Meet Your Microbes

You may think of yourself as a single being or a single creature, but your body is brimming with bacteria. Other than ‘you’, that’s about 100 trillion more creatures, more ‘bugs’, as they are called. They teem and brush up against each other, forming many microbial municipals in your mouth, nose, gut, skin and genitals. However, you’ve never properly met any one of them, because nobody can ever see a microbe with a naked eye. To get a glimpse of them, you would need a microscope. Yet, as small as they can be, their role in equipping us for life cannot be understated.


Despite that our bodies are now home to so many microbes, when we were first made in our mother’s womb, we were without bacteria, and we were bathing in the warm and sterile amniotic fluid of our mothers’ uteri. It is when the water broke that we received our first microbial gift.

When a mother gives birth to her child, she bestows the new-born with her own microbes. They come from her vagina and near it, her anus. This means that the baby gets a double dose of Mommy’s microbes, both vaginal and faecal ones. It sounds revolting, but this microbial rite of passage is needed to kick-start the baby’s immature gut to digest breast-milk.

The vaginal bacteria that a baby gets are mostly lactic acid bacteria, and they are milk-eaters. They take lactose, a sugar found in milk, and convert it ultimately into simpler molecules—glucose and galactose—that the baby’s small intestine can absorb. However, although the baby can now digest lactose, she cannot yet digest a complex sugar in breast-milk called human milk oligosaccharides (HMOs). These HMOs need to be digested by a kind of faecal bacteria called Bifidobacterium infantis, which have also colonized the baby’s gut. They have evolved to digest HMOs without problem, and when they do, they release nutrients that nourish the baby’s gut cells, shore up the gut lining and reduce inflammation.

As you can see, the breast-feeding mother isn’t just nourishing the infant. In fact, it is her and her microbes that affects and builds the child. Yet, aren’t microbes also disease-causing criminals?



Admittedly, infectious diseases like the bubonic plaque are caused by microbes, and they have been cast as villains for us to destroy, lest they destroy us first. But this urge to eradicate microbes is unwarranted, since most of them are either benign or beneficial to us. We need to abandon the thought that wherever microbes are, there is war.

In a study done by US scientists, mice were born into a world without microbes, and they continued to grow in a sterile environment. At first, they seemed fairly alright and nothing looked abnormal. But later, compared to their microbe-laden peers, these sterile mice had trouble on the inside. Their bones were weak, their guts poorly developed, and the blood vessels that tried to feed their organ systems, sparse. Perhaps most striking of all: their immune system was compromised. These microbe-free mice were miserable.

One way in which microbes make our lives worth living is that they play a starring role as they work with our own cells to modulate and balance our immune responses. This seems paradoxical, but contact with certain bacteria in the gut helps build the immune system. Once built, they continue to calibrate and tune it such that it reacts correctly to dangerous threats, but not overreact to harmless things—allergens like dust or pollen—from the outside world. Our microbes and the cells of our immune system keep each other in check, providing us with a strong and healthy immune system.



We’ve seen that microbes which coexist with us aren’t merely hitchhikers. In some cases, they can even provide their hosts with extraordinary abilities. The bobtail squid, for example, relies on a single species of bacterium—the Aliivibrio fischeri—to provide a bioluminescent light source on its belly that camouflages the squid against the water surface above it. Thanks to such bacteria, the squid has an invisibility cloak to hide itself from predators.

In the case of humans, the Japanese harbour seaweed-eating bacteria in their gut. Compared to plants that live on land, marine algae like seaweed have sulphur-rich sugars that are hard for us to digest. However, the marine bacteria, Zobellia galactanivorans, have genes which code for enzymes that can digest these sugars effortlessly. They thrive on seaweed. So, when sushi made it into the bellies of the Japanese, these bacteria tagged along. And once these marine microbes found themselves inside the gut, they passed on their seaweed-eating genes to other gut bacteria through a process called horizontal gene transfer.

Unlike hereditary gene transfer which pass down genetic material from parent to offspring of the same species, horizontal gene transfer allows bacteria to send their own genes to other bacterial species. No other kind of living creature except bacteria can do this naturally. This unique transfer of genes has empowered the rest of the gut bacteria with this special digestive ability.

Nevertheless, discoveries like these only look locally at individual microbes. What about the other 100 trillion of them within us? A better understanding of the human microbiome was needed.



Studies of our microbiome first began with Antonie van Leeuwenhoek, who, in the early 1680s, had examined his oral and faecal microbes. However, it is only recently that the microbiome caught the attention of scientists around the world, and so the Earth Microbiome Project was launched in 2010.

Since then, crowdfunded projects aimed at studying the human gut microbiome have also been launched worldwide, covering places such as the US (the American Gut Project), UK (the British Gut Project), and Australia (the Australian Gut Project). These projects see any one person’s microbes as forming a community. So, rather than studying the microbes individually, the goal is to study the microbial communities collectively, and to understand how this teeming mass works as a group, as a microbiome.

In 2016, the gut project reached the shores of Singapore as the Asian Gut Project, in effort to get more microbial data from Asian people. This is because people in Asian countries tend to eat more fermented food, and it was discovered that those who ate more fermented food had greater diversity of bacterial species in their gut—a sign of a healthy gut microbiome. With knowledge like this, our intimate relationship with our microbiomes puts our bodies and lifestyle into a new context. Who knows, because of this, people may be inclined to eat more tofu in the future.

As for the doctors and scientists, they think that understanding the microbial life within us could provide vital insights into illnesses from heart disease to cancer. Ultimately, it is from these gut projects that they want to use the information collected to rationally target the microbiome for various therapies. For instance, some scientists are looking to harness the power of poop.



Unlike our human cells, we can change our microbes for the better, and scientists are looking to do this via what’s called Faecal Microbiota Transplantation (FMT). It’s exactly what it sounds like. You take faeces from one person and put them into the gut of another.

The basis of FMT lies in our gut bacteria, of which most are beneficial for us, as we’ve seen. They’re crucial for our body to grow and function properly, and they sometimes aid in digestion, too. However, if a doctor administers antibiotics for a patient for whatever condition, the drugs can indiscriminately kill off these beneficial gut bacteria, allowing a ‘bad’ bacteria, called Clostridium difficile, to take over.

When C. diff dominates the gut, they release toxins that can damage the colon’s lining and cause inflammation, resulting in a condition called Clostridium difficile colitis. Normally, antibiotics are used to treat C. diff infections, but for patients with recurring cases, antibiotics become useless and the condition can turn life-threatening. This is where FMT comes in: the patient receives a stool sample from a donor with a healthy set of gut bacteria, and the patient’s bacterial balance is restored. C. diff’s reign over the gut is over.

Although we might have considered microbes to be bad, it now appears that we can intervene and get more of our microbes working on our behalf.



If the quality of our lives depends on microbes as much as they depend on us for food and a place to call home, we may need to stop thinking of ourselves as single organisms. Rather, every individual is superorganism. We are superorganisms, one consisting of us and our microbes. We are never without them, and because we live in intimate contact with them, we evolve together.

How can we come to understand ourselves without understanding them?


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