The Microbiome and the Gut-Brain Connection (Part 3)


In this final part of the Gut-Brain connection, I wanted to cover a topic concerning the blatant over use of spraying poisonous synthetic Pesticide chemicals on our food crops as you read through the article you will appreciate that this practice is another way of damaging the delicate balance of our bacterial ecosystem leading to the malfunction of our Gut-Brain connection. 

The most popular pesticide product has to date been ‘Roundup’ ready whose active ingredient is Glyphosate manufactured by Monsanto. Various studys have been completed on this product to ascertain if there is any evidence of damage to our health when consuming food that has been sprayed with this pesticide.

Monsanto, once an exclusive chemicals manufacturer who developed Agent Orange a herbicide and defoliant, causing 3 million Vietnamese and American combatants to suffer various illnesses including Leukemia and Hodgkinson;s lymphoma and damaging some 3 million hectares of forest, rebirthed itself into Biotech company producing genetically modified organisms specifically food crops known as GMOs. 

Corn, soy, beets become some of their GMO flagship products. The purpose of such products were touted to be pesticide resistant, whole crops were heavily sprayed with Monsanto’s pesticide ‘Roundup’ while everything around the crops died the GMO crops remained intact.  However, being a synthetic chemical and a registered antibiotic is was discovered that the GMO crops themselves became insecticides which were damaging the health of those who consumed these crops.

In this article we will explain the science behind GMO development and discuss how our Microbiome is damaged from such organisms.


The topic of GMO’s (Genetically modified organisms) is a forest fire still ablaze.  Both sides of the safety (for consumption) debate ravages the natural news wires, advocates for and against ‘duking’ it out with a myriad of arguments.  The pro-gmo movement professing that what the biotech companies have done is no different than what nature does.  

Stanley Cohen geneticist of Stanford University co-inventor of recombinant DNA (rDNA) technology (combining DNA from 2 different species, essentially the heart of genetic modification) said in Sept 1977:

“Compelling evidence that recombinant DNA molecules constructed in the laboratory simply represent selected instances
of a process that occurs by natural means,”


“Scientists can only duplicate what nature can already do.”  

Even at this time the issue of safety toward GMO was a concern and that Senator Edward Kennedy called for regulation by presidential commission which was eventually withdrawn due to overwhelming pressure from the scientific community that recombinant DNA was safe.

Erwin Chargraff, the biochemist wrote in Science,

“Bioengineering was warfare against nature.”

Jonathan King, professor at MIT alleged that deregulation of genetic modification was

“To protect geneticists not the public.”

Harvard biology professor, George Wald warned that rDNA technology,

“entails problems unprecedented not only in the history of science, but of life on earth, and to go ahead in this direction may not only be unwise, but dangerous.”

By 1979 the issue of safety vaporised in the wind so biotech had won the issue of regulation.

Does this sound familiar?  

(The 2008 financial meltdown: toxic assets, Glass-steagall regulation act, rescinded from its introduction to protect investors from a repeat of the 1927 stock market collapse).  

Anyway scientists were using E.Coli K12 strain for DNA insertion, that was originally cultured in the lab in 1922 from a Diphtheria patient and had been used for many years and declared harmless now.  As Steven Druker states in his book ‘Altered genes, Twisted Truth,’ “this was more of an example of Molecular Politics as opposed to molecular Science.”

In nature the transfer of genetic information occurs through natural reproductive processes either by pollination within plants or insemination within animals.  

However nature has distinct boundaries in terms of cross pollination and cross insemination in terms of species.

The process of transgenesis (the process behind genetic modification) can occur naturally. For example, biologists have found the sweet potato contains genes that have been inserted by a bacterial species Agrobacterium (a plant pathogen).

As a result the foreign DNA can interfere with a few plant hormones causing plant cells to proliferate forming tumor like growths, but the plant now produces 2 hormones to improve consumption.

This microbial DNA insertion was done an estimated 8,000 years ago and affects around 291 sweet potato varieties found in the US,Indonesia,South America and Africa.

However, this knowledge did not allay the fears of the anti-GMO camp, since they were also concerned about the heavy use of pesticide used on GMO crops, namely Glyphosate (tradename ‘Roundup’), and that Biotech companies have made seeds intellectual property (disallowing farmers who grow GMO crops to reuse the seeds and thus forcing them under the penalty of legislation to buy new seeds every year).  

Transgenesis between same species is naturally acceptable i.e cross breeding 2 different type of tomatoes. However, to insert a gene that protects an arctic flounder from freezing, into a sugar beet, allowing the tomato to be grown in harsh winter conditions crosses the boundaries of nature.  But this product, including the Fish-tomato was never commercially produced.  The original ‘flavr savr’ tomato failed since the genetic modification to adjust the ripening time, destroyed the integrity of the skin, so when the tomatoes were harvested the equipment turned the tomatoes into tomato puree.

Similarly to reduce pulping costs, the paper/pulp industry were looking at genetically modifying trees to reduce the lignin fibres, thus reducing the chemicals required to remove them during the pulping process.  However, by doing this the structural integrity of the trunk was in question, and the tree would risk collapsing 

‘If you mess with nature, you’re messing with the best.’

Why is Genetic Modification a Bad Idea?

One of various concerns of the anti-GMO establishment was, genetically modifying crops could introduce unknown toxins or allergenic properties.  

As you may know (or remember from previous articles) in cellular biology DNA strands contain nucleotides, and genes are made up of 3 nucleotide sequences:

  1. Coding regions that code for a specific protein sequence thus expressing the gene (these regions are called EXONS),
  2. Non coding regions used for epigenetic switching (called INTRONS)
  3. Regulatory regions that specify where the protein is made and how much is produced, this region also contains ‘Enhancers’ that turn the gene on for expression and to interact with RNA transcription, and ‘Promoters’ that allows transcription to occur.

The codon pairs (note : alphabetical letters A,T,G,C form biological codes called codons used to express specific amino acids i.e AGC is the code for Serine amino acid) are used differently between bacterial DNA and plant DNA, so there exists another incompatibility, specifically, the promoting aspect of gene expression.

Under normal circumstances this promoter protein which is essentially an on/off switch is activated by specific chemical signals e.g in a plant, one of the promoter proteins expresses a toxin to ward off or kill insects as a plant defensive mechanism.  

However, within the genetic modification process the ‘native promoter’ will cease to function under these foreign conditions so scientists have to replace it with another promoter, which is generally derived from a virus that infects the target organism keeping the promoter permanently in the ‘on’ state.

This means that excessive proteins are produced, known as ‘inclusion bodies’, that bio-scientists probably today have found a way to reduce, but if not, there is still a risk, with the promoter permanent on, excessive plant toxins will inevitably be produced. 

This was the case when the L-tryptophan supplement made by Showa Denko was released on the market disabling some 1500 people because the promoter that was permanently enabled produced excessive amounts of tryptophan that reached toxic levels causing Eosinophilia myalgia, creating abnormal levels of eosinophils (white blood immune cells used to fight parasites) and chronic muscle pain.

While the biotech industry were in discussions with government representatives, explaining the benefits to mankind that GMO technology provided to the food chain, and the precision that was involved to make this technology a reality, behind the scenes it was another story.

It was not the envisaged high tech laboratory manned with brilliant dedicated scientists designing this technology with precision, mimicking natural processes, but a Wild west show where genetic material was inserted using a BB gun or a 22 revolver firing a blank round at a buffer padded Petri dish hoping that some of the material would penetrate.

As Mae Wan Ho a geneticist from Hong Kong argued, genetic modification is designed to overcome natural barriers between species. Potentially, resulting in the failure of our natural enzymatic process when these foods are consumed, leading to a negative bacterial relationship between our own gut flora and the viruses and bacterias used in the GM process.

As she points out, its not easy to get a foreign gene to work in a cell which is why you need the aggressive ‘Gene switch’, the Promoter, as mentioned in the previous paragraph, which tells the cell “copy this gene and make a lot of protein and express the gene at a high level.

If this viral promoter gets into a mammalian cell (which is possible since it is of viral origin) it could make the cell multiply out of control which can lead to cancer.  

Genetic therapy, an experimental option to allopathic drugs, and surgery to treat genetic mutations follows the same techniques as genetic modification in plants and animals.  

If the transplanted cell gets into the wrong place within a DNA sequence it could express the wrong genes and cancer could erupt.

In addition, if the transplanted cell that uses a ‘gene carrier’ ( Vector ), which, itself is a virus (a disarmed virus), it conceivably could rearm itself by DNA injection into other cells and recombine (recombinant).

It must be said that development of more precise methods of  GM gene insertion exists, for example ‘Nucleases’ or ‘Genome Scissors’ (one example is referred to as TALENS – Transcription Activator-Like-Effector Nucleases ) that provide the ability to splice DNA and insert new DNA  fragments anywhere on the chromosome with efficient precision.

A few years ago French scientists genetically modified bone marrow cells outside of a patient and then reinserted the transformed ‘good ‘ cells back into the patient.

 It was deemed a great success until 2 of the 9 patients developed Leukemia 2 years later.  

The bio-scientists. Biotech industry and the pro-gmo advocates, proclaim that people ( who are unaware that GM substances are contained in hundreds of processed and fast food products ) have been consuming GM products since 1994 and nobody has died yet, so they must be safe.  

However, given the small quantities consumed, toxins if they exist, will take their time to bio-accumulate in the body and possibly cause people to become sick over decades and possibly advance the ageing process.

The most prominent litigation associated with GMOs was filed in May 1998 by Steven Druker a public interest attorney exposing the alleged ‘cover-up’ of the warnings of its own scientists pertaining to the risks of GMOs, lied about the facts and allowed these products into the national food chain without suitable safety measures.

However, the final ruling on the case was in favor of the FDA refuting the claims set out in the case which were that the FDA was not regulating GE foods, the FDA’s political appointees ignored the advice and warnings of the agency’s scientific staff, and that significant agreements existed among scientific experts regarding the safety of GE foods.

In conclusion it is irresponsible to make statements like :

“Monsanto should not have to vouch for the safety of biotech food.”

-Philip Angell Monsanto

But the EPA (Regulators of Glyphosate Herbicide) state :

The burden of generating the data to support a pesticide registration rests with the company.”

It would be beneficial if standards and regulations with respect to safety were standardised for both the GM crops and the herbicide sprayed on those crops because ultimately both products are ingested simultaneously.

The Herbicide Glyphosate

When genetic engineering was gaining acceptance, one its major ‘selling point’ was that it would increase yield and survive insects and pests invasion.  

This was the reason to genetically modify the plant in the first place; that is, it would survive while everything on and around the crop would perish when sprayed with the Bio-techs herbicide of choice, Glyphosate (the active ingredient of the trade name ‘Roundup’).  It is common knowledge that all herbicides, pesticides etc are poisonous ( DDT is a good example ), but Glyphosate is a unique poison since it has 3 patents, as a Herbicide, as a Chelator ( chemically binds with other substances ), and an Antibiotic.

According to Stephanie Seneff  a MIT research scientist who has done extensive research into GMOs and Glyphosate claims that Glyphosate is partially attributable to some of the diseases that have reached epidemic proportions including Autism, and Celiac disease.

Let us step back a moment, Glyphosate and all herbicides are designed to kill plants, and in general the toxicity of most herbicides is low, since plants are Autotrophic (organisms that produce their own nutrients from water and photosynthesis from light), but humans are Heterotrophic ( organisms that ingest nutrients from what they eat ). Glyphosate inhibits the production of 3 amino acids within the plant by blocking the enzyme that produce them. Since the original glyphosate patent expired in 2000 more than one company produce this chemical which has been subjected to hundreds of tests over its 40 year lifespan.

It may also be prudent to point out that researchers at Cornell analyzed toxicology tests in 1996 and concluded that glyphosate is practically non toxic by ingestion and is unlikely to be carcinogenic in humans nor cause birth defects, however, it is the chemical additives such as ‘adjuvants’ to increase its effect and ‘surfactants’ that act as foaming agents to increase penetration of the plant which may enhance toxicity.

The EPA ( the regulatory agency responsible for this herbicide’S regulation) originally stipulated an acceptable daily intake of glyphosate was 0.10mg/kg of body weight (so for a 180 kg human this would equate to 18 mg/day ). Given the maximum residue contribution it was calculated to be 1.39mg/day for a 1.5kg daily diet, so how can this low level be harmful ?.

Is Glyphosate Safe or Dangerous?

Some scientists are convinced that Glyphosate creates gut dysbiosis since this chemical destroys lactobacillus and Bifidobacteria that produce folate and cobalamin ( used in conjunction with Cobalt to produce Vitamin B12 ) which are both required for the bodies methylation cycle.  Since Glyphosate is a chelator it hijacks cobalt, iron,and molybdenum as well as causing iron deficiency, and B12 deficiency.

In animal studies, pathogenic bacterial strains Salmonella and Clostridium were found to be resistant to Glyphosate, but benefical strains such as Enterococcus, Bacillus and Lactobacillus ( as mentioned in the previous paragraph) were subsceptible thus promoting a gut bacterial imbalance.

Furthermore, the discovery of increased short chain fatty acids and Ammonia found the gut of autistic children suggests that an overgrowth of anaerobic bacteria such as Clostridia, Bacteriodes and Desulfovibrio, since these are common by products from anaerobic fermentation, while other by products from the same process include phenols, amines, ammonia and hydrogen sulphide are all toxic to the bowel.

Pseudomonas spp, a commensal pathogenic strain and an antibiotic resistant Bacterium actually breaks down glyphosate producing phosphate and carbon for amino acid synthesis, however the by product from this synthesis of Formaldehyde a known neurotoxin.

In addition, Phytates, found in grains and vegetables is broken down by  Phytase, an enzyme manufactured by lactobacillus and Bifidobacteria, so if they are destroyed, Phytate metabolism cannot occur and the undigested form of phytate can bind to vital nutrients making them inaccessible to the body.

Sulfite oxidase is a homodimeric ( meaning 2 molecules are needed ) protein located in the mitochondria of a cell.  

This enzyme which is made from a heme (iron) source and a molybdopterin ( molybdenum ) source, is used to catalyze the oxidation of sulfite to sulfate.

Sulfate is crucial for many regions of the body ( e.g the production of 7-Dehydrocholesterol to Cholecalciferol ( Vitamin D3 Sulfate  in the skin from sun exposure, Glutathione production, Heparan sulfate, a proteoglycan used in cells etc).  If Glyphosate chelates ( binds) iron and molybdenum then this important conversion from sulfite to sulfate fails which could lead to sulphate deficiency .

Other claims involve glyphosate’s inhibition of Cytochrome P450 enzymes. These hemoproteins are found in most cells of the body, most tissues of the body and in the liver.

They are responsible for metabolizing thousands of endogenous and exogenous chemicals (i.e  drugs), hormone synthesis, and to metabolise toxins.

Within the liver they activate Vitamin D, bile acid production and assist in detoxification, ridding the body of toxins and xenobiotics (drugs). They are basically the ‘efficient ‘cleanup crew or janitors’ of the body.

Since glyphosate blocks the production of 3 aromatic amino acids Phenylalanine, Tyrosine, and Tryptophan by blocking the ‘Shikimate’ chemical pathway in plants in order to destroy the plant, it is hypothesised that it will do the same within the human body, by blocking the same pathway that our bacteria use to produce these same amino acids.

In doing so it would inhibit the manufacture of key neurological hormones like Serotonin (made from Tryptophan), Melatonin and  Tyrosine (used to produce essential thyroid hormones).  

It is well known that brain starvation of Serotonin leads to various cognitive disorders including depression and behavioral problems, but a physiological side effect is in the bowel.  

Since serotonin is responsible for bowel movement, a deficiency would lead to constipation, but once the body receives tryptophan from dietary sources like wheat or bananas, the body will immediately overproduce serotonin causing diarrhea; the body’s intelligent decision to accomplish a critical function of elimination at the expense of the hosts discomfort.

Dan:   “Mr Hardy, your company contracts over 5000 broiler farms across the country”, How long do your chickens take to reach market weight?”

Hardy: On average 16, 17 weeks “

Dan:   “Clonestra is developing genetic technology that can cause rapid muscle growth in broiler chickens, our chickens can reach market weight in 5 weeks.

Hardy:“What is that, some kind of divine intervention?”

Dan:   “Genetic modification is nothing new, we have been breeding plants for a millennia, where do you think broccoli, cauliflower, and cabbage come from? It all comes from a wild mustard plant that humans have crossbred from traditional genetic mutation.  Our modern methods are just more precise”.

Paul:   “All you need to understand are 3 things, efficiency, better production, more precision”.

Quote from the movie ‘Consumed’ 2015

Check out the Previous Article in this series:

Microbiome and Digestion

Microbiome and Disease Part 1

Microbiome and Disease Part 2

Microbiome and the Immune system

Microbiome and the Gut-Brain Connection Part 1

Microbiome and the Gut-Brain Connection Part 2


  1. ‘Altered genes,Twisted truth’ (Book 2015)Steven Druker
  2. ‘Minerals for the genetic code’ (Book 2013) Charles Water, Dr Olree
  3. Science Daily ‘How gut bacteria communicate with our bodies to build special relationships (Article Norwich science institute )
  4. Sulfite oxidase (NCBI 2017 Summary )
  5. ‘The Blood brain barrier’ ( Wikipeadia)
  6. ‘Pericyte,Astrocyte and Basal Lamina association’ (the Davis Lab –University of Arizona)
  7. ‘Glyphosate’s Suppression of Cytochrome P450 Enzymes and Amino Acid Biosynthesis by the Gut Microbiome: Pathways to Modern Diseases’ (Article Stephanie Seneff, Anthony Samsel 2013)
  8. ‘Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders’  (NCBI 2015) J.Kelly, P.Kennedy, J.Cryan, T.Dinan, G.Clark, N.Hyland
  9. ‘The great glyphosate debate’ 2012 article Northern Woodlands website Dave Mance
  10. ‘GMO Myths and Truths’   Earthopensource 2014 J,Fagan, M.Antoniou, C.Robinson
  11. Mental Health may depend on creatures in your gut (article 2015)  Charles Schmidt  Glyphosate Toxicity’ Stephanie Seneff transcript Bulletproof 2016

Author: Eric Malouin