CAFOs, Your Gut, and Mental Health

Chicken Farm

Story at-a-glance

  • Nearly 25 million pounds of antibiotics are administered to livestock in the US every year, often for growth-promotion purposes
  • When you eat food that contains antibiotics, you not only get the drug but also antibiotic-resistant bacteria
  • Alterations to your gut flora can cause changes to your mental and emotional health and behavior


This is an older article that may not reflect Dr. Mercola’s current view on this topic. Use our search engine to find Dr. Mercola’s latest position on any health topic.

By Dr. Mercola

The majority of farmed animals (by some estimates more than 99 percent) raised for food in the US are raised in concentrated animal feeding operations (CAFOs).1 In fact, 80 percent of the antibiotics used in the US are used in agriculture.

The food – eggs, dairy, beef, pork, and poultry, for instance – shows up in your supermarket neatly packaged and for reasonable, often low, prices. But the cardboard egg cartons, cellophane wrapped steaks, and chicken breasts do not bear testimony to the true cost of the food.

There are serious moral implications to raising animals as though they are inanimate objects, not worthy of even basic requirements like access to fresh air and sunlight, space to move around and a clean place to sleep.

There are environmental implications, too, as CAFOs continue to pollute our waterways and air with massive quantities of waste. And then there are the health issues. CAFOs are putting public health at risk, all while claiming to offer an efficient way to feed the world.

But while CAFOs have mastered the art of growing profits, they’ve overlooked the basic natural laws that govern growing animals… the end result is a disaster already well into the making.

Reckless Use of Agricultural Antibiotics Has Led to a Crisis of Antibiotic-Resistant Disease

Nearly 25 million pounds of antibiotics are administered to livestock in the US every year for purposes other than treating disease, such as making the animals grow bigger faster.

Those antibiotics, and even worse, antibiotic-resistant bacteria, are transferred to you via meat and even through the animal manure that is used as crop fertilizer.

This is a much bigger issue than antibiotics simply being left behind in your meat; it’s a practice that is promoting the spread of antibiotic-resistant disease. According to Dr. Arjun Srinivasan, associate director of the US Centers for Disease Control and Prevention (CDC):2

"The more you use an antibiotic, the more you expose a bacteria to an antibiotic, the greater the likelihood that resistance to that antibiotic is going to develop. So the more antibiotics we put into people, we put into the environment, we put into livestock, the more opportunities we create for these bacteria to become resistant."

Bacteria often share genes that make them resistant. In other words, the drug-resistant bacteria that contaminate your meat may pass on their resistant genes to other bacteria in your body, making you more likely to become sick.

Drug-resistant bacteria also accumulate in manure that is spread on fields and enters waterways, allowing the drug-resistant bacteria to spread far and wide and ultimately back up the food chain to us. Now, we’re facing a crisis.

Antibiotic-resistant bacteria infect 2 million Americans every year, causing at least 23,000 deaths.3 Worse still, a report commissioned by UK Prime Minister David Cameron estimates that by 2050 antibiotic resistance will have killed 300 million people, with the annual global death toll reaching 10 million.4

And according to the CDC, 22 percent of antibiotic-resistant illness in humans is in fact linked to food,5 but a more accurate statement might be linked to food from CAFOs.

Low-Dose Antibiotics May Decimate Your Gut Health

Antibiotics are well known to disturb the microflora in your gut, and many studies make it clear that your gut health is pivotal in your ability to be healthy and avoid disease. When it comes to your mental health, your behavior and even your mood, we tend to think that the brain is in charge. In reality, your gut may be calling the shots.

In addition to the brain in your head, embedded in the wall of your gut is your enteric nervous system (ENS), which works both independently of and in conjunction with the brain in your head.

Your ENS contains 500 million neurons and is thought to be largely responsible for your “gut instincts,” responding to environmental threats and sending information to your brain that affects your well-being.

This communication between your “two brains” runs both ways and is the pathway for how foods affect your mood. For example, fatty foods make you feel good because fatty acids are detected by cell receptors in the lining of your gut, which then send warm and fuzzy nerve signals to your brain.

However, this gut-brain connection is far more than just comfort food or butterflies in your stomach. According to Scientific American:6

“The gut-brain axis seems to be bidirectional—the brain acts on gastrointestinal and immune functions that help to shape the gut's microbial makeup, and gut microbes make neuroactive compounds, including neurotransmitters and metabolites that also act on the brain.

These interactions could occur in various ways: microbial compounds communicate via the vagus nerve, which connects the brain and the digestive tract, and microbially derived metabolites interact with the immune system, which maintains its own communication with the brain.”

Are Antibiotics in Your Meat Messing with Your Mental Health?

The composition of your microbiome is somewhat like a fingerprint. It’s unique to you but, unlike your fingerprints, highly impressionable and constantly changing. As reported by Scientific American:7

The ecology of the gut microbiome may trigger or contribute to a variety of diseases, including autoimmune disorders and obesity, research suggests. Factors such as early environment, diet, and antibiotic exposure have a lot to do with why people differ from one another in the composition of their microbiomes.”

Unhealthy gut flora can have a detrimental impact your brain health, leading to issues like anxiety and depression. For instance, women who regularly ate yogurt containing beneficial bacteria had improved brain function compared to those who did not consume probiotics.8 Specifically, they had decreased activity in two brain regions that control central processing of emotion and sensation:

  • The insular cortex (insula), which plays a role in functions typically linked to emotion (including perception, motor control, self-awareness, cognitive functioning, and interpersonal experience) and the regulation of your body's homeostasis
  • The somatosensory cortex, which plays a role in your body's ability to interpret a wide variety of sensations

CAFO Animals Eat Genetically Engineered Feed That May Also Harm Your Gut Health

It’s worth noting that most CAFO animals are fed genetically engineered (GE) feed, like corn and soy. These crops are heavily treated with herbicides like Roundup, the active ingredient of which is glyphosate. Glyphosate is also patented as an antibiotic—and a very effective one at that— against a large number of beneficial organisms.

Unfortunately, like all antibiotics, it also kills vitally important beneficial soil bacteria and human gut bacteria. This is yet one more way that eating CAFO foods may harm your gut, your mental health, and your physical health. Dr. Don Huber explained:

“Lactobacillus, Bifidobacterium, Enterococcus faecalis—these are organisms that keep you healthy either by providing accessibility to the minerals in your food or producing many of the vitamins that you need for life. They’re also the natural biological defenses to keep Clostridium, Salmonella, and E. coli from developing in your system.”

When you take the good bacteria out, then the bad bacteria fill that void, because there aren’t any voids in nature. We have all of these gut-related problems, whether it’s autism, leaky gut, C. difficile diarrhea, gluten intolerance, or any of the other problems. All of these diseases are an expression of disruption of that intestinal microflora that keeps you healthy.”

The Antibiotics May No Longer Be Working to Make Animals Bigger

In other parts of the world, such as the European Union, adding antibiotics to animal feed to accelerate growth has been banned for years. The US Food and Drug Administration (FDA) has been aware of the problem for more than a decade. However, in 2013 they merely asked drug companies to voluntarily restrict the use of antibiotics that are important in human medicine by excluding growth promotion in animals as a listed use on the drug label. This would prevent farmers from legally using antibiotics such as tetracyclines, penicillins, and azithromycin for growth promotion purposes.  But it’s only a voluntary request. This is akin to letting the fox guard the henhouse, not a very astute or wise strategy to say the least.

Many meat producers have continued to use antibiotics for growth-promotion purposes, which is all the more reckless because some research suggests they’re not even doing this anymore. Past research suggested that antibiotics in animal feed improved the daily weight gain in young pigs by an average of 16 percent and the feed efficiency by 7 percent. However, studies conducted in 2000 and later suggest antibiotics increased average daily weight by just 0.5 percent and feed efficiency by 1 percent.9 As noted in Choices Magazine:10

“The growth response to antibiotics may have decreased over the past 30 years for several possible reasons. First, the growth response to antibiotics is less important when animal nutrition, hygiene, genetics, and health are optimal. The relative improvement in the growth rate resulting from supplementing the diet of pigs with antibiotics has been shown to be inversely related to the growth rate of animals not being fed antibiotics. With changes in the livestock industry over the past 30 years, all of these factors have improved. Second, increasing levels of resistance in animals could be diminishing the overall effectiveness of AGPs, although data are lacking to evaluate this hypothesis.”

Illegal Drugs in Your CAFO Milk

Antibiotics and other drugs are commonly given to dairy cows raised on CAFOs as well. Milk is tested for up to six commonly used drugs, such as penicillin, and if excess levels are found the milk cannot be sold. However, not all drugs given to animals are tested for, and there has been concern that illegal drugs might be showing up in milk too. In a new report released by the US Food and Drug Administration (FDA), samples of milk from 2,000 dairy farms were tested for 31 different drugs.11

About half of the farms were targeted because they had sent cows to slaughter that had drug residues in their meat (with the implication being that they probably had drug residues in milk as well). It turned out that 1 percent of the targeted samples, and 0.4 percent of the randomly collected samples, contained drug residues.12 Six different drugs were found in the milk samples, none of which are approved for use in lactating dairy cows. According to NPR:13

Because the survey was carried out for research purposes, the samples were collected anonymously, and the FDA cannot send investigators to the farms to find out what happened. Mike Apley, a researcher at Kansas State University's College of Veterinary Medicine, says that it is ‘totally illegal’ for dairy farmers to use two of the drugs that the FDA detected: Ciproflaxacin and Sulfamethazine.

In the case of other drugs, he says, the situation is more complicated. It's illegal for farmers to use those drugs on their own, but veterinarians are allowed to authorize their use in dairy cows under certain strict conditions. Veterinarians also are supposed to ensure that no residues enter the food supply. For whatever reason, that veterinary safeguard didn't work in these cases.”

Bird Flu Found in Arkansas Turkeys

Earlier this month, the USDA confirmed a highly pathogenic avian influenza virus was found in a flock of more than 40,000 turkeys in Arkansas.14 The animals will be culled to prevent the spread of infection. Although avian flu doesn't spread easily among humans, its capability to mutate has scientists worrying whether it could mutate enough to cause a human pandemic. CAFOs serve as the ideal place for this to happen, as there are millions, if not billions, of host birds among which the virus can flourish.

In the Netherlands, animal health authorities also recently discovered bird flu in samples taken from wild ducks.15 Chicken farms are suspected as the source of the disease and, so far, 300,000 birds at four CAFO locations were culled to ensure the infection doesn’t spread. There is already evidence of antibiotic-resistant superbugs “jumping” from farm animals to people. For instance, two human cases of infection with the antibiotic-resistant superbug MRSA were linked to livestock in Denmark.16

As reported by Mother Jones:17

The Danish study comes on the heels a 2012 paper by a consortium of US and European researchers, which used gene sequencing to show that another common strain of MRSA originated in humans as a common staph infection, jumped to livestock, where it evolved resistance to the common antibiotics tetracycline and methicillin, and then jumped back to humans. Of course, you can also contract antibiotic-resistant pathogens through contact with raw meat—as, for example, more than 100 people did when the agribusiness giant Cargill sent out tens of millions of pounds of ground turkey tainted with antibiotic-resistant salmonella in 2011.”

Costco Joins the Fight for Antibiotic-Free Chicken

Wholesale club Costco sells 80 million rotisserie chickens a year, so when they ask for change, suppliers and even regulators listen. The company has been involved in an ongoing push to end the use of human antibiotics in chicken and other livestock. The company has been working with the FDA and the CDC to help eliminate the use of so-called shared-use antibiotics (those used for both humans and livestock). Craig Wilson, vice president of food safety at the Issaquah, Washington-based Costco, told Reuters:18

We are working towards, and working with our suppliers and the regulatory agencies... to see how we can get rid of shared-use antibiotics in animals… I think all of us want to move to a point where we can get the human-use antibiotics out of the system. It's going to take time."

No target date has been set to reach this goal, but the company is the latest in a number of big-name corporations taking aim at agricultural antibiotics. For instance, McDonald’s recently announced they will only buy chicken raised without antibiotics important to human medicine, a change they plan to phase in over the next two years. Others in the industry who already offer antibiotic-free meat and poultry (or have committed to it) include Chipotle, Panera Bread, and Shake Shack. Chik-fil-A, which is actually the largest chicken buyer in the US, also announced last year that they would stop buying chicken raised with any antibiotics.

Additionally, late last year, six of the largest school districts in the US decided to switch to antibiotic-free chicken in their cafeterias, which is a major victory for schoolchildren and will put pressure on meat companies like Tyson, Perdue, and Pilgrim's Pride to adjust their production practices. Fast-food chain Carl's Jr. even recently rolled out a burger made with grass-fed, free-range beef, promising to be free of antibiotics, steroids, and hormones.19

It’s Time to Demand More from Your Meat (and Dairy and Eggs)…

Consumer demand is driving change to get antibiotics and other drugs out of the food supply. Toward that end, has organized a campaign, calling for Trader Joe's to exclusively source its meat from animals raised without antibiotics. You can sign the petition here. You can also download and print out a flyer and take it with you the next time you visit your local Trader Joe's store.

Finally, when shopping for truly healthy meat, that from CAFOs is not the best choice. Organic, grass-fed and finished meat, raised without antibiotics and other growth-promoting drugs is really the only type of meat that is healthy to eat, in my view.  This you will find at farmers' markets, family farms, food coops, and certain forward-thinking grocery chains and health food stores. When shopping, keep the following labels in mind to help you find truly high-quality meat:20

100% USDA Organic label offers excellent assurance that antibiotics have not been used at any stage of production.
"No antibiotics administered" and similar labels also offer high assurance that antibiotics have not been used, especially if accompanied by a "USDA process Verified" shield.
"Grass-fed" label coupled with USDA Organic label means no antibiotics have been used, but if the "grass-fed" label appears alone, antibiotics may have been given.
"American Grass-fed" and "Food Alliance Grass-fed" labels indicate that in addition to having been raised on grass, the animal in question received no antibiotics.
The following three labels: "Antibiotic-free," "No antibiotic residues," and "No antibiotic growth promotants," have not been approved by the USDA and may be misleading if not outright fraudulent.
"Natural" or "All-Natural" is completely meaningless and has no bearing on whether or not the animal was raised according to organic principles. "Natural" meat and poultry products can by law receive antibiotics, hormones, and genetically engineered grains, and can be raised in confined animal feeding operations (CAFOs).


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