Leisha New research reveals another remarkable way microbes communicate and survive. But it also raises a question about what happens when we repeatedly disturb the microbial communities that keep us healthy.
I came across a fascinating piece of research this week. Scientists have discovered that bacteria can actually share working proteins with one another, helping their neighbours survive when conditions become difficult. We already knew bacteria could exchange genes, but now we have evidence that they can pass along biological tools that another bacterium can immediately put to work.
Of course, the research is being discussed largely in terms of how bacteria survive medical treatments. Scientists are interested in finding ways to prevent that survival because drug-resistant infections have become a serious problem. But my mind immediately went somewhere else, back to the soil and to the incredible microbial relationships I have spent years studying.
What if we have been so busy trying to control microbes that we have overlooked how important their relationships are to our own health? And what happens when we repeatedly disturb the communities that have evolved alongside us?
The Bacteria Have a Delivery Service
The researchers worked with Escherichia coli, a bacterium that naturally lives in the intestines of humans and other animals. They discovered that bacteria can release tiny packages, called extracellular vesicles, containing working proteins that other bacteria can receive and use.
Imagine one bacterium sending a little parcel of functioning biological machinery to its neighbour. The receiving bacterium opens that parcel and puts the contents to work, gaining a capability it did not previously have. In the experiments, these exchanges also helped certain bacteria survive stressful conditions.
The scientists even observed proteins moving between different bacterial species. We are discovering that microbial communities have ways of sharing resources that we are only beginning to understand.
And here is what caught my attention. Bacteria are not simply isolated little organisms competing for survival. Their interactions can help entire populations respond to changes in their environment, and the abilities of one organism can influence the survival of another.
The research was designed to investigate bacterial persistence, but it opens up some fascinating questions about microbial cooperation and communication in the natural world.
What Happens When We Disturb Our Own Microbial Communities?
I have become increasingly concerned about the consequences of repeatedly disturbing the human microbiome. Our bodies depend on an enormous community of bacteria, fungi, viruses and other microorganisms that help digest our food, produce important nutrients, support our intestinal lining and communicate with our immune systems.
Yet many of these organisms are sensitive to the medications and environmental conditions we are exposed to. Research has demonstrated that certain treatments can dramatically change the composition of the gut microbiome, sometimes leaving particular microbial populations depleted for months.
In one study, healthy adults received a short course of powerful medication that substantially altered their gut microbiomes. Their microbial communities appeared to recover considerably over the following weeks, yet certain bacterial species remained undetectable in many participants six months later.
That is a rather sobering discovery when we consider how frequently people are exposed to treatments that disturb their intestinal ecology.
I wonder how many digestive problems, food sensitivities and other health complaints may be connected to microbial communities that have never fully recovered. We know that microbial disruption can contribute to certain intestinal illnesses, and researchers are investigating its possible involvement in other chronic conditions. There is still plenty we don’t understand, but I believe this area deserves far greater attention.
And adding a few probiotic organisms doesn’t necessarily recreate the original community. Microbes depend on one another, on the food we provide and on the conditions within the intestine. Restoring their relationships may be just as important as restoring their numbers.
I See This Every Day in the Soil
Here at Living Ground in southern Ecuador, we have spent years rebuilding depleted soils. My training in the Soil Food Web taught me to look beyond individual microorganisms and examine the relationships that allow an entire ecosystem to function.
When I put a soil sample under the microscope, I may find plenty of bacteria, but that doesn’t necessarily mean I am looking at healthy soil. Perhaps the fungi are missing, or there are too few protozoa and beneficial nematodes. Without these organisms and their interactions, the soil’s ability to cycle nutrients and support healthy plants can be compromised.
We can add compost and introduce beneficial organisms, but if the conditions are unsuitable, the biology may struggle to establish itself. Healthy soil needs organic matter, moisture, air, living roots and a diverse community of microorganisms interacting with one another.
I see a very similar principle at work within the human body. Our intestinal microbes depend on a steady supply of nutrients, particularly the diverse fibres and plant compounds that nourish different populations. Some microorganisms break down food compounds into substances that other microbes can use, creating an extraordinary network of metabolic relationships.
The human gut and the soil are very different environments, but both demonstrate something important. The health of a microbial ecosystem depends on the relationships among its organisms and the conditions that support them.
When those relationships are disturbed, simply adding organisms back may not be enough.
Growing Our Inner Garden
This is a large part of what has inspired my work with Plant & Kitchen Alchemy. I am fascinated by the connections between biologically rich soil, the plants we grow, the foods we prepare and the microorganisms living within us.
We grow herbs, vegetables and fruits in living soil, then bring them into our kitchen to explore fermentation, sprouting, cultured foods, medicinal vinegars and all kinds of other preparations. Each process gives us another opportunity to understand how plants and microbes transform nutrients and how the resulting foods interact with our own biology.
Different plant fibres feed different microbial populations. Fermentation transforms foods through microbial activity, creating new flavours and compounds. Some of the metabolites produced by our intestinal microbes nourish the cells lining our gut and influence our immune and metabolic functions.
I don’t believe there is a single food, probiotic or preparation that can restore every disturbed microbiome. Our microbial communities are far too complex for that. But understanding how to nourish them and create conditions that encourage biological diversity seems a sensible place to begin.
Just as we have learned to rebuild depleted soils by caring for the entire food web, we need to develop a greater understanding of how to support the living ecosystems within our bodies.
Perhaps We Should Be Listening to the Microbes
This new discovery has given us another glimpse into the extraordinary microbial world. Bacteria can package functioning proteins, release them into their environment and share them with other organisms. Under certain conditions, those exchanges can help neighbouring cells survive.
Scientists are understandably interested in how this knowledge might help them address dangerous infections. I am equally interested in what it might teach us about the relationships that exist within healthy microbial communities and what we lose when those communities are repeatedly disturbed.
How many other exchanges are taking place within our microbiomes that we haven’t yet discovered? What happens when important members of those communities disappear, and how do we encourage the recovery of the biological relationships on which our health depends?
These are the questions that keep me at my microscope, experimenting in the kitchen and working in our gardens. Every new discovery seems to reveal another layer of complexity in the living world, and another reason to pay attention to the extraordinary organisms that share our bodies and our planet.
Perhaps we need to spend a little more time learning how to live with our microbes and understanding what they need from us. After all, we are participating in these microbial ecosystems every single day, whether we recognise it or not.
References
- Antibiotics stimulate protein transfer to persister cells. Science, 2026.
- Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology, 2018.
