiomes of slim mice.
- The gut microbiome tells us when to eat. The bacteria residing in our stomach, namely Helicobacter pylori, tell us when we're hungry or full. Besides regulating the acidity in the stomach, this bug causes a decrease in the hormone ghrelin which is involved in appetite regulation. The absence of this bacterium in the stomach causes elevated ghrelin secretion, leading to a bigger appetite. Unfortunately, H. pylori has had a bad reputation throughout the last decades as a causative agent for peptic ulcers in susceptible people; it has almost been eradicated from our stomachs by antibiotics. As an example, two or three generations ago in the U.S., 80% of Americans harbored this bug, now less than 6% of American children are host to it, which may be one explanation for the increase in child obesity in the United States.