Alive with Microbiome

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Microbiome: the microorganisms in a particular environment (including the body or a part of the body). “we depend on a vast army of microbes to stay alive: a microbiome that protects us against germs, breaks down food to release energy, and produces vitamins”

Understanding the microbiome—human, animal, and environmental—is as important as the human genome.

As we have been taught, a human being is an individual who has grown from a fertilised egg which contained genes from both father and mother, right?

A growing band of biologists, however, think this definition incomplete. They see people not just as individuals, but also as ecosystems. In their view, the descendant of the fertilised egg is merely one component of the system. The others are trillions of bacteria, each equally an individual, which are found in a person’s gut, his mouth, his scalp, his skin and all of the crevices and orifices that subtend from his body’s surface.

The microbiome, like a rain forest or grassland, has all the complexities that an ecosystem entails. Just as the gorillas and leopards of African forests differ from the wolves and moose of American ones, so, too, do microbiomes vary around the world.

A healthy adult human harbours some 100 trillion bacteria in his gut alone. That is ten times as many bacterial cells as he has cells descended from the sperm and egg of his parents. These bugs, moreover, are diverse. Egg and sperm provide about 23,000 different genes. The microbiome, as the body’s commensal bacteria are collectively known, is reckoned to have around 3,000,000.

The entire microbiome accounts for about 1-3% of total body mass. Collectively weighing about three pounds — the same weight as our brain. Humans are like “bacteria in a suit.” Each of us is literally more bacteria than human. Not only do our bacteria outnumber us, their genes outnumber our genes. In many ways, their genes have more of an influence over our day-to-day life than our own genes do.

The microbiome of the gut has been characterised as a “forgotten organ”; and the only “organ” that can be replaced without surgery. Although it is not a distinct structure in the way that a heart or a liver is distinct, an organ does not have to have form and shape to be real. The immune system, for example, consists of cells scattered all around the body but it has the salient feature of an organ, namely that it is an organised system of cells.

The far larger genome of the microbiome has correspondingly greater capabilities, and complex carbohydrates are no match for it. They are relentlessly chewed up and their remains spat out as small fatty-acid molecules, particularly formic acid, acetic acid and butyric acid, that can pass through the gut wall into the bloodstream—whence they are fed into biochemical pathways that either liberate energy from them (10-15% of the energy used by an average adult is generated this way) or lay them down as fat.

The human microbiome may have a role in auto-immune diseases like diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, fibromyalgia, and perhaps some cancers. A poor mix of microbes in the gut may also aggravate common obesity.

Studies between metabolic products and disease, have shown that the amount of formic acid in someone’s urine is inversely related to his blood pressure—a risk factor for cardiac problems. The connection appears to be an effect that formic acid has on the kidneys: it acts as a signalling molecule, changing the amount of salt they absorb back into the body from blood plasma that is destined to become urine. Since the predominant source of formic acid is the gut microbiome, the mix of bacteria there is a factor in heart disease.

Perhaps the most striking claim, however, for links between the microbiome and human health has to do with the brain. It has been known for a long time that people with autism generally have intestinal problems as well, and that these are often coupled with abnormal microbiomes. In particular, their guts are rich in species of Clostridia. This may be crucial to their condition.

Interestingly, microbiomes go through a huge upheaval by the third trimester of pregnancy. They end up looking like the microbiomes of people with metabolic syndrome — a disorder that involves obesity, high blood sugar and a higher risk of diabetes and heart disease. These communities might indicate someone on the verge of chronic disease — or merely motherhood. Packing fat and building up blood sugar makes sense when you are nourishing a growing fetus.

During the last three months of pregnancy, antibodies from the mother are passed to her unborn baby through the placenta. This type of immunity is called passive immunity, because the baby has been given antibodies rather than making them itself. Antibodies are special proteins that the immune system produces to help protect the body against bacteria and viruses. The amount and type of antibodies passed to the baby depends on the mother’s immunity. For example, if the mother has had chickenpox, she will have developed immunity against the condition and some of the chickenpox antibodies will be passed to the baby. However, if the mother hasn’t had chickenpox, the baby will not be protected. Immunity in newborn babies is only temporary and starts to decrease after the first few weeks or months. Breast milk also contains antibodies, which means that babies who are breastfed have passive immunity for longer. The thick, yellowish milk (colostrum) produced for the first few days following birth is particularly rich in antibodies. Premature babies are at higher risk of developing an illness because their immune systems are not as strong and they haven’t had as many antibodies passed to them.

The microbiome is a teeming collection of thousands of species, all constantly competing with one another, negotiating with their host, evolving, changing. While your genome is the same as it was last year, your microbiome has shifted since your last meal or sunrise.

The microbiome is the sum of our experiences throughout our lives: the genes we inherited, the drugs we took, the food we ate, the hands we shook.

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