How Industrial Farming Is Harming Our Gut Microbiome


A greater number of us are becoming concerned about our health and the food we eat than ever before. While the driving factors that influence how and why we choose between different food options are complex, there are two questions that we should always be asking ourselves when shopping for food:

1. Where was this food produced?   

2. How was this food produced?

An awful lot takes place ‘behind the scenes’ of food production, and there are some intensive farming practices that could be seriously harming the make up of your gut bacteria – and your health in general.

What is Industrial Farming?

Industrial Agriculture – also known as Intensive or Factory Farming, came to prominence in the decades after World War II. A new system of agriculture was developed in the USA that significantly increased yield and decreased the cost of food production.

Through the expansion of highly efficient large-scale and intensive farming practices – such as single-crop farms and concentrated animal feeding operations – farmers were able to significantly increase their crop and livestock yields, resulting in more food at cheaper prices for consumers (2).

Today, a growing number of agricultural experts from around the world are joining forces to express their concerns about the effects of IA, including the resulting environmental damage, effects on workers and rural communities and animal welfare – as well as increasing concerns about the effects on human health (4).

The focus of this article will be about the effects of Industrial Agriculture (IA) on our gut and our health in general. 

Why is the Health of Our Gut So Important?

Our gut – also known as our forgotten organ – contains as many as 100 trillion organisms (5)– including bacteria, viruses and fungi – that make up our gut microbiome. This ecosystem of microbes has only gained significant appreciation in recent years as scientists have discovered the growing number of essential roles performed – from

  • Regulating our immune system and preventing infection from disease-causing organisms
  • Helping to controll our weight and metabolism
  • Influencing our mood and mental health, our sleep and even our circadian clock
  • And of course our managing digestive function. We also rely on our microbes to breakdown non-digestible dietary fibres, proteins into essential vitamins and chemicals for our body to function and biotransformation of xenobiotics (basically, the destruction and removal of chemical substances that shouldn’t be inside us, such as pesticides) (5).

So, How Does Industrial Farming Affect Our Gut & Our Health?

There are a number of industrial agriculture practices that affect the make up of our gut bacteria – and our health in general.


1. The Use of Pesticides

Pesticides: crop spraying from above
Pesticides are toxic chemicals that are designed to kill, repel or otherwise harm living organisms (7).

The growth of industrial synthetic pesticides accelerated after WWII. Today, there are now more than 1000 pesticides in use around the world, with the use (amount and type) of pesticides varying markedly in different countries.

It is estimated that the global consumption of pesticides is about two million tonnes per year (roughly 45% of this occurs in Europe, 25% in the USA, and 30% in the rest of the world) (9).

If you want to track your own country’s usage, you can use this tool from the FAO: https://www.fao.org/.

Pesticides significantly increase the yield of food producers by reducing large crop and livestock losses (10). However, the most commonly used pesticides today have been shown to be harmful to our health (11), with a strong body of literature linking pesticide exposure and chronic health effects.

Two systematic reviews published in 2007 revealed links with exposure of commonly-used pesticides and several forms of cancer, neurological issues, genetic issues, reproductive problems (including foetal death), and skin diseases (13,14); and in a study in 2011 certain pesticides were linked with diseases such as diabetes, obesity and metabolic syndrome (15).

How Do Pesticides Affect Our Gut Health? 

Humans can be exposed to pesticides by ingesting residues found on or within fruits and vegetables, or in contaminated animal tissues, including fish. Exposure can also occur through drinking contaminated water or even breathing contaminated air (particularly when pesticides are sprayed) (12).

How the pesticide affects us (its toxicity) will depend on its type, its dose (the amount you are exposed to), and the route of exposure (10).

Minimal research has explored the effect of pesticides on our gut ecology, but within the last several years some very important findings have come to light. Seminal research conducted in 2012 (17) suggested that certain pesticides directly alter our microbiome (leading to gut dysbiosis), which subsequently increases the risk of health problems such as diabetes, obesity and auto-immune diseases.

Furthermore, this research suggested that gut dysbiosis resulted in a higher amount of toxins being absorbed into the body due to the reduced ability of our gut microbiota to break them down.
Further research by Claus et al. (18) presented clear evidence that the toxicity of the exposed pesticide was dependent on its metabolism by gut microbes – basically, our gut ecology was protecting us from outside toxins, such as pesticides.


One particular type of pesticide that has attracted some recent attention is Glyphosate, which is the active ingredient in Roundup (the most widely used herbicide in the world). Glyphosate residues, which are most commonly found in sugar, corn soy and wheat, have been shown to promote the growth of some disease-causing bacteria by preferentially limiting the growth of common gut bacteria (11).

Roundup Glyphosate

In 2013, two contentious scientific reviews were published by Samsel and Seneff which argued that glyphosate, by disrupting our gut ecology, was likely to be an important causal factor of coeliac disease and gluten intolerance (19), as well as being a potential contributor to a range of diseases and conditions such as obesity, diabetes, heart disease, depression, autism, infertility, cancer and Alzheimer’s disease (20).

These two reviews received a lot of criticism, some of which had counter-arguments that were significantly flawed, such as the Huffington Post article ‘Condemning Monsanto with Bad Science Is Dumb’ (47, 48).

Whilst likely ‘over-playing’ their findings, there exists some consensus that there is a basis to some of the research’s important findings which should not be ignored (48).

The discussion around these two controversial reviews provides a microcosm of the often-dichotomous debate on the use of pesticides. However, many regulatory bodies have cited that they believe there is no objective evidence to suggest that glyphosate and other commonly used pesticides cause any harm to humans, such as the European Commission who recently renewed approval for the use of glyphosate for a further 5 years (21).

Many consumer rights groups and organisations however, such as the Union of Concerned Scientists and the European Citizens’ Initiative, are expressing their concern that there is enough evidence to show that certain pesticides, such as glyphosate, do cause us harm.

For the moment, there appears to be no clear-cut answer to this complex question, and further robust research is required to draw any substantial conclusions. However, we believe there is enough evidence to be genuinely concerned about the likely dangers of pesticide consumption.

How to Avoid Pesticides

Avoiding pesticides completely is no easy feat, but a good starting point is to be conscious of which foods contain higher concentrations of pesticide residues than others. Knowing this will depend on which country you come from, and in some cases, which part of that country you come from.

In 2017, the foods in the USA with the highest levels of pesticide residues were: strawberries, spinach, nectarines, apples, peaches, celery, grapes, pears, cherries, tomatoes, sweet bell peppers and potatoes (54).

In 2014, the European Food Safety Authority (EFSA) produced a report which showed that 45% of food products in the EU contained traces of one of more of 774 pesticides, with 1.6% containing residues exceeding legal limits. Bananas, aubergines, broccoli, virgin olive oil, orange juice, peas, peppers, raisins, wheat, butter and eggs were all found to have a higher chance of containing multiple residues (55).

The best way of reducing the risk of pesticide exposure is to eat organic food – although this is not affordable for many. While organic food can still contain traces of pesticides, the concentrations are much lower than non-organic foods (54). A 2015 study showed that people who ‘often or always’ ate organic produce had significantly less pesticides in their urine (57).
If you are unable to afford organic foods, it’s advisable to wash all fruit and vegetables thoroughly under running water, or better still soak in warm water and vinegar, scrubbing firm fruits and vegetables (such as root vegetables), discard the outer layer of leafy vegetables, and peel fruit and vegetables when possible. It is also recommended to trim fat and skin from meat, poultry and fish to reduce the ingestion of pesticides that accumulate in the fatty tissues of animals.


  • There are hundreds of pesticides in use today, the use of which is common in industrial agriculture.
  • Many pesticides have been linked with chronic health issues such as cancer, endocrine disorders, genetic issues, reproductive issues and neurological disorders. Some pesticides can also directly disrupt our gut ecology (gut dysbiosis), potentially leading to further chronic health issues such as diabetes, obesity and chronic gastrointestinal issues.
  • The debate surrounding pesticide use is often confusing and muddled. Consumer advocates routinely produce papers highlighting evidence of health risks, which are often countered by regulatory bodies with papers stating the evidence is not conclusive.
  • The simplest way to reduce the amount of pesticide consumption is to eat organic foods; otherwise, it is recommended that you wash and/or peel your fruit and vegetables thoroughly using running water.
  • Fruit and vegetables containing skins – such as bananas, oranges and avocadoes – will require less cleaning. However, fruits such as grapes, apples, guavas, plums, mangoes, peaches, and pears, and vegetables such as tomatoes, aubergine and okra, may contain more pesticide residue due to their crevices in the skin.



How Pesticides in Industrial Farming Harm our Health

2. The Use of Antibiotics

antibiotic use in livestock
In 1951, the first antibiotics were approved for use in animal feed in the USA, following studies showing how low dose antibiotics helped chickens, pigs and other livestock gain weight. This opened the floodgates worldwide, and for a long period of time giving low levels of antibiotics (sub-therapeutic levels) to livestock was common practice globally.
In 1997, WHO published a report recommending that the same antibiotics used in humans should not be used to promote growth in animals. WHO cited they had concerns about the spread of antibiotic resistance, which was a fear that ultimately led to the European Commission banning this practice in Europe in 2006 (49). It wasn’t until 2017, however, when the US FDA finally caught up (23).

Current Regulations

While regulations on the use of antibiotics have improved, Antibiotics can still be given for the purpose of treating a sick animal, or treating a batch of animals when at least one is ill (metaphylaxis), or even for complete preventative treatment against a disease (prophylaxis). These uses are frequently blurry:
One study from the US showed that 16% of all lactating dairy cows were receiving antibiotic therapy for mastitis (inflammation of the breast tissue) each year. However, the same study showed that nearly all dairy cows were receiving infusions of prophylactic antibiotic doses after each lactation to prevent and control future mastitis (24).

In 2010, global consumption of antibiotics and other antimicrobials in food production was conservatively estimated to be over 63,000 tonnes. This is projected to rise to well over 100,000 tonnes by 2030, with a concerning percentage of this increase attributable to more animals being raised using methods of industrial agriculture (25).

Antibiotic Use in Industrial Farming and Our Gut Health

Any living creature’s gut ecosystem – whether you are a human, cow, chicken or a pig – becomes exposed to antibiotics when they are ingested. This exposure can then result in a number of changes: Some that affect the individual (such as chronic gastrointestinal issues), some that can affect the surrounding environment (through excretion), and others that can affect all of us (through the creation of ‘superbugs’).

Current evidence suggests the amount of antibiotics in the animal products we eat is probably very low (26). This is largely due to strict legislation in many places around the world that ensures animal products (including dairy and eggs) go through obligatory drug withdrawal periods to ensure they are ‘antibiotic-free’ before being allowed to be used as food.
The caveat is that, in many places around the world, there can sometimes be gaps between policy and practice. Often, consumers have no choice but to trust that industrial agriculture is abiding by the law (26).

The Effects of Environmental Pollution on Our Gut

However, recent research has highlighted that we could be ingesting antibiotics, not through direct consumption of contaminated meat, but as a result of contaminated waste being absorbed into crops via the environment (55).
It is estimated that 75% of antibiotics given to livestock are excreted in waste (meaning that more than 45,000 tonnes of antibiotics entered the environment via animal waste in 2010 alone). Antibiotics have varying biodegradability, with some still being present in soil for up to 5 months. Antibiotics can accumulate in plant tissue, with a study in 2013 showing that certain antibiotics had accumulated in corn, lettuce, potato, carrots, onion and cabbage crops (55).
This study also hypothesised that the consumption of antibiotic residues could be fuelling the obesity epidemic by altering our microbiome, leading to gut dysbiosis.

Antimicrobial Resistance (AMR) and Our Gut Health

Antimicrobial resistance (AMR) is a serious public health concern, with the use of antibiotics in food animal production being a significant contributor. When huge amounts of antibiotics (particularly when given at low doses) are given to a large number of animals that contain enormous numbers of gut bacteria, it becomes statistically inevitable that a mutated strain of bacteria develops that can resist the given antibiotic. What’s incredible is that the stress of the antibiotics can encourage bacteria to mutate and develop resistance, much the same way as humans develop immunity after receiving a vaccine (24).

“Although previously unthinkable, the day when antibiotics don’t work is upon us. We are already seeing germs that are stronger than any antibiotics we have to treat them.”

  • Dr Arjun Srinivasan of the Center for Disease Control and Prevention (CDC) (27).

This means that certain antibiotic-resistant bacteria can become a part of the gut ecology of livestock, which can then spread directly to humans through ingestion (24, 28). Whilst not necessarily causing an acute illness, we can become symptomless carriers of superbugs as they integrate into our gut ecology. The implications of this are huge, as we can then spread these superbugs unknowingly and unintentionally onto others (28).


  • The practice of giving low levels of antibiotics to livestock to promote growth is now banned by most regulatory bodies; however, large numbers of livestock are still given antibiotics for other purposes, such as disease prevention.
  • The level of antibiotics passed from animal products to consumer is likely to be negligible. However, antibiotics spread through the environment via animal waste can accumulate in plant tissue, and certain crops have been shown to contain low levels of antibiotic residues.   Research suggests that this could be linked to obesity, but the results are not conclusive at this stage.
  • The prescription of antibiotics to livestock is a main contributor of antimicrobial resistance. Antibiotic-resistant bacteria can be passed onto the consumer, subsequently becoming a part of the consumer’s gut ecology.



3. Reduced Quality and Diversity of Food

Crop Quality & Diversity
Fruit, vegetables and grains that have been grown using methods of industrial agriculture have been shown in several studies to have significantly lower nutritional content than the same foods a century ago (38), findings well documented by a paper published in 2009 (39). For example, protein concentrations in wheat and barley have declined by up to 50% in this time, and the calcium content of broccoli decreased by almost 3-fold from the 1950s to the 2000s (38).

Why is this occurring? There are potentially two main reasons for this. One is called the environmental dilution effect, where industrial agriculture tends to decrease the concentrations of minerals found in crops due to intensive monoculture practices. The second reason is due to the genetic dilution effect, where genetic preference is given to high yielding crops, often at the expense of nutrient content(39).

Certain mineral deficiencies could directly impact the health of our gut. An example is selenium deficiency, a mineral found in some fruit and vegetables. In humans, selenium plays an important role in maintaining the antioxidant pro-oxidant balance in our gut, which is important for regulating the inflammatory pathway (40, 53). Research in mice showed that selenium deficiency significantly increased the likelihood of inflammation and oxidative stress of the gut lining (40).

The genetic dilution effect has not just resulted in reduced nutrient composition, but it has also caused a significant decline in the diversity of crop species and strains produced. Of the known 250,000 edible plant species, we use less than 200 for food, with 75% of the world’s food coming from just 12 plant species and 5 animal species (60). It is known that a decrease in dietary variety results in a reduction in gut microbiome diversity, which has been linked with health issues such as obesity, diabetes and inflammatory bowel disease (61). The limited species of crops produced are also increasingly being used to make processed food (41). Discussing the health impacts of processed foods is a gigantic topic, but it is arguably one of the most important driving factors of the obesity epidemic (41). 


  • Industrial agriculture can reduce the nutritional content of food through the environmental and genetic dilution effects.
  • Certain mineral deficiencies, such as selenium, could potentially impact our gut health through oxidative stress pathways, leading to inflammation
  • Certain practices of industrial agriculture are contributing to a reduced number of crop species and strains being used for food production. This is resulting in reduced dietary variety and subsequently decreased microbiome diversity – something that is linked with obesity, diabetes and inflammatory bowel disease.



 4.  Contaminated Animal Feed

Contaminated Animal Feed Lots
Intensive industrial farming of livestock has brought with it feedlots, where animals are confined indoors for the majority of the year, raised in pens and are given food designed to speed growth and minimise costs.

Diets are designed to maximise gain and reduce costs – so shift away from a natural diet of high-cellulose foods (such as grass) towards grain-based diets which can result in serious gastrointestinal problems (sometimes fatal) for some livestock such as cows, goats and sheep (35). In addition, research findings show that the type of animal feed affects the quality of the meat. For example, cows that are fed grass are more likely to produce meat with lower saturated fat levels, which subsequently may reduce the risk of heart disease (35, 56).

So How Does This Affect Our Gut Health?

Heavy metals contaminants (such as cadmium, lead and arsenic) have been shown to build up in these engineered animal feeds, and in turn build up in the fatty tissues of the animals, which is then passed on to the consumer (36).  Evidence from a study published in 2013 suggests that our gut health could be directly affected by heavy metals (notably lead and cadmium) found in animal feed. Both of these heavy metals have been shown to disrupt the gut ecology in mice, and could potentially affect the gut ecology of humans via similar mechanisms (37).


  • Certain substances such as heavy metals in engineered animal feeds can be passed on to humans through the meat and fatty tissue.
  • Heavy metals such as Lead and Cadmium have been found to harm our own gut microbiome.



5. Increasing Risks of Acute Gastroenteritis Outbreaks

Gut dysbiosis could result in MS in young adults
Industrial agriculture can increase the risk of outbreaks of acute gastrointestinal illness (31), particularly those caused by E.Coli, Campylobacter and Salmonella. In concentrated animal feeding operations, the unnaturally high concentrations of animals in a confined space, which also results in the unnatural production of huge amounts of waste, facilitates the growth and rapid dissemination of these dangerous bacteria. In 2010, a multi-state outbreak of Salmonella in the US occurred as the result of the dissemination of mass-produced eggs from one facility, and was estimated to have resulted in 2,000 cases of gastroenteritis (50).

Large single-crop producing facilities be exposed to these dangerous bacteria through the use of contaminated water. Their produce, exported in large quantities in a short period of time thanks to very efficient distribution systems, are then exposed to many consumers within an enormous area. In 2006, an outbreak of E.coli 0157:H7 (a particularly violent strain of E.coli) occurred in 26 states of the US, and was due to the consumption of spinach produced from a single manufacturing facility on a particular day. Three deaths were confirmed during this outbreak (51).

Research shows that acute gastroenteritis from these bacteria can lead to longer term health complications, such as an increased risk of ulcerative colitis, reactive arthritis and aortic aneurysm (ballooning of the aorta) (52). 


  • Industrial Agriculture can increase the risk of acute gastroenteritis outbreaks caused by dangerous E.coli, Salmonella and Campylobacter strains.
  • Bacterial gastroenteritis can result in longer term health complications such as ulcerative colitis, reactive arthritis and aortic aneurysms.




A Viable Alternative? Sustainable Agriculture

Sustainable Agriculture - A Viable Alternative?

Sustainable Agriculture, put simply, is the production of food, fibre, or other plant or animal products using production techniques that protect the environment, public health, human communities, and animal welfare (42). Sustainable agriculture is by no means a new concept, and has been in place for millennia.

From our gut health’s perspective, sustainable agriculture is the only way we can protect our gut ecology, as it is the approach that avoids the harmful practices of industrial agriculture.

Remember to ask yourself: Where was this food produced? And how was this food produced? There isn’t one fixed path that everyone should follow when it comes to shopping for food. Firstly, it is important to work out what is important to you. What type of values and principles do you feel are important to uphold? How important is health to you? How important are the other factors that differentiate industrial from sustainable agriculture to you?

Sustainable Table have a very useful article for readers who are interested in eating more sustainably, which includes some of the often-challenging first steps to take: (https://www.sustainabletable.org/568/do-you-have-to-eat-100-local-sustainable-and-organic).

A Parting Thought: Can Sustainable Farming Feed the World?

Many advocates of industrial agriculture (most with vested interests) argue it is the only realistic way to feed the world’s growing population. However, this is a claim that has never really been backed by any sort of hard evidence. A Working Group on the Global Food Crisis consisting of distinguished US experts tackled the topic. They reviewed available scientific evidence about the relevant components of sustainable agriculture from around the world, and concluded that the answer to this question was clear and simple: Yes (43, 44, 45). Not only can sustainable agriculture feed the world, it is the only viable way to do so (46).



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About Author

Benjamin Wood [MScIH, MBBS] is a medical doctor from Tasmania with a background in public and humanitarian health. He is passionate about improving the health consciousness of the public on a wide range of health and nutrition topics.

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