” We are Our Bacteria & Virus”

Over the past few weeks, my interests have diverged from the biological sciences, and moved
back towards the intertwining of scientific and philosophical ideas. It’s become clear to me that our
response to Covid-19 — initially, ongoing, and planned — is flawed in many ways. More importantly, I
have learned that this pandemic will ultimately serve as part of humanity’s evolution. Our response
brought out much of the compassion that resides within all of us; however, it has also shined a light on
our own moral failures and narrow-mindedness. I think it’s critical that we learn from what this situation
brought to our awareness and begin considering alternative paths that may bring about more happiness
and minimize human suffering. We are presented with an opportunity to enact change based on the
compassion that arose, while also recognizing where our decision-making appears to have been
shortsighted or narrow-minded. The primary problem that I now recognize with our response to Covid is
that it was based on our consideration of ourselves as separate from our environment, when in fact, we are
very much dependent on and connected to the environment that we live in, including the bacteria and
viruses that surround us.
In December 2018, I wrote a paper for my philosophy class called “The Nonexistence of The
Conventional Self and Its Metaphysical Implications.” I argued that the self that we are familiar with, and
that we continually identify with, is an illusion appearing in consciousness. By combining logic, science,
and the growing Western understanding of nonduality, I argue that it is solely another object in the totality
of our experience in the present moment. The key realization is that we have a tendency to continually
identify with the contents of consciousness, and by doing so we neglect our real identity, which lies in the
context. This is a difficult idea to understand, and has taken me years to understand deeply. A simpler
way of saying it is this: We are all one. The world’s problems are my problems. Over the next several
years, I foresee many more people coming to understand this insight. When one does come to understand
this, it becomes clear that separation in the long-term — as Harvard officials say will be necessary until
2022, and as we have collectively agreed to do in some form permanently by foreseeing the dissolution of
handshakes and hugs — will not be the best way for humanity to advance: I believe our advancement will
depend on us coming to understand our interconnectedness to each other and nature, and coming to
agreements based on this fact.
At first glance, none of this may seem very relevant to biology, bacteria and the microbiome. But
I see it differently: in order for the world to begin seeing past the false self, and recognizing the true
nature of the individual, science and philosophy will need to begin to coincide far more than they
currently do, so that we can begin to reveal an objective truth behind spirituality: science is already
beginning to point us towards an understanding of oneness, and the relationship between bacteria, viruses,
and our minds is a key area of research in eventually dissolving the materialist worldview. In this report, I
will be showing that bacteria and viruses are an integral part of who we are, and that the health of the
mind-body relationship is deeply intertwined with the health of our microbiome. I intend to show this by
shining a light on probiotics: we have seen for many years now that a healthy gut is fundamental to not
only our physical health, but our mental health as well. I hope it will become slightly more evident that
bacteria (and though it will not be the focus of this report, viruses as well) support the growth and
evolution of both our minds and bodies. To satisfy the computational requirement, I will be considering
the Cell paper on resistance to gut colonization on a person by person basis, and analyzing the efficacy of
probiotics on the individual. I will also consider ways in which individuals that are resistant to absorption
may be able to improve their gut health in other ways.
My view is that bacteria and viruses should not be as feared as they are, and that we will need to
begin seeing them in a more sensical way moving forward — namely, as part and parcel of our evolution.
As part of this scientific report, I will be including my own personal experience over the past two months:
since quarantine began, I have seen the number of psychological stressors on my life vastly decrease, and
I have started taking probiotic supplements. I have all but sorted out the psychological problems that I had
personally been struggling with, and I hypothesize that the health of my gut microbiome has coincided
with my increase in mental strength.
The human gut has three times more neurons than the spinal cord, and contains over 100 trillion
bacterial cells. That is over ten times the number of human cells every individual has: simply as a matter
of cell count, we are mostly bacteria; no argument needs to be made here. Nevertheless, the neural
connections between the gut and brain, and the effect these connections have on our minds, is what I am
interested in. In their 2014 work, “Gut Microbes and the Brain: Paradigm Shift in Neuroscience,” Mayor
and Knight of the Neuroscience Journal summarize the recent history of research pertaining to the gut
microbiome and mental health. Several preclinical trials have indicated bidirectional signaling occurring
between the microbiome and brain: in the brain-microbiota direction, scientists have found that in animals
experiencing psychological or physical stress, the metabolic activity of the microbiota decreases. They
explain that “maternal separation, restraint conditions, crowding, heat stress, and acoustic stress” have all
been shown to be triggers that can lead to an unhealthy microbiome.
The relationship also exists in the microbiota-brain direction: Mayor and Knight report that when
experimental change is conducted on the microbiome, such as through ingestion of a variety of different
types of probiotics or prebiotics, anxious behavior, depression, and memory dysfunction have all been
shown to reduce significantly in some patients, but not all. They also mention that an increase in bacterial
metabolites due to probiotics (or prebiotics) can play a significant role in epigenetic modification, which
also has a growing body of research showing links to changes in brain and behavior.
Clearly, an effective increase in probiotics, whether absorbed through fermented foods or created
internally through prebiotic supplements, appears to alter the health of our guts, and our mental
well-being alongside. Our brains live in a reciprocal relationship with the gut microbiome: the research
discussed indicates that positive or negative effects on one coincides with the other. There is a strong case
to be made that individuals suffering from mental health problems should be evaluating their probiotic
intake, absorption and innate creation from prebiotics, and obviously most importantly, finding ways to
manage or overcome the psychological stressors that are being placed on their life (in my case, that meant
dropping my course load from six to four classes, and creating a positive lifestyle that supported my
growth) that are negatively affecting their bacterial health. Of course, for most people that’s not possible
due to the current state of humanity: the lack of basic care we provide keeps billions of people enchained
to their psychological stress. I believe we will see this change in the decades to come as our
compassionate response evolves to be more fully encompassing and based in reason.
The importance of bacterial health is clear, but the most significant problem that computational
biologists continually confront is effective absorption into the gut: microbiome researchers consistently
find that there is a person-specific gut colonization resistance to probiotic ingestion.
Concluding with how bacteria and viruses are part of our evolution: mention what Eisenstein
brings up about viruses being able to transfer DNA and change the germline