You may have heard it said that our genome is “99% chimpanzee”. As surprising as this may sound to some, what is even more shocking is that more than 90% of “our” cells are actually bacteria.
How is this possible? Read on to find out more!

Immediately after we are born, we begin to acquire bacteria from our surroundings. We call these bacteria “commensals”, a word from the Medieval Latin “commensalis,” referring to a companion at the table. This is a good name for our intestinal bacteria, since these microbes break down food for energy alongside our own cells in the gut. The human gut is more than 25 feet long and is the home to one hundred trillion bacteria. This means that there are 10 times more bacteria in your gut alone than there are human cells in your entire body! The sheer number and diversity of commensal bacteria in the gastrointestinal (GI) tract makes it one of the most ecologically-rich and densely-populated microbial habitats on the planet, even richer than the menagerie of bacteria you would find in the soil. Interestingly, the density and diversity of bacteria vary depending on where you look along the GI tract. The density and diversity of bacteria is relatively low in our acidic stomach, but rise to a maximum towards the colon, where anaerobic bacteria that live in the absence of oxygen are abundant.

Living in a microbial world

The mucosal surfaces of our body, like our airways, reproductive tract, intestine, and some skin, are in direct contact with the environment and are highly susceptible to invasion and infection by pathogenic bacteria, viruses, fungi and parasites. However, commensal bacteria compete much more efficiently for food and space and colonize these nutritionally rich surfaces before pathogenic bacteria get a chance to invade. With a hundred trillion bacteria inside our bodies, we can imagine these microorganisms to be a sort of “microbial organ” placed within one of our own. This microbial organ is composed of cells that communicate with one another, carries out important functions necessary for our survival, and can maintain itself through regeneration. The particular species of bacteria in our gut today are descended from bacteria that formed a mutually-dependent, or symbiotic relationship with mammals millions of years ago, co-evolving with us to the point where we need them as much as they need us.

Scientists recently discovered one particular gut bacteria type found in Japanese people that allows them to digest complex carbohydrates that are abundant in the seaweed used to wrap sushi. These carbohydrates, called porphyrans, would have otherwise been impossible for our human cells to break down. Interestingly, the gene in the bacteria that makes this possible was acquired by the gut bacteria from marine microorganisms that are often found on seaweed. Such foreign genes acquired by our microbial organ allow us to perform functions that we have not been able to evolve ourselves. Indeed, there are 100 times more genes in the 500-1000 species of bacteria of our gut than in the human genome.

Commensal bacteria control your immune system

While commensal bacteria live happily and cozily in our intestines, we also benefit greatly from them — they help us with efficient digestion, absorption, synthesis and storage of nutrients. But this is not all. Small experimental mammals that are raised to be completely commensal bacteria-free don’t just have problems with digestion. They also have poorly developed immune systems, with fewer white blood cells and fewer antibodies circulating in the blood, making them highly susceptible to infection by certain bacteria, viruses and parasites. Our gut bacteria also help train our immune system to react in the way it needs to when a real infection comes.

Our immune system and commensal bacteria have co-evolved such that our immune system recognizes the commensal bacteria as our allies and commensals prepare our immune system for attacking pathogenic bacteria. This two-way communication involves secretion of numerous pro- and anti-inflammatory factors by the bacteria and the gut, involving numerous complex carbohydrates, peptides and lipids. We are still discovering and learning more about these chemical signals as our knowledge of the microbial organ is growing.

Relationship status: It’s complicated

And yet, while most of our interactions with the microbes in our gut are beneficial, sometimes the relationship with our commensal bacteria can go awry, and this has been linked to disease. This is most clearly evident in inflammatory bowel disease (IBD), like Crohn’s disease, which is a crippling disorder in which the immune system inflicts severe inflammatory damage on the gut wall. Compared to unaffected individuals, patients with IBD also have higher levels of antibodies against their own commensals, suggesting that the immune system in these individuals is overreacting to the bacteria in their gut, and the various tissues in the digestive tract are suffering as a result.

There are two groups of bacteria that dominate the human gut, the Bacteroidetes and the Firmicutes. The ratio of these two bacteria correlates with and reflect the status of our health. The community of bacteria in IBD patients often lacks these two groups, both of which are very common in non-IBD individuals. Interestingly, a difference in bacterial types and ratios has also been seen between healthy and obese individuals. Obese individuals have fewer Bacteroidetes and more Firmicutes. After diet therapy, however, this ratio is reversed. To study this effect, there have even been some experiments to test microbial “organ transfer”. Mice lacking the leptin gene that controls appetite are morbidly obese. If commensal bacteria of these leptin-deficient obese mice are transferred into mice with a normal leptin gene but lacking any commensals in their gut, their mean body fat goes up, suggesting that there is a complex relationship between our microbial organ, our diet and our health.  As we come to better understand these relationships, we might be able to design bacteria that could regulate our microbial organs to selectively decrease inflammation or alter our digestive capacity.

The Human Microbiome Project

Following the completion of the Human Genome Project, there is now a growing support for the sequencing of all the bacterial genomes that constitute the human microbial organ, or “microbiota”. The human microbiome is several times larger than the human genome but remains unexplored. Modern sequencing technologies will help scientists figure out how human microbiomes vary across populations and how they impact disease.  We will better understand the role of commensal microbes in infections, obesity, diseases such as IBD and even arthritis and invent novel ways to engineer our microbial organs for human health.

–Grace J. Yuen, Harvard Medical School

For More Information:
Bacteria Thrive in Inner Elbow; No Harm Done:

Japanese people have special seaweed-digesting gut bacteria:

Human gut microbes hold ‘second genome’:

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