Fighting Microbes with Microbes

Story at-a-glance

  • Microflora in soil influences plant health, helping to provide nutrients and suppress disease; there are more than 30,000 varieties of microbes in soil
  • In humans, antibiotics are often overprescribed, killing off beneficial bacteria and promoting the formation of antibiotic-resistant ”super germs”; in plants, pesticides, herbicides, fungicides and other chemicals also kill off both good and bad microbial communities, prompting a similar reaction
  • Plants, like humans, can harness the power of beneficial microbes to help ward off disease, and those benefits are passed on to future generations
  • Researchers recently revealed that breast milk contains more than 700 species of bacteria (more than previously thought), further confirming the important role of microbes for health

You’re probably aware that your body is teeming with bacteria, fungi, viruses and other microbes that together make up your microbial inner ecosystem, or microflora.

Your body actually contains about 100 trillion cells, but amazingly only one in 10 is “human.” The others are made up of bacteria and other microorganisms. What may also surprise you is that soil has a microflora of its own, sharing many similarities with the microflora in the human body.

Soil Contains More Than 30,000 Varieties of Microbes…

For comparison, the human body contains about 10,000 different bacterial species. And just as in humans, the microflora in soil influences plant health, helping to provide nutrients and suppress disease, these microorganisms are also susceptible to agricultural chemicals to which they’re so widely exposed.

In humans, antibiotics are often overprescribed, killing off beneficial bacteria and promoting the formation of antibiotic-resistant “super germs.” In plants, pesticides, herbicides, fungicides and other chemicals also kill off both good and pathogenic microbial communities, prompting a similar reaction. As reported in The Scientist:1

“Although the medical community now warns that overprescribing antibiotics kills beneficial organisms and encourages the formation of resistant strains, a similar change in opinion has not occurred in agriculture, where a kill-all approach to plant pathogens has given rise to biocides that indiscriminately wipe out the beneficial along with the pathogenic.

‘Biocides can nuke the soil, but they never kill everything,’ says Mike Cohen, a biologist at Sonoma State University in California. ‘This creates a biological vacuum that becomes filled by opportunistic survivors and organisms from the surrounding soil.’

Biocides create a strong selective pressure: the few pathogens that survive face little competition and proliferate, giving rise to pathogenic communities that can evade standard treatments.”

Microbes Could Help Reduce the Need for Agricultural Chemicals

Soil is very much “alive,” and the microbes it contains create a powerful synergy with the plants, recycling organic material, making the soil more resilient and better at holding water and nutrients, and nurturing plants more effectively.

Microbes need carbon for food, and we’re depleting our soil of this element by using chemical fertilizers, overgrazing, over-plowing, and burning stubble in fields to accelerate crop turnover. Add to this genetically engineered (GE) crops, and our soil is under a constant assault.

According to Dr. Don Huber, an expert in an area of science that relates to the toxicity of GE foods, glyphosate, the active ingredient in the herbicide Roundup, which is widely used on GE crops, is one of the biggest threats.

About 20 percent of the glyphosate migrates out of the plant’s roots and into the surrounding soil. Once in the soil, the glyphosate kills beneficial soil microorganisms in the same way it kills weeds, because they have the same critical metabolic pathway.

The important point we must all understand is that once you destroy the beneficial microbes in the soil, you’ve destroyed the food grown in it, because the quality of the food is almost always related to the quality of the soil, which depends on a healthy balance of microorganisms.

The solution, of course, is to stop assaulting our soil with chemicals that are killing off its microorganisms, and one of the best ways to do this is by utilizing the microbes themselves. As in the human gut, beneficial microorganisms in the soil can help keep disease-causing varieties at bay.

For instance, one study found that plants can communicate with each other underground, via underground common mycorrhizal networks (CMNs) that interconnect roots of multiple plants.2
Through this pathway, neighboring plants can ‘eavesdrop’ on defense signals coming from nearby plants that have been infected with a pathogen, allowing them increase their defenses and improve their resistance to the disease. This communication via the CMN was linked to the beneficial fungus Glomus mosseae.

“Bagged tomato plants grown in soil that lacked this underground network were unable to receive the ‘activate-defenses!’ signal from infected neighbors and did not produce disease-fighting compounds. In contrast, in soils containing Glomus mosseae, uninfected plants detected the warning signs of disease and produced higher levels of six defense-related enzymes,” The Scientist reported.

“…Because the mycorrhizal network can extend from one set of plant roots to another, it’s possible that the network of fungal mycelia acts like telephone wires, allowing the plants to communicate underground. If this hypothesis is proven by identifying compounds that relay the chemical signal through the fungi, it might be possible to prevent plant disease by cultivating an appropriate mix of microbes in the soil.”

Beneficial Microbes are Passed on to Future Plant Generations

Natural practices such as crop rotation, tillage and non-chemical fertilization are proving to be far superior in establishing healthy microbial communities in the soil than chemical treatments of any kind. And once that beneficial microflora is established it benefits not only the current plants but also the next generation, which can prosper from its predecessors’ heightened disease response.

For instance, the Bacillus subtilis bacteria colonizes soil around plant roots and produces an antimicrobial peptide that may help keep pathogens away when the plant is compromised.3 The next generation of plants also becomes better able to fight off disease if the parent plants were exposed to B. subilis, even if they were never exposed directly. Interestingly, plants are highly intelligent and can even secrete the necessary food sources to attract specific beneficial bacteria needed to help ward off a particular pathogenic invader.4

Over 700 Bacteria Identified in Breast Milk

If there were any ever doubt about the importance of microbes to living creatures, one need look no further than human breast milk, which researchers recently revealed contains more than 700 species of bacteria (more than previously thought).5 Just as soil microflora is easily influenced by environmental and other factors, the study also found that the composition of breast milk microflora is influenced by the mother’s weight, as well as her method of delivery.

Researchers noted:6

“Milk from obese mothers tended to contain a different and less diverse bacterial community compared with milk from normal-weight mothers. Milk samples from elective but not from nonelective mothers who underwent cesarean delivery contained a different bacterial community than did milk samples from individuals giving birth by vaginal delivery, suggesting that it is not the operation per se but rather the absence of physiological stress or hormonal signals that could influence the microbial transmission process to milk.”

We now know, of course, that breastfed babies develop entirely different gut flora compared to bottle-fed babies as well. Infant formula is not a healthy replacement to breast milk, for a number of reasons, as it cannot duplicate the diverse microbial species found in breast milk, and therefore leads to altered gut flora.

Breast milk, but not formula, appears to promote a healthy colonization of beneficial biofilms (these biofilms are essentially thin, sticky bacterial “sheaths” that adhere to your intestinal wall, where they serve as a shield, effectively blocking out pathogens and infectious agents).7 And previous research has already established that breast milk reduces diarrhea, flu, and respiratory infections in babies, as well as lowers their risk of developing allergies, type 1 diabetes, multiple sclerosis and other diseases, once again reaffirming the importance of nourishing and supporting your microbial communities.

Agricultural Antibiotic Use May be Linked to Urinary Tract Infections

It’s not only the soil that is being impacted by agricultural chemicals… animals are also exposed to such chemicals, including antibiotics. The United States uses nearly 30 million pounds of antibiotics annually in food production. Livestock antibiotic use accounts for 80 percent of the total antibiotics sold in the United States, and unnecessary use of antibiotics in food animals (cows, pigs, chickens, and turkeys) is a major driving force behind the rampant development of antibiotic-resistant bacteria.

Unfortunately, last year the U.S. Food and Drug Administration (FDA) reneged on its plan to withdrawal approval of penicillin and tetracycline antibiotics intended for use in food-producing animal feed – a measure it had been planning since 1977. The quiet withdrawal of their intent to ban low-dose antibiotics in animal feed means that the spread of antibiotic-resistant “super-germs” linked to this practice will continue unabated, although there may be a light at the end of the tunnel.

A federal judge ruled twice in 2012 that the FDA must reconsider petitions urging them to revoke approvals for all nontherapeutic uses of antibiotics in livestock production, but it remains to be seen whether any meaningful action will be taken.8

Meanwhile, a joint investigation by the Food & Environment Reporting Network and ABC News revealed that the rising number of antibiotic-resistant urinary tract infections may, in fact, be due to antibiotic-resistant E. coli bacteria from chickens.9 So again we’re seeing problems arising from antibiotics that are indiscriminately killing off both good and bad bacteria – just as fungicides and other chemicals do in the soil. And taking it full circle, research shows that frequent consumption of foods containing beneficial bacteria – including fermented foods such as kefir, sauerkraut and other fermented vegetables – can promote good urinary tract health.

Even Shrimp Are Being Raised on Antibiotics

When you think about agricultural antibiotic use, you probably think about cattle, pigs and chickens – not shrimp. But they, too, are being raised on factory-style farms, which includes often includes the excessive use of antibiotics. Japan even refused shipments of shrimp from Vietnam (the fifth largest shrimp importer to the United States) because of the significant amounts of antibiotics they contained.

In 2007, the FDA also banned several species of farmed seafood, including shrimp, from China because it contained unsafe drugs, including fluoroquinolone antibiotics and antimicrobials.10 Even to this day, the FDA has acknowledged that its oversight of unapproved drug residues in imported seafood is “limited.”11 As Wired reported:12

“…[Shrimp] represent the sort of antibiotic misuse that has consumers wary of antibiotic resistance and suspicious of beef, pork and chicken in the United States – and they may have been produced with even more antibiotics, and even less oversight, than we have here.”

If You Want to Help Protect Microbial Biodiversity in the Environment and in Your Own Gut…

On an environmental level, organic agricultural practices promote ideal soil conditions, while conventional farming methods threaten to completely deplete our soils worldwide, which will only worsen nutrition as time goes on. This is vital, since the continued destruction of our soils will ultimately lead to the demise of the entire food system.

In order to qualify as certified organic, a product must be grown and processed using organic farming methods that recycle resources and promote biodiversity. Crops must be grown without synthetic pesticides, bioengineered genes, petroleum-based fertilizers, or sewage sludge-based fertilizers. Eating organically and supporting farms whose practices are sustainable is currently one of the best ways to protect your health, the environment and the very future of our food supply.

On an individual level, the advent of processed foods dramatically altered the human diet, and we’re now reaping the results in the form of rapidly rising chronic health problems. I believe the shunning of traditionally fermented foods has a lot to do with this. Cultured or fermented foods have a very long history in virtually all native diets and have always been highly prized for their health benefits.

The culturing process produces beneficial microbes that are extremely important for your health as they help balance your intestinal flora and produce a wide range of metabolic byproducts that benefit our health, e.g. lipoic acid, beta glucans, infection-killing bacteriocins, etc. If you do not regularly consume traditionally fermented foods, a high-quality probiotic supplement will provide similar benefits.

Along with eating naturally fermented foods and/or taking a high-quality supplement, it’s essential that you avoid sugar, including fructose. Sugar feeds the growth of pathogenic bacteria, yeast, and fungi in your gut, which may actually harm you more than its adverse impact on insulin resistance. One of the major results of eating a healthy diet like the one described in my nutrition plan is that you cause your beneficial gut bacteria to flourish, and they secondarily perform the real “magic” of restoring your health.

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