The End of All Days
How Our Microbiome Shows the Path to Survival
Our modern lives are dominated by monumental harbingers of doom: potential nuclear war, the looming climate catastrophe, and future pandemics. The newspapers are filled with tales of the ultimate, all-encompassing disaster: total annihilation. It almost seems as if they aim to satisfy the reader’s yearning for the definitive end, as if to say, “Then at least there’ll finally be some peace and quiet.”
And it’s understandable: The noise around us has become overwhelming. Like a raging hurricane, catastrophes, doomsday scenarios, wars, viruses, and ballistic missiles swirl around us, threatening to drag us into the abyss. The louder, the better. Deafeningly loud.
In this cacophony, trying to convey a message – let alone leave a lasting impression – has become impossible. Speaking in a normal tone? Whispering? Forget it! Instead, we shout, crank up the volume even more – and amplify the chaos to unbearable levels. Luckily, space absorbs all sound. Otherwise, we’d risk waking up distant aliens who might drop by and add to the general apocalyptic mood.
But apparently, even that’s not enough: disaster movies flood the cinemas, hammering home the image of a crumbling humanity, even in our spare time. So, is the end truly near?
Madness everywhere
One could almost believe it and simply close their eyes – with a beloved partner by their side. Cuddled up close, like in the movie “Seeking a Friend for the End of the World,” waiting together for the final detonation.
Eckhart Tolle has proposed the hypothesis that humanity is collectively insane
Speaking of madness: One of our time's most influential spiritual teachers, the German author Eckhart Tolle, has proposed the hypothesis that humanity is collectively insane. After all, how else could one explain the 100 million deaths caused by human actions in the 20th century? It’s a good explanation for the past – and for a possible future. Though these days, 100 million deaths hardly seem sufficient. Surely, apocalyptic scenarios today should involve at least a billion people. After all, we are living in the 21st century, an era where anything still seems possible.
“I” is “We”
But when I look out the window and watch the autumn wind gently playing with the leaves, I still haven’t swept off the driveway, and the idea of an impending exodus somehow seems unrealistic from this perspective. I wonder: Did I miss something? At this point, reflecting on the “I” in the sentence above seems appropriate.
“I” is “we.” Every human being is a symbiotic organism composed of approximately 30 trillion human cells and 30–40 trillion bacteria. Add to that another 10,000 trillion viruses, though, for the sake of simplicity, let’s leave those aside for now.
“Every human being is a symbiotic organism”
We – that is, our human cells and bacteria – exist in a world to which we have no direct access. Through our sensory cells, we perceive only stimuli that create an image of the world out there, without knowing what it truly looks like. Our brain generates a picture of this world based on the stimulation of various neurons within us – a world whose very existence we cannot even confirm. The movie The Matrix addressed this in a rather accessible way. But let’s not go that far and instead focus on ourselves – on “we.” Because that is exactly what we lose sight of amidst all the external catastrophes.
Through our upbringing – by our parents, but especially through our schooling – we have been conditioned to feel almost ashamed when dealing with our “I,” or rather, our “we.” Isn’t it extreme selfishness to focus solely on ourselves? Is that even acceptable today, given the looming catastrophes, the suffering in developing countries, and the much-proclaimed decadence of Western civilization? Yes, it is.
Or to put it differently: It must be.
The inner view
In Buddhism, it is said that everything – absolutely everything – is already within us. All the knowledge of the entire universe resides within us, because we are part of it.
Yet the announced catastrophes distract our gaze, pulling it away from ourselves and out into a world that is ultimately imaginary, a construct created by our neurons.
When we turn our gaze away from ourselves and focus only on the external – the problems handed to us from the outside – don’t we completely lose ourselves in the process? It’s like going to the cinema, where we are drawn so deeply into the story that we start to believe we are actually part of the film. Or worse, we fail to even realize that it’s just a film. We become trapped in it. However, since it is only limited to being three-dimensional at most, an escape is always possible.
The author Michael A. Singer described an interesting thought experiment in his book The Untethered Soul: What if we were trapped in a film with all our senses fully engaged – for instance, in a future cinema where we could move freely within a three-dimensional space? We would soon lose all connection to our true self – until hunger, thirst, the operator, or some other external stimulus brought us back to ourselves.
This is precisely the danger of today’s society. We are becoming playthings of the external world, and by extension, of all those who have a vested interest in ensuring that we lose our connection to our true self. That we abandon – or, in a broader sense, forget – our “I,” or our “we.”
But we are so much more.
The decline of our microbiome diversity
Humans have evolved over several million years. Homo sapiens, our direct lineage, has existed for approximately 300,000 years. Our bodies were formed through a symbiosis between human cells and bacteria. While human cells have around 20,000–25,000 genes, bacteria have expanded our genetic pool to 3 million genes. The endosymbiont theory suggests that even our mitochondria – our energy powerhouses where ATP, the universal currency of energy, is produced – originated from bacteria that integrated into the proto-cells of our ancestors. This integration enabled us to survive in an otherwise hostile environment dominated by a then-toxic substance: oxygen.
Without our bacteria and the abilities they provided us, we would not be able to survive. And this is exactly where the problem lies: the diversity of our microbiome – the entirety of our microorganisms – has declined dramatically during the industrial age. Various factors such as our lifestyle, increased use of antibiotics, processed foods, medications like proton pump inhibitors, and much more have led to a drastic reduction in key microbial populations. Populations that faithfully accompanied us for millennia are now simply eradicated. Scientists believe that these extinct populations can never return.
They are gone forever.
Anyone who thinks that vaccines can rejuvenate a deteriorating immune system is merely trying to fight fire with fire
The decline in microbial diversity becomes particularly evident when comparing people living in rural areas with urban dwellers. An industrialized microbiome has emerged in cities, which differs significantly from the more traditional rural microbiome. Microorganisms adapt to our lifestyle. However, the way we navigate our industrialized lives seems to primarily attract pathogenic, disease-causing bacteria, while increasingly pushing back the "good" bacteria – those that have adapted to us over millions of years and taken over some of our functions. Studies suggest that changes in the microbiome are associated with a significantly increased risk of diseases of civilization, such as obesity, chronic inflammatory conditions, and possibly neurodegenerative diseases like Parkinson’s and Alzheimer’s.
The many inflammatory processes in our bodies, which are a response to the shifting microbial balance, indicate a kind of resistance – a final attempt to fight against the increasing deterioration of our internal shields. Anyone who thinks that vaccines can rejuvenate a deteriorating immune system is merely trying to fight fire with fire.
Our body, inhabited by bacteria, contains so-called microbial guilds. These are microbial populations that work together to perform a specific function. They do not need to be related to one another. The cohesion of these guilds is crucial for maintaining certain functions. What makes them unique is that if one bacterial species within the guild is lost, it can be replaced by another. However, this replaceability has its limits.
“microbial guilds and keystone taxa are extraordinarily important”
Additionally, there are so-called keystone species, also known as keystone taxa, in our body. These act as mediators between individual microbial populations and are essential – not only for the stability of the microbiome but also for critical processes such as energy flow and nutrient cycling. The loss of a keystone taxa is particularly significant for the body, as it cannot be compensated for like in a guild, leading to a failure of functionality.
Both microbial guilds and keystone taxa are extraordinarily important for the stability and functionality of our body. However, unlike microbial guilds, the loss of keystone taxa can have catastrophic consequences.
The tipping point
And this is exactly the case with tipping point theory. It states that complex systems can suddenly transition into a new state through gradual changes once they cross a critical threshold (the so-called tipping point). This transition is often abrupt, difficult to predict, and can have long-term, sometimes irreversible and dramatic consequences.
The challenge of tipping point theory lies in its non-linearity. Small changes may have little to no impact before the tipping point but can become disastrous after it.
Our microbiome is a highly complex network of various microbial populations. The different "sub-microbiomes" are in highly efficient communication with one another. For example, the microbiome of the mouth communicates with the microbiome of the esophagus and stomach; the latter, in turn, connects with the microbiome of the small and large intestines. The gut microbiome communicates bidirectionally with our brain via the gut-brain axis. Everything is interconnected.
While a sudden collapse of the entire system is unlikely, it could, in the worst case, lead to death
The loss of certain keystone taxa and the disappearance of essential microbial guilds can significantly impair the stability of the microbiome. This promotes inflammatory processes, weakens the immune system, and increases the risk of chronic diseases. While a sudden collapse of the entire system is unlikely, it could, in the worst case, lead to death.
This hypothesis is supported by the fact that bacteria can divide rapidly, while human cells regenerate only slowly. Skin cells can divide within 19–27 hours, but liver cells take 200–400 days. Mature nerve cells do not divide at all; however, neurons responsible for learning, located in the hippocampus, are capable of division.
As a result, the human organism is sluggish in terms of adaptation – and for good reason: if evolutionary advancements that took hundreds of thousands of years to develop were lost within a few days, the organism's chances of survival would be minimal.
In contrast, microbial cells can multiply very quickly, some within 15–20 minutes (e.g. Escherichia coli). The short generation times mean that bacteria can change and adapt very quickly.
Due to humanity's industrialized lifestyle, various adaptations occur. Microorganisms evolve rapidly because of their high division rates, while entire keystone taxa die out, and humans, with their slow adaptation, cannot keep up. This discrepancy can lead to shifts in microbial balances and the loss of essential functions. As a result, the microbiome is impaired not only in its functionality but also in its ability to effectively support the human organism.
“The ultimate apocalypse for humanity is the complete collapse of our microbiome”
Even Michael Gorbachev is said to have remarked, "Life punishes those who come too late." While it’s unclear whether he actually coined this phrase, it can certainly be applied to the microbiome and its interplay with the human organism. If the human body fails to compensate for the loss of microbial functions – or does so too late – illness and, ultimately, death are the logical consequences.
There are, therefore, compelling reasons to examine the microbiome, our lifestyle, and these complex interconnections – especially if we wish to avoid falling victim to disease or even extinction.
This brings us back to the apocalyptic scenarios mentioned at the beginning of this article. The ultimate apocalypse for humanity is the complete collapse of our microbiome, which would inevitably lead to the extinction of humankind.
The shift of our attention
To prevent this catastrophe of biblical proportions – this "Microbial Apocalypse Now" – humanity needs a fundamental shift in focus. No pharmaceutical company will save our microbiome from self-destruction if we do not take responsibility for it ourselves. There can be no drug capable of replacing the functions of the trillions of microorganisms – functions we are only just beginning to understand. So, while we sit on the couch, engrossed in the evening news with a bottle of beer and a bag of chips, the war rages not only on the screen but also within us. Unnoticed and insidiously, it worsens until we reach the aforementioned catastrophic tipping point.
We should – and we must – shift our attention away from external distractions and turn it back toward ourselves. Why, after all, did Buddha achieve the end of suffering 2,500 years ago as he attained enlightenment under the tree? Not because he tried to eliminate the world’s collective suffering – an impossible task. Rather, because he turned entirely inward instead of outward.
“to prevent this catastrophe of biblical proportions – this "Microbial Apocalypse Now" – humanity needs a fundamental shift in focus”
That is why we must start with ourselves. Just like the safety instructions on every flight remind us to secure our own oxygen mask first before helping others, we must prioritize ourselves. Yet this is precisely what we have long since stopped doing.
The matrix
We sit transfixed, like a rabbit before a snake, unable to move or become aware of ourselves. We allow ourselves to be flooded by external stimuli like news and events, without pausing to look inward. We are, quite literally, dissolving from within. Our microbiome is disintegrating, and we are incapable of recognizing it.
It is time to turn our gaze away from the outside world and look inward, to become aware of ourselves. No one will take care of us – not the pharmaceutical industry, not the food industry, and certainly not politicians – unless we take responsibility for ourselves. We must act now. For ourselves. And we must see through the deception. This is exactly what the looming collapse of our microbiome is trying to tell us.
“we must see through the deception. This is exactly what the looming collapse of our microbiome is trying to tell us”
Like Neo in The Matrix, when he finally realized that his entire life had been an illusion. We must reach for the red pill and face the uncomfortable truth that we are living in a deception – from our indirect sensory perceptions to the bombardment of external stimuli of every kind. We must begin to counteract the eradication of our microbiome.
If we are unwilling or unable to do so, then we might as well take the blue pill and wait for the end of the world, hand in hand with a loving partner.
The choice is ours!
Sources and further readings:
Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., … & Dominguez-Bello, M. G. (2015). The microbiome of uncontacted Amerindians. Science Advances, 1(3), e1500183. https://doi.org/10.1126/sciadv.1500183
De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., … & Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences, 107(33), 14691-14696. https://doi.org/10.1073/pnas.1005963107
Gupta, V. K., Paul, S., & Dutta, C. (2017). Geography, ethnicity or subsistence-specific variations in human microbiome composition and diversity. Frontiers in Microbiology, 8, 1162. https://doi.org/10.3389/fmicb.2017.01162
The Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207-214. https://doi.org/10.1038/nature11234
Larsen, O. F. A., & van de Burgwal, L. H. M. (2021). On the verge of a catastrophic collapse? The need for a multi-ecosystem approach to microbiome studies. Frontiers in Microbiology, 12, 784797. https://doi.org/10.3389/fmicb.2021.784797
Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016). The healthy human microbiome. Genome Medicine, 8, 51. https://doi.org/10.1186/s13073-016-0307-y
Requena, T., Martínez-Cuesta, M. C., & Peláez, C. (2018). Diet and microbiota linked in health and disease. Food & Function, 9(1), 12-27. https://doi.org/10.1039/C7FO01820G
Sonnenburg, E. D., & Sonnenburg, J. L. (2016). Diet-induced extinctions in the gut microbiota compound over generations. Nature, 529(7585), 212–215. https://doi.org/10.1038/nature16504
Sonnenburg, J. L., & Sonnenburg, E. D. (2019). Vulnerability of the industrialized microbiota. Science, 366(6464), eaaw9255. DOI: 10.1126/science.aaw9255