Photo by Martin Michener

by Martin Michener, PhD
Health Impact News

Healthy Gut Flora: Key to Health

Americans are beginning to realize that our gut flora is extremely important to our health, both daily and for the long term. But most folks have little idea about how to ensure the balance of their natural digestive environment.

The flora (or microbiome) has been recently found to have very complex signaling connections to our brain, and small imbalances as to exactly which bacteria are flourishing can readily shift our mood and thinking [1]. We rely on these organisms, mostly bacteria, which outnumber our own cells about ten to one, not only for the proper sequential passage of every meal, but for the absorption of our food, and for providing the many vitamins they create which are essential to our maintenance. We read daily of antibiotic-resistant overgrowth of the wrong creatures (dysbiosis), such as “C. diff” (Clostridium difficle) outbreaks in hospitals and nursing facilities, yet medical doctors are almost completely ignorant of the true causes and how to deal with each case.

Humans are designed and built as omnivores, able to eat a wide range of food materials. We lack the specialized digestive structures of herbivores. Our system more nearly resembles that of an efficient meat-eater (carnivore) [2]. Herbivores usually have long digestive systems, well adapted to extracting nutrients from plant materials with lower nutrient densities.

Cattle and bison (ruminant herbivores) have the most extremely modified systems, including their rumen, a huge basin where in the absence of oxygen specialized microbes breakdown roughage (leaves, stems, grass) into digestible nutrients. Very few animals are able to do this, and ruminants critically depend on their microbiome balance even more than we humans do.

Previously, for most of us, the culture of bovine husbandry for meat or for dairy has held very little interest, except at the dining table. But we are not alone at having gut troubles in this age of pesticides.

Modern Bovine Gut Problems

During the last decade, even well-cared-for pastured cattle have developed serious acute digestive problems, seemingly at random. Symptoms include apathy, severe indigestion, wasting and weight loss. All too often, the result is fatal. But even the minor cases may adversely affect a cow’s dairy or meat production, and the veterinarians have been unable to pin down the causes.

The symptoms closely match those of botulism poisoning, but the diagnosis is far from simple. In several publications authors have called this “visceral botulism,” but this bacterial toxin is so powerful that a mammal can die from tiny amounts so small that they are chemically untraceable [3].

Because of the timing, many experts suspected this epidemic to be one more of the health impacts from the active ingredient in the world’s best selling unregulated pesticide Roundup: glyphosate (N-methyl phosphonyl glycine).


Study: Glyphosate Affects Microbiota in Ruminants

A team of German veterinarians and microbiologists from U. Leipzig, Saxony published a fascinating study detailing several experiments with ruminant gut diseases [4].

In short, they transferred samples of the rumen contents plus specific diets into warm reaction chambers where this “cud” was cultured for two days. They then analyzed what microbes remained after different treatments. They wanted to establish dosage cause-and-effect by adding glyphosate in ways we never could with human digestion. The rumen and its in vitro mechanical incubator “Daisy” would thus make possible the comparison of the world’s most critically adapted microbiome under the stress of an added herbicide. In a second series, they also added to some samples the microbe which produces the notorious toxin, “botox” or BoNT.

The Danger of Botulism

Botulism is a disease that is surely one of the most bizarre stories of poisoning in all biology.

The bacterium is called Clostridium botulinum, although it represents three or four distinct strains and about seven different toxin versions as well. While the toxin is rare, the germs are not: their inactive spores reside commonly in most upper soil horizons. But they only grow and produce the toxin in nutrient rich, neutral liquids, where no oxygen is present (anaerobic conditions).

Salts, nitrites and/or acids make conditions impossible for growth this bacterium, (which is why we lactoferment many foods in a 3% salt brine).

Like other infamous members of the genus Clostridium (e.g. tetani, perfringens), they are quite resistant to many antibiotics. The spores are immune to pasteurization, and can even survive boiling in water at 100°C (212°F) for ten minutes!

This makes botulism the potential scourge of home canning, where non-acid foods are boiled and sealed in glass jars, then stored at room temperature (non-acid, no oxygen). Many will tell you this is why pressure cookers were invented: to elevate food temperatures for canning to above the tolerance of botulinus spores [5].

The toxin is hardly a simple compound, (C6670H10290N1716O1983S32Zn) but an elegantly complex, two-chain molecule, normally surrounded by protective proteins. It poisons animals by a series of specific actions allowing it to pass from gut to blood, enter a nerve synapse (communication passage between nerve cells), attach to an axon and lastly permanently block the release of the neurotransmitter Acetylcholine, (ACH). This terminates all messages moving along that nerve pathway, producing paralysis in the muscles served by that motor neuron [6].

The toxin is degraded by temperatures about 80°C (176°F), but spores can survive. As a nerve poison (neurotoxin, called BoNT) it is reportedly the most poisonous compound known to be produced by any living thing: only 75 micrograms ingested with food can paralyze and kill an adult person of average weight. For a more intuitive reference, a teaspoon of salt contains about 7.5 grams, or about 100,000 times that dosage amount.

A Healthy Microbiome Normally Protects Against Botulism

So, we immediately have a puzzling contradiction: if the spores are everywhere and will grow anywhere with no air, why are illness cases so very rare?

For the answer, quick rewind to our friends, the microbiome: our gut bacteria routinely detoxify BoNT by several subtle but effective mechanisms. Gut bacteria release proteases and “bacteriocines” (short peptides) which digest or deactivate the protective proteins around the BoNT, and even destroy the BoNT molecule itself [4].

It is tempting to point out here, this produces one more exception to the US FDA ruling about “cures”: the bacteria found in fermented sauerkraut, yogurt and Kim chi can really cure botulism.

How? By neutralizing this most potent nerve poison and lowering the pH of the medium so the bacterium cannot grow or produce more toxin.

Yes, lacto-fermented foods can and do neutralize botulism, even though the FDA forbids anything (food or supplement) from curing anything (disease) unless it is a pharmaceutically registered, regulated drug. Perhaps the bacteria in raw milk also detoxify BoNT as many farm families and activists often claim.


Photo by Martin Michener

We now understand better how a cow might die, but the BoNT causing the death could be so dilute as to be undiagnosable.

But what about the digestive flora and their protective relationships?

Here is where the experiments of Ackermann, Coenen, Schroedl, Shehata and Krueger, 2014, move closer to establishing a definitive answer. Their paper [4], just published in Current Microbiology, establishes the lengthy protocol for two actual experiments, two purposes following much the same methods.

Testing Effects of Glyphosate on Microbiota

Realizing that even following the biochemistry and cultures in an actual cow would be subject to many random uncontrolled events, such as the cow suddenly eating another food, the authors took elaborate care to follow these steps (which, for brevity, I have simplified, here):

  1. Take measured amount of rumen contents from a single, healthy, adult, non-lactating grass-feeding Holstein cow;
  2. strain out the large particles,
  3. mix this cud containing hundreds of different protozoa as well as bacteria with a sterile mineral buffer solution;
  4. add measured amounts of one of two diet foods
    a. mainly grass, with sweet potato pellets.
    b. richly supplemented diet for a milk-producing cow.

Each sample then had added to it sufficient glyphosate (the pure chemical, not the weed-killer commercial mixture Roundup) to produce a known concentration. Then it was incubated for 48 hours at 39°C (102.2°F), and analyzed for bugs and toxins.

In the first experiment, concentrations of glyphosate were then added to each flask to produce these values: 0, 1, 10, 50 and 100 micrograms per milliliter, (or parts per million, PPM, since a milliliter weighs a gram). Here we note these chosen levels units result in quite a lot of glyphosate being added; the lab results for grains and soils are typically reported in micrograms per LITER, or parts per billion, PPB. This experiment was run using both diet a and b, that of pasture grass and that used for a dairy cow giving milk.

In the second experiment, actual spores of C. botulinum were added to each sample, then again glyphosate to create increasing levels of the herbicide. In this experiment, however, another dose, higher than 100, was also added, to bring the glyphosate in the last sample flask to 1000 micrograms/milliliter, or one milligram per gram, of 0.1% glyphosate. This indeed is a high concentration. Again, after 48 hours at 39°C the contents were checked for microbiome and toxins.

Results of the Experiments on Glyphosate

The results of both experiments, in short, showed the C. botulinum survived the glyphosate, but the protozoa and helpful bacteria much less so.

The protozoa are mostly ciliates, identified with a stain and high power light microscope. They disappeared at low glyphosate additions. In the rumen, these protists are essential to breaking down the coarse cellulose in grass and leaves into food materials the other bacteria can use.

So we can see that without these ciliates, removed by the lowest glyphosate levels, the rumen food chain cannot get started, and a cow could become very sick from herbicide-mediated dysbiosis.

In the second experiment, C botulinum spores grew well, and were found at all levels of glyphosate addition, but BoNT was only found in the mix at the highest level, 1000 micrograms/milliliter. I take this to mean that until the normal bacteria (Enterococcus, Lactobacillus, etc.) were all diminished, their bacteriocines and or proteolytic enzymes degraded the actual toxin.

The methods used in this study were very sophisticated and would require pages to fully report. But to do the authors work justice, I will summarize in a few sentences.

Counting the bacteria was not a simple culture-and-count on diluted plates, because potentially hundreds of different species are present. Special RNA oligonucleotide probes [7] with attached specific fluorescent dyes where used, requiring many stages of drying the bacteria and preparing them to open their walls to allow the RNA probes to hybridize with the RNA inside each dead bacterium. Then the unattached probes and fluorescent dye is washed away and the preparation dried for the counting by fluorescent color.

In the second experiment, determining trace amounts of the toxin, BoNT, was done with ELISA (also fluorescent) reagents, as described in previous work at the University of Leipzig [8].

The results confirm many recent works showing glyphosate can wreak havoc in a mammal’s intestine [1].

The Glyphosate Epidemic: Mainstream Medicine has no Answer

These results confirm many recent works showing glyphosate can wreak havoc in a mammal’s intestine [1].

In a recent discussion [9] I have explored the interactions between Aluminum (the toxic immunity-stimulator) and glyphosate, as they combine to produce the widespread gluten food allergy. This study adds materially to that analysis, in providing another example of the importance of both dietarily avoiding “glyphosate the selective antibiotic”, and avoiding “glyphosate the mineral chelator”.

Of course glyphosate is the same unregulated food pollutant, now found in certified organic grains from the American Midwest [10].

The Samsel-Seneff report [1] predicts the process behind all these findings: glyphosate blocks the production of healthy amino acids (tryptophane, phenylalanine) by our native microbiome, and instead produces strong oxidant irritant chemicals (m-cresol). It also blocks the Cytochrome P450 detoxifying enzyme production in the liver, by which the inflammation could have been abated.

What this study shows is how, even at huge glyphosate levels in an anaerobic cow’s rumen, the surviving normal bacteria stop the overgrowth of botulinus and degrade its monstrous neurotoxin, BoNT. These are live-saving processes, for cows and us, of which neither mainstream medicine nor the victims of modern food are aware.

Care of Gut Bacteria: The Answer

Filling jars. Photo by Shannon Stonger.

Filling jars with homemade Kim chi. Photo by Shannon Stonger.


How to make homemade Saurkraut. Photo by Shannon Stonger


Care of gut bacteria is both a new area of developing science and a rediscovered ancient art [11]. Consuming healthy foods is a large part of modern (ancient!) restorative measures.

First prebiotics, then probiotics, in that order. Eat food your biome will like as it arrives, then add live bacteria of the right mix. Natural yogurts are famous for being the right culture, but there are doubts about live bacteria surviving the acid stomach. Naturally fermented vegetables, combining the cabbage-mustard family and the onion family (sauerkraut, Kim chi) which have not been pasteurized, are hard to find unless you make them yourself, but they have four unique survival advantages:

1. These foods have lots of organic sulfur, which has recently been found to be deficient in our diets [1]. Sulfur eaten with flavenoids, such as carotenoids or turmeric, allow sunlight on your skin to combine cholesterol and vitamin D3 with sulfate, both of which help maintain healthy membranes (muscles and nerves).

2. The culturing process makes the batch turn “sour,” and by the end-point most of the original bacteria die off from this acidity. Clostridium bacteria are placed on hold. This is why these ancient processes were invented: to preserve healthy food values without refrigeration. Although the live bacteria diminish, they leave behind acid-proof spores, able to survive a trip through your stomach acid, and ready to spring into action as soon as the pH rises (aka, they reach your small intestine, as needed).

3. The fermented cabbage and onions are softened a lot in the fermentation process, but they are still very healthy roughage, able to make it through 90% of the digestive process to your lower gut, offering some protection to bacteria and providing surfaces on which those replacement bacterial spores can begin to grow.

4. As we age, our digestive tracts may lack adequate stomach acid for some meals; regularly eating lacto-fermented products provides an acid mix around pH 3.5, and is able to help digest proteins in meat and legume dishes without becoming overly acidic.

The regular consumption of this natural nutrition system has worked for thousands of generations. We even recommend it to our bewildered physicians, recently frustrated by C. diff. infection cases resistant to big pharma’s famous antibiotics, and with nowhere else to turn for healing.

About the Author

Dr. Martin C. Michener  has over fifty years experience as a teacher, ecologist, zoologist and botanist. He has a B.S. from Cornell University, and a Ph.D. in biology from Harvard University Graduate School.

healthy-traditions-GMO-Tested-med Glyphosate-Tested250



[1]          http://www.drdooley.com/gut-dysbiosis-therapy.php

Samsel A, Seneff S  (2013) Glyphosate’s Suppression of Cytochrome P450 Enzymes and Amino Acid Biosynthesis by the Gut Microbiome: Pathways to Modern Diseases. Entropy 2013, 15(4), 1416-1463; doi:10.3390/e15041416.  http://people.csail.mit.edu/seneff/Entropy/entropy-15-01416.pdf

[2]          Keith,  Lierre.  2004. The Vegetarian Myth: Food, Justice and Sustainability.  http://en.wikipedia.org/wiki/Lierre_Keith

[3]          Bohnel H, Schwagerick B, Gessler F (2001): Visceral botulism-a new form of bovine Clostridium botulinum toxication. Journal of Veterinary Medicine A – Physiology, Pathology, Clinical Medicine 48, 373–383. http://www.ncbi.nlm.nih.gov/pubmed/11554495

Lindstrom M, Myllykoski J, Sivela S, Korkeala H. (2010): Clostridium botulinum in cattle and dairy products. Critical Reviews in Food Science and Nutrition 50, 281–304. http://www.ncbi.nlm.nih.gov/pubmed/20301016

[4]          Ackermann W, Coenen M, Schroedl W, Shehata A, Krueger M (2014). The Influence of Glyphosate on the Microbiota and Production of Botulinum Neurotoxin During Ruminal Fermentation. Current Microbiology 2014. doi:10.1007/s00284-014-0732-3.

[5]          U. Florida IFAS Extension. Preventing Foodborne Illness: Clostridium botulinum. http://edis.ifas.ufl.edu/fs104

  1. Todar’s Online Textbook of Bacteriology. Pathogenic Clostridia. http://textbookofbacteriology.net/clostridia.html

[6]          http://en.wikipedia.org/wiki/Botulinum_toxin

[7]        Loy A, Maixner F, Wagner M, Horn M (2007) ProbeBase—an online resource for rRNA-targeted oligonucleotide probes: new features 2007. Nucleic Acids Res 35:D800.

[8]          Krueger M, Shehata AA, Schroedl W, Rodloff A (2013) Glyphosate suppresses the antagonistic effect of Enterococcus spp. on Clostridium botulinum. Anaerobe 20:74–78

[9]          Michener M (2014) Gluten Intolerance and the Herbicide Glyphosate: A National Epidemic – http://healthimpactnews.com/2014/gluten-intolerance-and-the-herbicide-glyphosate-a-national-epidemic/#sthash.OAMuBgoZ.dpuf

[10]        Shilhavy B (2014)  http://healthimpactnews.com/2014/the-glyphosate-contamination-of-organic-food-an-update/

[11]        Stonger S (2014)  http://healthimpactnews.com/2014/a-simple-homemade-kimchi/