The Gut as a Living Archive

By: Siobhan Gray, MD

In my book club we read Sirens, a novel where children “remember” their parents’ conversations.

It sounds like fantasy, but the idea unsettled me in the best way. As we passed wine and laughter around the table, I found myself wondering: could memory really be inherited? Not in the form of stories told or photos kept, but in the body itself, passed down in cells, in whispers of biology that we don’t consciously hear but still carry forward.

That curiosity lingered, and weeks later it tangled itself with another story.

This one not from fiction, but from a Radiolab podcast called The Elixir of Life. The episode unraveled the mystery of breast milk. Scientists had discovered that many of its sugars, called human milk oligosaccharides, were indigestible by babies. Which makes no sense at first glance: why would a mother’s body pour energy into producing a food her infant cannot even use?

The answer is almost mythic. These sugars are food, yes, but food for bacteria. Specifically, a species called Bifidobacterium infantis, an organism passed from mother to child for thousands of generations, nourished by milk itself. It was as if nature had written into the body: “This microbe belongs with you.”

And yet today, that very organism is disappearing. In much of the industrialized world, B. infantis is nearly gone, eroded by antibiotics, formula feeding, C-sections, diets that starve microbial diversity.

We are unraveling an ancient inheritance without even realizing it.

It made me pause and wonder: what parts of ourselves are we letting slip away? What ancestral agreements, forged in the deep past, are we breaking with our modern lives? gut is not only a digestive organ; it is an archive, recording where you’ve been and who you’ve come from.

The foods you eat, the air and soil of your childhood, the microbes passed from your mother during birth...all of it leaves a trace.

In rural communities still eating traditional, high-fiber diets, the gut microbiome blooms with diversity. It holds onto species that have long since vanished from Western guts. Compare stool samples from children in Malawi or the Amazon to those in New York or London, and you see two very different microbial “libraries.”

One is vast, teeming with stories. The other has whole shelves missing.

This is what fascinates me: our gut carries memory the way language does. Words can be lost from a culture when not spoken; microbes can be lost from our bodies when not nourished. And once gone, both can be painfully hard to recover.

Cellular Memory: When the Body Remembers

Gut memory is one layer of this story. Another lies deeper, in our very cells.

Scientists call it epigenetics; the way experiences etch chemical marks onto DNA, shaping how genes are turned on or off.

The most famous example comes from the Dutch Hunger Winter of 1944–45. Pregnant women starved through one of the harshest famines of the twentieth century. Decades later, their children, conceived during famine, showed higher risks of obesity, heart disease, and metabolic dysfunction. Their cells “remembered” hunger, even though they grew up in times of plenty.

What we endure can leave echoes that ripple across generations. Trauma, famine, stress, they leave their fingerprints not only on the psyche, but on the genome itself.

When I think about the gut and epigenetics together, it feels like a chorus of memory. The microbes telling one kind of story. The cells telling another.

Together, they are not “memory” in the way Sirens imagined, but they are inheritance all the same. Biological stories, carried silently, shaping us before we ever speak our first word. Think of the gut as a living archive.

What We Know, What We Imagine

Science is clear on some things:

We know that breast milk is not simply nourishment for a baby, but a carefully coded gift for microbes, especially Bifidobacterium infantis, that in turn shape the infant’s immunity, metabolism, and even risk of allergy and asthma (Zivkovic et al., 2011; Marcobal et al., 2010).

We know that the gut microbiome changes across geography and diet. Children in non-Westernized communities harbor twice as many microbial species as children in industrialized nations, many of them specialists in fermenting fibers nearly absent from the modern Western diet (Yatsunenko et al., 2012).

We know that early life exposures matter. Babies born by C-section have microbiomes that differ from those born vaginally, with potential consequences for immune development (Dominguez-Bello et al., 2010). Antibiotic use, particularly in the first year of life, has lasting effects on microbial diversity.

We know that trauma and scarcity can inscribe themselves on the body. Epigenetic studies show that famine during pregnancy alters DNA methylation patterns in children decades later, influencing metabolism, fat storage, and disease risk (Heijmans et al., 2008). Similar epigenetic signatures are found in descendants of Holocaust survivors (Yehuda et al., 2016).

And yet…there is so much we do not know.

We do not know the full constellation of microbes once carried by our ancestors, nor which losses matter most. We do not know why some people seem resilient to epigenetic scars, while others carry them like heavy shadows. We do not know whether restoring a missing microbe can truly “restore” a lineage of health.

Here, imagination steps in.

Perhaps the gut remembers more than digestion. It remembers forests walked, soils touched, foods gathered. Perhaps our cells hold not just scars of famine but the resilience that survived it. Perhaps we are not only recipients of memory, but living co-authors, choosing each day what will be remembered, and what will be forgotten.

A Living Inheritance

I return to that question often: what are we carrying forward, and what are we letting die?

Every choice we make, food, medicine, environment, writes itself into our bodies. We are not just individuals, but living archives of those who came before us.

Gut health, then, is not only about digestion or bloating or probiotics. It is about stewardship. It is about tending the microbial and cellular stories we’ve inherited, and choosing carefully which ones we want to pass on.

Because in the end, we are both memory and maker. We inherit, yes. But we also create.

So I’ll leave you with this: what stories are your body and your gut carrying? And what new ones do you want to write for the generations that follow?

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References

Book & Podcast

Radiolab. (2017). The Elixir of Life. WNYC Studios. https://radiolab.org/podcast/the-elixir-of-life

Meyer, J. (2019). 

Sirens. Macmillan. https://www.goodreads.com/book/show/42444390-sirens

Scientific Sources

Dominguez-Bello, M. G., Costello, E. K., Contreras, M., Magris, M., Hidalgo, G., Fierer, N., & Knight, R. (2010). Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences, 107(26), 11971–11975. https://doi.org/10.1073/pnas.1002601107

Heijmans, B. T., Tobi, E. W., Stein, A. D., Putter, H., Blauw, G. J., Susser, E. S., … Lumey, L. H. (2008). Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proceedings of the National Academy of Sciences, 105(44), 17046–17049. https://doi.org/10.1073/pnas.0806560105

Marcobal, A., Barboza, M., Froehlich, J. W., Block, D. E., German, J. B., Lebrilla, C. B., & Mills, D. A. (2010). Consumption of human milk oligosaccharides by gut-related microbes. Journal of Agricultural and Food Chemistry, 58(9), 5334–5340. https://doi.org/10.1021/jf9044205

Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., … Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222–227. https://doi.org/10.1038/nature11053

Yehuda, R., Daskalakis, N. P., Bierer, L. M., Bader, H. N., Klengel, T., Holsboer, F., & Binder, E. B. (2016). Holocaust exposure induced intergenerational effects on FKBP5 methylation. Biological Psychiatry, 80(5), 372–380. https://doi.org/10.1016/j.biopsych.2015.08.005

Zivkovic, A. M., German, J. B., Lebrilla, C. B., & Mills, D. A. (2011). Human milk glycobiome and its impact on the infant gastrointestinal microbiota. Proceedings of the National Academy of Sciences, 108(Supplement 1), 4653–4658. https://doi.org/10.1073/pnas.1000083107