Can gardening improve your gut microbiome?

In this Article (Index)

• The Loss of Gut Microbial Diversity
• Why have we lost microbial diversity?
• Soil Microbes and Your Skin and Gut
• The Soil Microbiome
• Benefits of Eating Garden-Fresh Foods
• Diet and gut microbiome diversity
• Closing Comments

The Loss of Gut Microbial Diversity

As people have moved from rural settings to cities over the past century, they have lost contact with the plants and soil that humans have lived with for the past 300,000 years.

Modern city dwellers have lost about half their gut microbes E. Pennis, (10)

Research shows that of the 85 microbial genera found in the guts of wild apes like Bacteroides and Bifidobacterium, only 55 genera are found in the guts of people living in U.S. cities.
People living in less developed countries have a higher variety, with 60 to 65 of those bacterial groups, reflecting the positive impact of a rural setting. (10)

This lack of contact with the microbes living in a biodiverse natural setting has led to a loss in the diversity of the microbes living in the gut. At the same time, chronic inflammatory diseases have become prevalent in urban societies.

Why have we lost microbial diversity?

There are many factors leading to these changes in our gut microbiota. We list them below.

Antibiotics

The use of antibiotics starting in the 1940s, to treat human infectious diseases and also to keep farm animals (pigs and cattle) healthy, has led to an increase in the number of antibiotic-resistant bacteria, which can swap genes with others who aren't resistant, and make them so. This altered the microbiome because antibiotics don't only eliminate pathogens, they also wipe out beneficial microbes that live in our bodies.

A negative side effect is that antibiotic-resistant microbes are a serious health risk for all of us, as they can't be eliminated with antibiotics.

Fortunately, as we will see further down (see Diet and gut microbiome diversity), people who consume more than 30 types of plants per week have fewer antibiotic-resistant bacteria in their guts.

Farming Practices

Agrochemicals and large-scale farming reduce the variety of microbes in the plants we eat.

The use of pesticides and insecticides alters the microbiome in the soil, decreasing its diversity. These microbes also colonize plants and interact with their roots where they fix nitrogen, so the plants' microbiomes are also affected as well as their nutrient content.

Modern farming focuses on large-scale farming and single-crop production (monoculture) to optimize yield, It uses hybrid seeds that are mass-produced. This results in a lower variety of crop plants, and also reduces the plant microbiome to which we are exposed.

Traditional smallholder farming and organically grown vegetables ensure a higher biodiversity in the microbiome. (1)

Genetic selection of plant varieties and altered soil microbiomes reduce the production of compounds known as plant secondary metabolites (PSMs) that help protect them from pathogens, and insects. They comprise phytochemicals such as phenolics, terpenes, steroids, alkaloids, and flavanoids, all of which are beneficial for human health. (1)

A lower variety of plant-based foods (see Diet and gut microbiome diversity) reduces the diversity of gut bacteria.

Food Processing

After harvesting, fruits and vegetables go through industrial processing like cleaning, washing, milling, mixing, hydrating, drying, steaming, storage, packing, and distribution which further modify the existing microbiome.

The higher intake of processed and ultra-processed foods alters the gut microbiome and has negative health effects.

Urbanization

Our modern urban lifestyle has isolated us from interacting with a more diverse natural microbiome. We are no longer immersed in nature, in contact with the soil and plants. Forests and fields have been replaced by concrete and bricks. Scientific evidence shows that Being Outdoors is good for your health.

The Circuit Between Gut Microbiome and Nature

The following image shows the former, rural (green arrows), and current, urban (red arrows) interactions with natural microbiomes.

In the past, in a rural setting, plant-based food was consumed fresh ①, people were in frequent contact with the soil and its microbiome ②, and their feces returned to the soil (blue arrow) ⑤
They also interacted indirectly with the feces microbiome ③ which also enriched the soil ④.

The modern urban cycle is different. Plants are processed ❶ in industrial facilities, and humans consume food that is more or less processed ❺.
Other manufacturing sites produce agrochemicals ❷ and pollution ❸ (airborne pollutants can taint the soil modifying its microbiome). Agrochemicals ❹ modify the plant and soil microbiome. Humans are now removed from contact with their feces (blue arrow ⑤) which does not return to the soil, instead, it is sent through sewage ❻ and processed before being dumped into waterways ❼

Soil Microbes and Your Skin and Gut

A study by Parajuli, Hui, Puhakka et al., (2020) in Finland (7) reported that the contact between the skin and organic gardening materials modifies the gut microbiome. They found that shrubs and flowering plants in the yard and gardens were "associated with a reduced abundance of Clostridium... and an increased abundance of Faecalibacterium and Prevotellaceae" bacteria in the gut of the people living there, while built-up areas showed a predominance of Bacteroides.

They suggest that the microbes in the environment find their way into the gut of the residents through "everyday nature contacts and transfer of environmental microbiota indoors" and that living in areas with a diverse plant community can "have cascading effects on health associated gut microflora in urbanized, developed societies" improving the gut microbiota.

A 2022 study (11) reported that "soil exposure through gardening was associated with a small but detectable change in the gardeners' gut microbiota composition."

A 2023 paper by Dr. Gynne Mhuireach also investigated the microbes in urban garden soil to learn if these germs transfer onto people's hands during gardening, and how long they stay there. (8)

The study found that bacteria did move from soil to skin, and remained there for up to 12 hours. However, as the study took place during the COVID-19 pandemic, the subjects tended to wash their hands more frequently (between 4 and more than 10 times a day) and also used hand sanitizer and/or antibacterial soap, which surely reduced the staying time of the bacteria on the skin.

The authors mention that recent research "suggests that more microbial diversity on skin may help reduce allergies."

A recent randomized trial by Saarenpää et al., (2024) (3) investigated if direct contact with the soil during gardening modified the microbiota and improved immunity. It took two groups, one, that received a substrate for growing plants that had a rich and diverse growing media, and the other one, the control group, received peat that was poor in bacterial content and diversity. The trial found that five different groups of bacteria increased on the skin of the "rich medium" group, namely Bacteroidetes, Planctomycetes, Proteobacteria, Cyanobacteria, and Verrucomicrobia, and Bacteroidia, while no changes were observed in the control group. Immunity improved in the "rich medium" group, as immunomodulatory cytokine interleukin 10 (IL-10) an anti-inflammatory, and interleukin 17A (IL-17A) increased their blood levels in comparison to the control group.

The participants were also exposed by eating their crops which could have affected their gut microbiota and caused the observed immune response.

The Soil Microbiome

A study by Roslund, M. I., Laitinen, O. H., & Sinkkonen, A., (2024) (2) investigated the benefits of ingesting soil (yes, eating soil).

There is evidence that soil microbes improve the gut microbiome and its immunological resilience.

How Can Soil Exposure Improve Immunity?

Different studies have shown that exposure to soil and its microbes improves immunity by increasing the blood levels of IL-10, and TGF-β1 both of which are anti-inflammatory cytokines with immunological properties. It also modulates IL-17A, a pro-inflammatory cytokine, and Treg cells that regulate the immune system and help prevent autoimmune disorders.

Risks and Adverse Effects of Esting Soil

This doesn't mean that you should eat soil.

Soil contains traces of toxic heavy metals like lead (Pb), cadmium (Cd), arsenic (As), and nickel (Ni), Polycyclic aromatic hydrocarbons (PAHs), drugs, petroleum, and other pollutants that can pose a health risk. Some of them are obesogens.

Soil also contains eggs of parasites like helminths (worms) which can survive for many months in the ground as well as fungi (saprophytes) that can have negative health effects. (8)

Antibiotics used by the farming industry to keep animals healthy leach into the soil and evolution has promoted the natural selection for antibiotic-resistant microbes in farm soils, which if ingested could alter your gut microbiome.

Benefits of Eating Garden-Fresh Foods

You don't have to go to the extreme of eating soil. Consuming fresh produce instead of processed veggies can do the trick.

Gwynne Mhuireach, (2023) (4) points out that "we eat billions of microbes (bacteria, fungi, viruses) inhabiting our food... a single apple harbors about 100,000,000 bacteria, not to mention an unquantified number of fungi, viruses, and other microorganisms."

Supermarket produce and garden-fresh foods undergo different degrees of processing. Supermarket veggies are washed more thoroughly and handled as they move from farm to your table. Garden produce, on the other hand, is subjected to less washing and sanitizing, so it still harbors some native plant and soil microbiota, exposing you to a wider diversity of microbes.

Traditional Farming produce is good for your gut health

Evidence suggests that exposure to diverse microorganisms, such as those associated with traditional farm environments, can help train the immune system and reduce inflammation Mhuireach (2023) (4)

Rosberg (2021) (5) found that the vegetables and fruit that we buy at supermarkets after being washed and handled as they move through the supply chain only retain 2% of their original microbes by the time they reach the point of sale. The actual bacterial count is unchanged, but now 98% of them were acquired in the processing plants.

They end up containing more "abundance of spoilage bacteria. E. coli was detected after the washing... At expiry date, bacteria thrive equally well in commercially washed and unwashed leafy vegetables."

Brown, M.D. et al., (2022) (6) reported that during the peak harvesting season, families that garden and also consume their produce, have more soil-associated bacteria, a more diverse gut biome with more fiber-fermenting bacteria in their colon than families that don't garden.

Soil-derived bacteria were found in all family members even though there was only one primary gardener per family, showing that sharing the garden produce in their meals shared the soil-sourced bacteria.

Diet and Gut Microbiome Diversity

Diet plays an important role in modulating the gut microbial diversity. Fruits, nuts, vegetables, whole grains, and legumes are rich in dietary fiber.

A large study using data from over 10,000 subjects (9) found that those who ate more than 30 different plant foods each week had a higher diversity of gut bacteria than those eating less than 10 plant foods per week. Since different plants contain different types of fiber and resistant starches, a diverse diet will nourish a more diverse microbiome. Furthermore, it also reported that those who consume more than 30 types of plants per week had fewer antibiotic-resistance genes. This means that their gut harbors fewer bacteria that are resistant to antibiotics. Microbes that have resistance to the commonly used antibiotics put people at higher risk of infection, and death.

Closing Comments

If you have a garden and a library, you have everything you need Marcus Tullius Cicero (106 BC-43 BC)

Contact with soil and plants through gardening, and eating a diverse (+30 different plant types per week) plant-based diet, sourced from organic gardens or small-scale farms can improve the diversity of your gut's microbiome and provide health benefits.