This question continues to arise in every faction – doctors, scientists, media, even the general public is starting to take an interest. How many species of bacteria exist in a healthy human microbiome? The sheer number of bacteria on the human body is huge – anywhere from 100 trillion to 1.5 quadrillion (the latter is likely more accurate). The challenge of identifying these species is due to a few factors. One is the plasticity of the microbiome, which can change from minute to minute, even swapping DNA from virus to bacteria to human. Another is the fragile and extremely unique microecosystems that are represented on your body surfaces, orifices, and even within the internal organs that we now recognize harbor a microbiome workforce. We cannot reach the sites of the majority of these microecosystems and cannot recreate these diverse microecosystems in petri dishes to preserve and grow the species that would live there.
Every nook and cranny of the human body is filled with microbiome, including the skin, eyes, ears, mouth, nares, tonsils, and colon. We cannot reliably get culture data from any site – including the skin – to define the vast species variants. This is due to the very sensitive ecosystems each species needs to survive long enough to get set up in culture. Less than 1% of species present are thought to survive long enough to grow in culture. As such, we have underestimated the number of species that actually exist in different parts of the human body. When we culture wounds or body spaces in the clinical or research settings, a few will grow, and so we come to assume that these are representative of the microbiome that is present. This is not at all the case.
For example, we cannot get to the living human small bowel for good specimen collection and this is likely the site of extraordinary diversity that goes unseen in colon and stool samples due to its unique anaerobic environments. We discovered, only in the last few years, that the appendix is a repository of a vast ecosystem with different bacteria thriving at each millimeter as you go deeper into the tube-like pouch. Just last year an additional 1600 metagenomes were added to the database which will result in at least that many more species of microbes categorized on top of the 10,000 already known in the human microbiome.
Since we cannot rely on culture data to define the complexity of the vast microbiome we need new technological advances to get us to the quantification and categorization of the human microbiome. Genomics and proteomics are two science fields that are advancing quickly and will play a role in this future accomplishment, with additional data coming from the new world of microRNA and retrovirus detection.
In the meantime, when you hear someone say, “this is how many bacterial species are in the human microbiome…”, recognize that this is akin to the estimates of the galaxies in the universe before we launched the first space-based telescopes that would reveal millions of previously unseen galaxies filling the darkest pixel of the night sky. I fully expect that we will, in the decades to come, discover many tens of thousands of bacterial species, along with hundreds of thousands, if not millions of species of fungi, viruses, and parasites that help maintain health in the optimal human system.
We should all stand in humility of how little we know at this stage of microbiome science, and be in fear of the extinction of bacterial, fungal, parasite, and viral species never recognized as we continue to pour antibiotics, herbicides, and pesticides into our animals, humans, soils, rivers, and oceans. The journey into the microbiome is one of the most prescient missions of our generation; through it we will discover a whole new universe. Buckle up and enjoy the ride with all of us at Biomic Sciences as we join so many other scientists around the world to dare to go where no man or woman has gone before…
Zach Bush, MD
CEO, Biomic Sciences
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