Microbiome: The gut-soil connection

Pablo Ramírez
Director of Innovation at Horizon

If we look closely at the inside of our gut and compare it to the roots of a plant, we notice they are very similar in morphology. Both organs are made up of microscopic protrusions (villi in the intestines and root hairs in plants) that absorb water and nutrients from their environment. And if we look even closer, the analogy holds beyond just form and function, applying also to the millions of micro-organisms both tissues are in contact with.

Although the soil and gut microbiomes differ in composition and metabolism, there are many similarities in how plants and animals relate to and depend on their microbiomes for important functions such as nutrition, warding off pathogens, resilience in the face of changing environments and general health.

Born to work together

According to the theory of endosymbiosis, the close relationship between higher organisms (animals and plants) and micro-organisms (bacteria, fungi and viruses) has evolved over history from our origins, when single-celled organisms evolved by merging with bacteria, which became mitochondria (the powerhouses of animal cells) and chloroplasts (the photosynthetic cells in plants). So, we can say that without this original joining of forces with microbes, neither plants nor animals would exist today.

I feed you, you feed me

Later on, the relationship between microbes and animals shaped the evolution of our digestive tract.

Our genome doesn’t code for all the enzymes we need to extract energy from the food we ingest. Our gut microbiota, especially in the lower part of the intestines, digests and absorbs the nutrients that escape us and produces substances that are beneficial to our cells. Symbiosis in its purest state.

This mutualistic relationship starts early in our lives. At birth, we are primed with our mother’s microbiome and soon start feeding it with the nutrients we get from her breast milk (human milk oligosaccharides or HMO), which we can’t digest because they have been developed through evolution to nourish our microbes. Over time, these human milk oligosaccharides are replaced by oligosaccharides we produce, anchored in the intestinal mucosa, providing both food and shelter for our guests. All this bacteria food, plus the fibre in fruits and vegetables, is what we now call prebiotics.

Similarly, the first algae left the oceans roughly 400 million years ago by merging with fungi, which allowed them to get nutrients from rocks and spread to find new water sources.

Today, plants invest 30% to 40% of their photosynthetic production into feeding the micro-organisms in the rhizosphere (part of the soil in contact with their roots) with root exudates. In exchange, the bacteria and fungi that live there help the plant by extending its roots, giving the plant key enzymes it lacks and mobilising nutrients that wouldn’t otherwise be available. One clear example is phosphorus, which is mainly found in organic phosphates that the plant can only absorb after they are liberated by phosphatase.

Plants get an estimated 90% of their biomass as food from their symbionts.

First line of defence

The microbiome is the first line of defence against infection and pathogenic micro-organisms, both in intestines and in roots. Our allies there protect us with several mechanisms.

In some cases, the best defence is a good offence. Certain fungi in the soil trap and immobilise nematodes, which are potential parasites for plants, and then feed on them. Other symbionts produce toxic substances or antibiotics that get rid of harmful microbes. And in other cases, as tends to happen in the intestines, defence occurs through direct competition for space and food. In any biological ecosystem, greater biodiversity means more competition and fewer opportunities for a pathogen to get stronger and grow unchecked.

And occasionally, the mechanism works indirectly. Because everything is connected, and microbial activity and their nutritional contribution to the soil and the intestines also helps develop and boost the host’s immune system, making it more resistant to infections, pests and diseases.

Diversity is key

Today, it is very difficult to define a healthy microbiome, for plants or animals. In the soil of a meadow or forest, micro-organisms are mainly found in the top 15 centimetres of the organic layer with a concentration somewhere between 100 million and 1 billion bacteria per gram. In the intestines, concentration can range from 10,000 in the jejunum and 10 million in the ileus to 1 trillion in the colon. Of course, the concentration varies, but in both cases the number and diversity of micro-organisms is key to the ecosystem’s homoeostasis and benefits both parties.

It is scientifically proven that higher microbe diversity is associated with a healthier, more resilient ecosystem, whether plant or intestinal, and a loss of this diversity, a process known as dysbiosis, can mean a loss of functions and open the door to diseases.

We’ve all heard about the risks of misusing antibiotics and the impact of our modern diet and lifestyle on the microbial diversity in our gut, leading to serious health issues such as obesity, inflammatory diseases and cancer. Exactly the same happens with modern agriculture where intensive farming and misuse of chemical fertilisers and pesticides have a negative impact on soil health and the biodiversity of its microbial ecosystems, with detrimental effects to plant health.

For centuries, we have underestimated the role microbes play in the health of our ecosystems, and our diet, medicine and agriculture have worked against this collaborative association that all plants and animals on Earth depend on.

Not all is lost

Little by little, we are learning that the microbiome is not only a bunch of “bugs”, but can be considered another organ, invisible yet essential, whose genome complements (in both plants and animals) our metabolic capacities and boosts our potential to grow and live a healthy life. This is why we have to care for and nourish it, encouraging its diversity and resilience.

In terms of the intestine, this is mainly achieved through an active lifestyle and a balanced diet, low in processed foods and high in fibre, which can include prebiotics, probiotics and other supplements to boost microbial diversity, strengthen the intestinal barrier and keep the immune system working properly.

In terms of the soil, it is about promoting practices to regenerate organic material and restore biodiversity, such as crop rotation, cover crops and replacing chemical fertilisers and pesticides with organic products like those developed by Horizon that stimulate and provide nutrients for the micro-organisms and plants naturally, without upsetting their delicate balance.

Thanks for reading us. We look forward to seeing you for the next #HorizonWorld post.

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