The Human Microbiome, the Self You Never Knew

By Jacob Devaney on Monday May 9th, 2016

The Living Organisms Sharing Your Body

Can a basic understanding of the Human Microbiome change the way we think of ourselves and provide substantial food for thought as we reflect on who and what we are as a species?

We know that we are made of bones, blood, cells, muscle, etc. and we tend to think that these are what makes us human. However, we often overlook the Human Microbiome. This is a naturally occurring community microorganisms (microbes) in our body – including diverse viruses, fungi, and protozoa – that outnumber human cells almost two to one! While this might sound scary, this thriving community of microbes in our body is working in harmony with our human cells to create life as we know it.

Each region of our body has its own distinct community of microbes living on or in it. – Lita M. Proctor

Thanks to Louis Pasteur, a cornerstone of our modern medicine has been based on the notion of killing germs (i.e. bad microbes). This “war with germs” was born from a history of “battling” bubonic plague, small pox, yellow fever, typhoid, and others, but science is telling us that struggling against germs is not an accurate portrayal of what it means to be healthy.

This thriving community of microbes in our body is working in harmony with our human cells to create life as we know it. A thriving community of microbes working in harmony with human cells.

Rather than thinking of our bodies as a battlefield (fighting off bad germs etc.), humans and microbes must now be seen as a co-evolved system for the mutual benefit of both the host and resident microbes. Health is the result of balanced harmony between resident microbes and human cells, and though antibiotics are helpful in certain applications, there is much reason to be cautious and prudent in their usage.

Routine practices, including the use of antibiotics, may alter the human microbiome by reducing nontargeted bacteria and creating antibiotic resistant strains. -Blaser, M.J. (2011) from Antibiotic overuse: stop killing our beneficial bacteria

Before we dive into the science of the microbiome, let’s consider how this belief structure of war, separation, and homogeneity is applied in other aspects of our life. For example, in politics we draw national boundaries and fight over immigration. We mono-crop ideas as much as we do our agriculture in a fictitious quest for purity. In reality, on a biological level, we aren’t even “purely” human. Our conquest of nature over the centuries has revolved around our fear and inability to seek greater harmony with our environment and embrace the bio-diverse web of life. Luckily, times are changing and science is a guiding force.

We should stop thinking of our bodies as a battlefield (fighting off bad germs etc.).We should stop thinking of our bodies as a battlefield (fighting off bad germs etc.).

So What is a Microbe?

Simply put, a microbe is any living organism that is too tiny to be seen with the naked eye. This includes bacteria and archaebacteria, protists, some fungi and even some very tiny animals that can only be seen with a microscope. These microbes can include germs that are beneficial, as well as those that are harmful. Overall, most of the microbes are beneficial, like enzymes that can provide energy for metabolism, help the body synthesise vitamins, act as a defence against pathogens or help us digest food. The human microbiome is the sum of these communities, which is primarily composed of bacteria and other microbes, such as viruses, protozoa, and fungi. Our emerging understanding of these communities within the human body will continue to bring breakthroughs in every aspect of medicine and well-being.

Scientists now believe that infants are sterile (meaning free of microbes) in the womb and receive their first inoculum of microbes from the mother during natural childbirth. This inoculum goes on to colonize the newborn and initiate a succession of events leading to the development of the child’s own microbiome. The newborn relies on this maternal vaginal microbial inoculum and the additional inoculum of microbes from mother’s breast milk for microbial colonization of all exposed surfaces in and on the infant’s body (e.g., oral, nasal/airways, gut, urogenital, skin). -Lita M. Proctor, Ph.D.

A microbe is any living organism that is too tiny to be seen with the naked eye.A microbe is any living organism that is too tiny to be seen with the naked eye.

It Starts at Birth

The immune system is completely entwined with the human microbiome, and birth will leave life-long imprints on us. From the moment we are born, our bodies start to learn all different kinds of microbes, distinguishing the helpful ones from the ones that cause diseases. This means that creating a sterile environment in the first weeks, months and years won’t allow the child’s immune system to develop properly. Playing in the dirt, walking around barefoot, putting random things in the mouth should be supervised, but not discouraged.

The latest scientific research is now starting to indicate that if the baby is not properly seeded with the mother’s own bacteria at birth, then the baby’s microbiome, in the words of Rodney R Dietert, Professor of Immunotoxicology at Cornell University, is left “incomplete”. Consequently, that baby’s immune system may never develop to its full potential, leaving that infant with an increased risk of developing one or more serious diseases later in life. –Toni Harmon, Huffington Post

Playing in the dirt should not discouraged.Playing in the dirt should not discouraged.Image from Jiva Photography.

It’s All About Lifestyle Choices

Our hormones, where we live, how we interact with our environment (do we get our hands in the dirt enough?), and what we eat are all influencing factors on our microbiome. Knowing this, you may want to consider how your daily lifestyle may affect your microbial colonies. What kinds of soap do you use? Do you really need to shampoo every day? What kinds of food do you eat and which kinds of microbes are you feeding?

Many researchers believe that certain bug-guts or parasites are actually causing us to crave certain foods. With discipline, we can learn to feed our bodies food that encourages happy and healthy colonies of microbes and maybe even eat our way to enlightenment. Significant research shows us the importance of eating live foods because they are rich in enzymes. Healthy serotonin, and dopamine levels, as well as mood are also related to gut flora and food. Eating cultured and fermented foods are also important.

We can learn to feed our bodies food that encourages happy and healthy colonies of microbes.We can learn to feed our bodies food that encourages happy and healthy colonies of microbes.

Human Microbiome Project (HMP)

Much of the inspiration and information for this piece came from a longer and more in-depth article by Lita M. Proctor, Ph.D. Lita is Program Director of the Human Microbiome Project (HMP), which is, “an 8-year, $194M trans-NIH Common Fund Initiative to create a community resource of data, research resources and clinical and scientific approaches for this emerging field.” Medical and scientific initiatives like this are very hopeful as they invite us to look at the big picture, think holistically, and consider new ways to embrace health in a community context.

We are a web of interconnected organisms, we are an organism within a larger organism called Planet Earth. Having a good relationship with our internal and external communities requires mindfulness, awareness and healthy lifestyle choices. We are only at the very beginning of being able to comprehend the magnificence that is life within this biological diverse realm that we inhabit. Keep learning, growing, talking with friends, and raising the overall vibration, be good to your microbes and they will be good to you!

How do you feel about this article? Join the conversation.

Jacob Devaney

Founder and director of Culture Collective, creative activist, musician, and producer.



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Lita M. Proctor, The Human Microbiome: A True Story about You and Trillions of Your Closest (Microscopic) Friends. Action Bioscience.

Toni Harman, Microbirth: Why 'Seeding Baby's Microbiome' Needs to Be on Every Birth Plan. Huffington Post.


7 Responses to The Human Microbiome, the Self You Never Knew

  1. I agree with those who believe it is helpful to consider that any division of the Universe into parts is arbitrary and political. We did not discover that there were parts called Plants and there were parts called Animals and then discovered that there were Microbes too! It may seem to be comforting to imagine that there is some ideal arrangement of Parts and Processes that once discovered, human beings can live in harmony with, but you might want to think again. Do all of the human beings who live before the time of sufficient discovery live lesser lives? Just try to divide the Universe into Parts. Does organic parts and inorganic parts work for you or do you get tangled up with organic parts being made up of inorganic parts and organic parts turning into inorganic parts when life leaves them? Okay, can’t we at least decide that Nothing can be discerned to be different than Something? Well, when we try and discover nothing we keep coming up these days with dark mater and dark energy and sub – atomic particles winking in and out. When it is discovered that not all microbes are bad, things may have just got bad for people who just discovered that . They may have recently decided not to squish invading spiders, but now are forced to think about antibiotic medicine differently. We will never discover that the Universe is infinite, if it is, because we can’t travel to the place where we can see that it goes on forever. We can’t amass and analyze enough data, solve enough mathematical equations to discover that the Universe is constantly changing, always has and always will be. We become human when we divide the Universe into parts and put labels on those parts so we can play with them. Is there any other way to do it? Can we be a little bit more playful with our discoveries? Parts that I have the most trouble letting go of are good and not so good, ease and disease. Yet in the moments that I have given up on all of these parts I can laugh the most delightful of laughs and sense infinite, timeless, ever changing beauty. It is jarring going back to remembering to wash my hands before I handle food. I suppose I should now apologize to all of the good bacteria I kill when I apply hand sanitizer. I realize that I am a social being, that exists within a politically shaped, ever changing culture. My discovery that there is no discovery is still fun.

  2. I took a Coursera course about this, and then went on to read one of the recommended books–it’s all extremely fascinating, and has already changed the way I eat. Keep it comin’–thanks!

  3. I love the way this article highlighted what is inside of us, and especially how good bacteria needs to be nurtured. More focus on needs and solutions. It was a real eye-opener for me. Thank you.

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