Our Microbial Organ

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.

Human gut microbes hold 'second genome'

The human gut holds microbes containing millions of genes, say scientists.

In fact, there are more genes in the flora in the intestinal system than the rest of our bodies. So many that they are being dubbed our "second genome".

The human body carries some four pounds of microbes, primarily in the gut, and understanding their biomolecular functions, their impact on human hosts, and the metabolic and functional roles of microbial communities generally is one of the key areas of study enabled by high-throughput sequencing.

The Human Microbiome Project: the large effects of small inhabitants

The Human Microbiome Project (HMP). If asked what it is, perhaps you would see that the name resembles that of the Human Genome Project and guess that it is a large effort devoted to some sort of DNA sequencing involving humans. This is partially correct.
So what exactly is a microbiome? First, we have to wrap our heads around the astounding fact that the human body has 10 times more bacterial cells in and on it than human cells. That’s a lot of bacteria! Together, all these bacteria and other microorganisms associated with the body are called the microbiota (referring to “small life”). Second, just as a genome is the collection of all the genes of an organism, the microbiome is the collection of all the genes present in the microbiota. The HMP aims to characterize and understand the role of the human microbiome, and this summer, the culmination of years of work on the HMP has been unveiled.
Before we move on, let’s make one thing clear: bacteria have gotten a bad rap. Understandably, many people associate bacteria with disease. While pathogenic bacteria that cause disease usually get the most press, in reality, bacteria provide many benefits for both our planet and us. They are the workhorses of the world, from performing photosynthesis in the oceans, to fixing nitrogen (think of it as creating fertilizers out of thin air) to feed much of the world’s vegetation. They probably make up more of the global biomass than all other living organisms combined . Not only are bacteria important on a global scale, they are also an integral part of us. Bacteria are associated with every surface of the human body, from the external skin to the internal gastrointestinal tract. Some studies even investigate the microbiome of the eye!