Microbes to the Rescue
Helping develop our immune systems is only part of what microbes do for us. They are in charge of digesting most of our food, including fiber and complex proteins, and chopping them into more digestible forms. They also supply the essential vitamins B and K by synthetizing them from scratch, something our own metabolism cannot do. Without the vitamin K from microbes, for example, our blood would not coagulate.
Good bacteria and other beneficial microbes also help us combat disease-causing microbes. Experiments in our lab have shown that infections from Salmonella, a diarrhea-causing bacterium, are far worse when antibiotics are given before the infection actually occurs. Similarly, many of us have experienced the side effects of a long bout of antibiotics: abdominal cramps and watery diarrhea. The microbes we harbor live in a balanced state that provides us with so many benefits, all in exchange for a portion of our daily calories and a warm, dark place to live with regular feeding and watering.
But changes in our modern lifestyles are altering this balance, especially during a critical window in early life. In many developed countries, about 30 percent of babies are born by cesarean section, antibiotic usage is a lot more frequent, and most children do not suffer serious infections thanks to vaccines. Far from suggesting that any of these things should be avoided, our aim is to educate parents, as well as parents-to-be, grandparents, and caregivers, about the potentially life-changing decisions we make on a daily basis by raising children in an environment that’s much cleaner than ever before. As parents ourselves, we understand that most of us do the best we can with what we have, and it is not our intention to dictate how other people should raise their children. However, as microbiologists, we are becoming increasingly aware of the key role our resident microbes have in shaping our bodies’ development. The microbial communities of babies and young children are being altered in ways that may make them sicker later in life, by the very same practices intended to keep them healthy. Talk about a double-edged sword!
The scientific community is just beginning to grasp this new knowledge, and the general public is just starting to hear about it in news articles of (often misinterpreted) studies. Preventing serious illnesses should always be one of our biggest concerns, but we can also do a great deal to try to distinguish between a necessary intervention, such as giving an antibiotic to fight a life-threatening bacterial infection, and an unnecessary and hyperhygienic practice, such as applying antimicrobial hand sanitizers every time a child plays outside. Not all children will or should be raised like Jedd or Jacob, but we can certainly change those unneeded aspects of our far-too-clean world.
In our classical training as microbiologists, we studied only the microbes that cause diseases and the ways to kill them. Now we acknowledge that we have, for many years, ignored the vast majority of microbes that keep us healthy. Our research labs are changing focus, and we are beginning to think it’s time for everyone to become better hosts to our microbial guests.
BUBBLE BOY
David Vetter was born in 1971 in Houston, Texas, with a rare genetic disorder that left him without a working immune system. Any contact with a nonsterile world would mean certain death. Because of this, he was delivered by C-section and placed in a sterile bubble immediately after his birth. In a controversial medical decision, he lived in the hospital in a bubble that grew with him. His medical treatment included many courses of antibiotics to prevent any bacterial infection. Being devoid of bacteria meant that doctors also had to feed him a special diet, along with the essential vitamins K and B, which are normally produced by intestinal bacteria. David’s story reflects the impossibility of living without an immune system in a world full of microbes, as well as a human’s dependence on microbes and what they produce for us. Sadly, David died at the age of twelve from a viral infection a few months after a bone marrow transplant was finally performed.
2:A Newly Discovered Organ: The Human Microbiome
Invisible Life
The idea of humans being inhabited by countless microbes invisible to the naked eye is as old as the first microscope. Born in 1632 in the city of Delft, in what is now the Netherlands, Antoni van Leeuwenhoek was a tradesman with a special interest in lens making. His desire to see the intricacies of the cloths he marketed drove him to shape glass rods into spheres using a flame. These almost perfect spheres allowed him to magnify not just threads, but anything else he wanted to view in great detail. Although he wasn’t formally trained as a scientist, he was one at heart and he soon began to put the oddest things under his rudimentary microscopes: water from a creek, blood, meat, coffee beans, sperm, etc. He methodically wrote everything down and sent his findings to the Royal Society of London, which began publishing his curiosities-filled letters.
One day in 1683, he decided to scrape the white residue between his teeth and place it under his lens, writing in his notes:
An unbelievably great company of living animalcules, a-swimming more nimbly than any I had ever seen up to this time. The biggest sort (whereof there were a great plenty) bent their body into curves in going forwards . . . Moreover, the other animalcules were in such enormous numbers, that all the water . . . seemed to be alive . . . All the people living in our United Netherlands are not as many as the living animals that I carry in my mouth this very day.
Naturally, Leeuwenhoek’s observations of a never-before described world filled with microscopic “animalcules” were met with great skepticism and ridicule. It wasn’t until other British scientists saw it with their own eyes that they began to acknowledge that Leeuwenhoek was not hallucinating. Leeuwenhoek had written many letters to the Society, but discovering microscopic life is what sealed his long-lasting fame. As a result of his many discoveries, Leeuwenhoek is considered the “Father of Microbiology.”
Still, these findings remained nothing more than curiosities of the natural world, with no real connection to human biology until scientists discovered that those “animalcules” caused diseases. This revelation took place almost two hundred years later, when Robert Koch, Ferdinand Cohn, and Louis Pasteur each separately confirmed that diseases such as rabies and anthrax were caused by microbes. Pasteur’s work also showed that microbes caused the spoilage of milk, and he thus designed the process known as pasteurization, in which microbes are killed with the use of high heat. Milk contamination led Pasteur to the idea that microbes could be prevented from entering the human body, and together with Joseph Lister, they developed the first antiseptic methods. These began to be widely adopted, with one of them still in use today: Listerine.
Avoiding Contagion at Any Cost
The work of Pasteur, Cohn, Koch, and others led to the widespread knowledge that diseases could be avoided by preventing contact with microbes, and by killing them, and so the quest to eradicate them began in earnest. Health departments opened in London, Paris, New York, and other big cities. Garbage, which had previously been left to pile high on sidewalks, was now collected and disposed of; drinking water was treated; rats and mice were hunted; sewer systems were built; and people with contagious diseases were often placed in isolation. It was through all this that the word “bacteria” gained its bad reputation and inherent connotation of disease, contagion, and plague. Germs were (and still are) entities to be feared, avoided, and fought.
Fast-forward another two hundred years and an equally astounding discovery is now in progress: in our quest to clean up our world, we have been killing more