Gut Instinct: Invisible but Indelible

Written by Nita Jain, from Lilburn, USA. Nita, 26, is an independent researcher and freelance writer. Please read her article and leave your thoughts and comments below.

To know the self is impossible as the self is  constantly changing, growing, and adapting. To paraphrase Heisenberg, we cannot simultaneously know our position and direction. Perhaps that is the paradox in the command from the Oracle at Delphi. To know thyself is to know that the self is unknowable. The self doesn’t really exist.

We think that we exist as individuals. Singular beings. A drop in the ocean. A pixel on a screen. A speck of dust suspended in a sunbeam. But we are the ocean. We are the screen. We are the personification of the universe perceiving itself. The focus on knowing the individual as an entity is entirely misplaced. Even without knowing ourselves, we have continually demonstrated the capacity for progress since the inception of our species.

Contrary to Darwin’s assertion that evolution only occurs by natural selection, populations do indeed evolve even during the course of their lifetimes, adding a Lamarckian twist to our current understanding. To isolate the genes of an individual as the sole drivers of evolution is to ignore the contributions of billions of years of symbiotic co-existence, at a dangerous cost. Forging ties with our microbial symbionts have allowed us to achieve what we never could in isolation.

Our human chromosomes provide an incomplete picture of the genetic repository we possess. To only consider the aforementioned would be to neglect the bacterial, archaeal, fungal, protistan, and viral genetic information that is equally integral to human identity, if not more so. If we accept and acknowledge that we are not individuals but living ecosystems, comprised of hundreds of trillions of microbes, it is not difficult to envision how we can evolve leaps and bounds faster than if we really were the individuals we perceive ourselves to be. Enter the hologenome.

The hologenome accounts for the genetic material of a host, or holobiont, plus all its symbiont microbiota. Many bacteria that live in and on our bodies multiply rapidly enough to go through several generations of offspring within the span of 24 hours, accounting for why antibiotic resistance evolves so rapidly. Bacteria reproduce, mutate, and therefore evolve very quickly. In this manner, the hologenome can evolve at a much more rapid pace than the human genome. As science writer Ed Yong expounds in I Contain Multitudes, “By partnering with microbes, we can quicken the slow, deliberate adagio of our evolutionary music to the brisk, lively allegro of theirs.”

Microbial symbiosis provides the crucial complement to features missing in the host’s core genome. Consider the case of lactose intolerance. Tolerance to lactose is usually assessed based on the activity of the human lactase enzyme. The lactase enzyme breaks down lactose into its monosaccharide constituents, glucose and galactose. In the majority of humans, the gene that encodes for the lactase enzyme shuts off shortly after weaning, making lactase persistence rare and lactose intolerance the default status. However, many bacteria belonging to the genus Lactobacilli also have genes that encode for the lactase enzyme. Therefore, if an individual did not have a functioning human lactase gene but nonetheless carried enough lactose-degrading symbionts, he would nonetheless be able to tolerate some amount of lactose, depending upon the activity of his fellow inhabitants’ lactase enzymes.

Critics of the hologenome theory question whether the microbiome can be transmitted with sufficient fidelity across generations to be considered a unit of selection in evolution. However, another school of thought argues that transmission of specific species is irrelevant as long as the metabolic processes enabled by the microbiome are conserved. In other words, while humans harbor taxonomically unique microbial communities, the functions those communities carry out do not exhibit much variability. Evolutionary biologist W. Ford Doolittle expressed this idea in a 2017 article entitled, “It’s the song, not the singer,” an inversion of a popular Rolling Stones song.

Revisiting the question of who is really in charge, researchers at Cornell University tracked the changes in the gut microbiome of a newborn for over two years and made a tantalizing discovery. Metagenomic analyses revealed that polysaccharide-digesting functional genes appeared in the gut microbiome while the baby was still exclusively consuming breast milk, several weeks prior to the introduction of polysaccharide-containing solid food in the diet, suggesting a microbial priming of the infant gut in preparation for an adult diet. This metabolic preprogramming implies that perhaps our microbes are the ones pulling the puppet strings, a humbling insight in the context of our anthropocentric view of the world.

Through our partnerships with our resident microbes, we have transformed so quickly as to become unrecognizable to our former selves. Though we may have spent most of our lives blind to the microscopic bonds we have formed, the interactions have nevertheless left indelible imprints on our lineage. While we may not have always been aware of the existence of our co-evolutionary comrades, we still had a gut instinct that our species would find ways to not merely survive but thrive. If the perilous infancy of our species is any indication, proper perception of the self need not be prerequisite for progress.

64 comments on “Gut Instinct: Invisible but Indelible

  1. Roshan Shrestha on

    There are many gut bacteria than the number of stars in our entire universe. Isn’t that amazing? A quality article on our gut health which we take for granted, not anymore as Nita explores in this brilliant and lucid article. She deserves all the accolades.

  2. Nisha Bansal on

    Excellent article on the influence and significance of the gut microbiome! A very illuminating and valuable perspective. Great work Nita!

  3. Anupama Jain on

    A very nice and informative article on the role of microbes in the lives of humans. Very well presented. Superb Job Neeta!

  4. Kesha Chanel Palmer on

    Insightful article! Never thought of humanity and microbes together. Always affiliated microbes with a science lab. New perspective. Thanks Nita!

  5. CJ Canton on

    That makes a lot of sense actually, I took 23&me and found out I should be lactose intolerant, but I’ve always and to this day love drinking milk. Missing out on all of those microbes must be bad for the baby, no wonder breast feeding has so many benefits.

  6. Cayden on

    Immaculately well put! It’s been a pleasure to see more holistic, systems-based approaches taking root across the different fields of scientific inquiry. And right at the epicenter is of course ourselves, blooming, buzzing orchestras of biomolecular and cellular automata. Thank you for eloquently reminding us of the inconceivable complexity and beauty to be seen, if we just take a moment to look.

  7. ECC on

    I really enjoy how you destabilize conceptions of anthropocentrism by attending to the multitudes inside humans that are so central to our survival. I also enjoy how you connect scientific knowledge to philosophical questions. It makes the scientific material more accessible to people in the Arts and Humanities. Great work!

  8. Cecil (CJ) John on

    I loved the opening paraphrase of Heisenberg’s uncertainty principle. I actually see the same dynamic with human relationships: you can’t primarily focus on friendship and business, or love and power respectively.

  9. Tom Hanratty on

    Fascinating article, Nita. The importance of the gut bacteria in everything from immune response to brain function means we have a lot of helpers in our body. I suspect many maladies of humans, other than lactose-intolerance, could be treated with proper bacteria transplants. And the relationship with the immune system may impact type one diabetes or asthma. As usual, your articles make me think.

  10. Kurt Keefner on

    As informative as the science in your essay is, I have to disagree with its philosophy. A human being is an entity, despite having many human cells and hosting many non-human cells. A human being lives and dies as one, and more importantly, a human being is conscious and makes choices as one. I don’t mean that this cognitive oneness is simplistic. There are multiple systems at work, but they ultimately, especially if one does try to know oneself, pull together as a single unit. Still, despite my disagreement, I think your essay is a valuable reminder that we contain many lives within us.

    • Nabil ALOUANI on

      Intresting point of view Kurt. I agree with the fact that human beings are conscious entities.

      However, being conscious being doesn’t translate into making conscious choices only. In fact, most of our behaviors are automated. Our decision-making and reaction mechanisms are run by our subconscious mind.

      Plus, whether conscious or subconscious, the mind is not limited to our thoughts, it takes into account emotion and body experiences like pain, hunger, thirst, sexual impulses and so on.

      The mico-ecosystems, living within us, are responsible for a huge part of our desires such as eating. In fact, the flora of our guts affects our food choices. Here’s a video that explains it quickly and accurately.

      The food that we ingest transforms into data processed by our brains. For instance, carbs give energy fairly quickly. When the brain is aware of the energy reserve it has, its behavior changes. If someone is feeling energetic, they are more liable to go for a walk, write down an essay, clean the house, basically doing an activity. When someone eats protein, the body would want to rest and relax because digesting protein takes time. Hence, the person finds themself wanting to lay down or chill on the sofa watching TV.

      Thus, we could say that the bacteria in our guts relatively rules our behavior in specific ways.
      Furthermore, it goes without saying that our behavior over time shapes who we are.

      Yes, we are conscious beings but most of our behaviors are subconscious. Put differently, many of things that define who we are, drive from the subconscious mind.

      Being aware of what happens in our guts and how it evolves is one of the keys to understanding the hidden mechanisms that define us.

      This take on the gut’s flora is a valid approach of exploring who we are: one whole entity composed of multiple entities. Each sub-entity plays a role in defining and building The “Self”.

  11. Anu G on

    An eye-opening perspective that I had not thought of….. Keep sharing your insights on these kind of topics. Always interesting reads!

  12. kylie on

    Great piece, Nita.

    Evolution would dictate that if bacteria CAN influence our behaviour to benefit themselves , then they will. They will proliferate, and be more successful. They’ve had many millions of years to perfect this on other species before humans. It’s as good as fact in my mind.

  13. Alex Walsh on

    A thought provoking read. As a person who has spent quite a bit of time and effort trying to “know myself”, I actually found the beginning of this article slightly disheartening as I began to think of all the the time I have wasted. As I read on, I started to remember the complexities of life and the extremely limited extent of our understanding. As the title of the article suggests, I have chosen to lean into my gut instinct and attempt to follow the path which I believe is best illuminated by my instincts. As per the article, I am aware that sometimes I may be led by beings which could be considered separate from my “self.” I suppose I am as accepting and understanding of these facts as I can be at this point in my life, and I know I must be willing to make changes based on my current knowledge and “gut instinct” as I go along. Thank you Nita for a great article.

  14. Christine Houghton on

    A keen mind and a clever turn of phrase are evident in the author’s treatment of a scientific topic in which she has embedded elements of philosophy, evolutionary biology and history, all written in an entertaining and eloquent style.

  15. Rakesh Kumar Jain on

    Congratulations Nita Jain for such a beautiful article. Really an inspiring work on the indispensable role of microbiota in our lives. In religious Jain epics, it is written that there are innumerable microbes that can lie on the tip of a needle in this universe.

    Commendable job Nita. Thanks to you, equivalent to the number of microbes in our gut!

  16. Jenny on

    I absolutely love this perspective on the role of microbes in our evolution and how they shape us. We are mailable….adaptable and cannot neglect the role that our microbes play in our individual and collective evolution. Thank you Nita for this thoughtful recognition of our symbionts.

  17. Meagan Mendoza on

    These truly are humbling points in humanities constant questioning of the “perception of self.” Interesting article.

  18. Lorenz Duremdes on

    Really nice article on identity. I like the different perspectives including not just simply adhering to just the “Gene-centered view of evolution” (something which I, however, do).

    Many fail to see their dependence on their environment. This article, however, doesn’t.

    It reminds me of this:
    Like a plant that won’t grow without good soil, water and sunlight, creative thinking needs the right organic setting. Without it, creative and innovative ideas fail to sprout.

  19. Rafael González Hidalgo on

    Clever title for a well written article where some fundamental insights questioned our cherished individuality. Here, hologenome, living ecosystem, and symbiotic relationships are living ideas attempting to describe ourselves as living communities rather than isolated individuals where Nita is just one more member. Evolution is communal and the gut instinct after all seems more like a consensus act of our indelible micro friends than our volatile, ghostly self.

  20. Nash Brooks on

    Dear Ms. Jain, After reading this my heart races, I love your concise and razor-sharp writing style. I wrote a paper called “Inherent Memory,” the premise was that we as humans must be born with some sort of inherent memory in order to survive. I referenced instinct, communal memory, and the like supporting the claims with scientific and religious holdings. You just blew out the whole side of my paper. I kept hammering the “OK what came before that” scenario. I defended the paper successfully but I wish I had your database. Always a pleasure.

  21. Nash Brooks on

    Dear Ms. Jain, After reading this my heart races, I love your concise and razor-sharp writing style. I wrote a paper called “Inherent Memory,” the premise was that we as humans must be born with some sort of inherent memory in order to survive. I referenced instinct, communal memory, and the like supporting the claims with scientific and religious holdings. You just blew out the whole side of my paper. I kept hammering the “OK what came before that” scenario. I defended the paper successfully but I wish I had your database. Always a pleasure.

  22. Ken Lassesen, M.Sc. on

    One aspect that need to be emphasised, at least from my perspective. Bacteria are a population that communicates with each other. One example is quorum sensing but another that is more important is RNA sharing and exchange of DNA.

    In human terms, this is the equivalent of knowledge sharing (todays often alleged Intellectual Property stealing). A bacteria that is resistant to a specific antibiotic due to some RNA fragment, will circulate that RNA with the general community of bacteria. Other bacteria, “reading this RNA” realize that it is an better idea and incorporates it into it’s structure and thus become resistant.

    Back in the 1970’s, my statistics prof was a specialist in the statistics of infectious diseases. From her after class talks then, in terms of statistics, we will keep running out of effective antibiotics and then finding new ones. Some new disease will come along and wipe out 90% of mankind, but mankind will survive. It is all part of the Yin and Yang of nature – which we are part of!

    Many people have a “science is all powerful and will conquer every issue” attitude. It’s not, if you believe that you lack a solid understanding of science and its history.

  23. Keith Bell on

    Thanks, Nita Jain, for connecting us eloquently with the web of life. I like to think real and positive change can take place with this newfound awareness. We can no longer depend on egoistic “progress” because our environment can no longer withstand the pressure of oblivion. On the contrary, what you’ve described is a window to connection with all things, including and especially true self. Feel free to cry now. Those Lactobacilli mentioned are known to raise oxytocin receptors in the brain via the vagus nerve, and that’s all about social connection, love and empathy. That’s what’s real and the opposite of narcissistic, antibiotic mindset. “Perilous” indeed.

  24. twahiru musa on

    This article is so beautiful, simply because it can help us to know a lot about human being and other living things. Thanks very much madam NITA JAIN for this brilliant article i hope you will continue to give us lecture. I really appreciate even more and give you 97 % .

  25. Cody on

    Really nice thought piece. I read somewhere that we actually assimilate genetic material from bacteria, viruses, and fungi. And then new microorganisms introduced to earth from asteroids could also play a part in the direction of our evolution.

    At the same time, what part does the human mind play in this evolution???

    When we look at the placebo effect, this is the mind essentially driving the healing process.

    If I believe I am healed, I am healed.

    Do you wonder how our minds might impact our microbiome? It’s well documented that some microbiome species create chemicals analagous to hormones and neurotransmitters.

    So what can our minds to do them?

    What if you send happy thoughts to your critters?

    • Nita Jain on

      We do indeed incorporate genetic material from microbes into our own chromosomes. transposable elements or transposons, often referred to as “jumping genes” in the vernacular, are remnants of ancestral viral and parasitic infections that subsequently became integrated into the human genome in a manner somewhat analogous to the CRISPR defense system in bacteria. More than 45 percent of the human genome is derived from transposons, whereas coding regions called exons comprise less than two percent.

      The role of the human mind is absolutely instrumental, and microbes even influence our social evolution. Butyrate, a SCFA byproduct of bacterial fermentation, increases histone acetylation and promotes the expression of genes that facilitate memory consolidation, neurogenesis, and neuroprotection. So our microbes promote social behaviors in the hosts and drive evolution in that manner as well.

      As you’ve alluded to, the communication is bi-directional, and happy thoughts do have physiological effects. Stress and cortisol production tend to weaken gut barrier integrity, which could in turn lead to lower goblet cell turnover and less mucin available for anti-inflammatory species such as Akkermansia muciniphila to feed on.

  26. Arv J on

    A very good read on the “Who is really running the show?” Good to know about the inner workings of ourselves.
    Keep up the good work Nita!

  27. Nabil ALOUANI on

    This great breakdown made me rethink my vision of my passions: self-growth and neuroscience.

    I am familiar with the fact that our gut micro-ecosystem is considerably intervening in our eating behaviors. Nevertheless, I never considered establishing the link between the little creatures in our bodies and our overall way of being including our thought mechanisms.

    Thank you very much Nita for enlightening me with your amazing take on the subject. I have definitely something to ponder on and read about.

  28. Jamie on

    Absolutely brilliant. Well put together and captures the importance of microbe communities and the critical role they play in who/what we are. Well done Nita!

  29. Dr Sabine Hazan on

    Very nicely written and very well put. All we are and will ever be is bacteria, viruses and fungi living in symbiosis. Our bacteria control our mental health and understanding that could help some achieve healing. We need more people like you educating the world. Understanding this concept makes one think twice about hating a person based on religion race or gender. Understanding the microbiome is a path towards peace. We should reproduce what we see at the microscopic level… symbiosis of microbes.
    Keeo doing great work Nita.

  30. Dennis Smith on

    Very deeply touched by your writing and your breakdown of your Breakdown of gut micro ecosystem is a Amazing, And yes I feel that our body is the make up of life itself yet but we go deeper than that And what you wrote makes one think deeper and look at all facets of life and 1 that has reached out to me so deeply is our spirit. All Though the human body is so complexed one can’t help but think about the spirit man as well, That resides in the body as well Amazing work.

    • Tracey on

      At the 6 month mark of a pregnant but still nursing mum the breast milk changes flavor putting the nursing baby off the mothers milk in preparation for the next nursing baby❤️

  31. Brian Batiste on

    WOW! A very brilliant, thought provoking article. I am in awe of both the topic & the writing style.
    Absolutely excellent in every way!

  32. Christopher K on

    Extremely thoughtful and informative. Really well written by an author who clearly understands the material on a deeper level. I learned a lot, thanks for sharing!

  33. David Wood on

    > Metagenomic analyses revealed that polysaccharide-digesting functional genes appeared in the gut microbiome while the baby was still exclusively consuming breast milk, several weeks prior to the introduction of polysaccharide-containing solid food in the diet, suggesting a microbial priming of the infant gut in preparation for an adult diet.

    Well that is fascinating but it raises another question: How was that triggered?

    A very speculative explanation would be that the microbiome carries a kind of “instinct”… but I have a feeling the explanation might turn out to be far more simple; perhaps the polysaccharide profile of the mother’s milk starting to change (since breast milk changes composition across the period of breastfeeding).

    But of course, if that prior state-change was also observed in formula fed babies… 🙂

  34. Gregory A Kieser on

    A great, quick exploration of the hologenome as a mode of inheritance, and an angle i did not consider: that while our biomes tend to vary greatly their metabolic functions don’t vary nearly as much.

    This will have me thinking for a bit.

  35. Colleen Harrison on

    Thank you Nita for this insightful article about our connection to our gut Microbiome. This field of science while not mainstream yet is fast changing lives, one microbe at a time. I’m living proof of these changes.

  36. Robin on

    I was drawn to read this piece after glancing at the clever title, but the body of the article surpassed my expectations. Nita Jain’s piece explores the intriguing topic of the microbiome in the most fresh and fascinating way. By calling the reader’s attention to the dichotomy of the individual self and the mass of organisms that exist in harmony with that self, the reader is left contemplating one’s place in the world. One walks away from this piece feeling significantly less alone in the world due to the not so invisible impact of the invisible microbiome. I am eager to read more of Nita’s insightful articles.

  37. Trafton Crandall on

    I found this article to be thoughtful and intriguing.

    In her writing, Nita possesses a talent for merging the rigor and precision demanded by science with the poetic and artistic world of the imagination, as she sheds light on the new frontier of the Microverse within our bodies and the vast multitudes of the microscopic beings that dwell there.



  38. Erin on

    Love Nita’s take on the symbiotic relationship between humans and microbes. Truly humbling to think of ourselves as the puppets with microbes leading the way. I look forward to seeing where this area leads in the years to come and have a feeling it will really redefine what we believe to be “self” and “other.” Thanks for the great discussion Nita!

  39. Josh Taylor on

    A beautifully written take on such a vastly important subject. Life and nature is symbiotic and constantly changing by design. Science isolates variables as a necessity, but we shouldn’t lose sight that these incredibly complex relationships.


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