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The humans omnivores dilemma- Meat consumption, probiotic bacteria, inflammation, and the gut

by Milos Pokimica ND

by Milos Pokimica ND

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"Are humans omnivores in a true anatomical sense? There is a fundamental difference in the way the digestive tract works in plant vs meat-eating species."

Are humans omnivores in a true anatomical sense? There is a fundamental difference between the way the digestive tract works in plant-eating and meat-eating species. There are no bacteria in the colon of the meat-eating species because this type of meat-eating bacteria is very aggressive and it is not probiotic. Transit time of food through the digestive tract in meat-eaters needs to be short, no more than five to ten hours or the immune system can be overstressed when meat begins to rot in the colon. That will create inflammation and food poisoning. Also stomach acid in meat-eaters is much more corrosive and their upper digestive tract is essentially sterile.

Penny on the right was retrieved from the belly of 17 lb Shih Tzu
Penny on the right was retrieved from the belly of 17 lb Shih Tzu

The large intestine (colon) of carnivores and omnivores is thus simple and very short since its sole purpose is to absorb salt and water. It has almost an identical width as the small intestine and, consequently, has a limited capacity to function as a reserve. Although a microbial populace is still present in large amounts in the colon of carnivores, its activities are essentially putrefactive.

In herbivorous animals, the large intestine is a highly specialized organ involved in the absorption of water and electrolytes, the production of vitamins, and the fermentation of plant fibers. The colons of herbivores are always more comprehensive than their small intestine and are relatively long and filled with probiotic bacteria. The microbiome of the colon in humans has an essential role in the normal functioning of the body.

Herbivore vs. Ruminant herbivore vs. Insectivore vs. carnivore digestive tract
Herbivore vs. Ruminant herbivore vs. Insectivore vs. Carnivore digestive tract

Somehow we underrate the importance of the colon and think it is just some waste material organ. In carnivores, it is, in us, it is not. In Homo sapiens and other primates colon is subject to a different array of functions. For example, water and electrolyte absorption and vitamin production and absorption. There is also extensive bacterial fermentation of fiber that results in the different metabolites and short-chain fatty acids production and absorption from the colon that also provides significant amounts of energy and other health benefits. We are not able to utilize the entire energy value of the fiber as grazers can do but we can utilize some of it. The extent to which the fermentation and absorption of metabolites take place in the human colon has only lately started to be studied, and research into the microbiome is a new big thing because of all of the chemicals that these bacteria can secrete and the effect that they have on our bodies. It is not just the vitamins that probiotic bacteria create. Every chemical is one possible drug.

The composition of the microbiome depends on the food we eat. One type ferment fiber another type putrefies the meat, and not all of them are probiotic.

Fiber rich vs protein rich diet effects on GI-microbiota and modulation of host health
Fiber rich vs protein rich diet effects on GI-microbiota and modulation of host health

Think about it in this way, if bacteria putrefy the beans for example and we get gases as a result, it does not have a considerable interest in us. We are not her food. Bacteria likes the beans only. Bacteria are organisms that are specialized to a great extent. They do not eat everything. One type eats fiber, another type eats meat. It likes you too but in a different way. You are her host, and you give her all that food and place to live with moisture and warmth so she may help you live longer because she likes you, but in a different way, she does not like your meat.

However, when we have bacteria that putrefy corpses, then we are on the menu too. Meat is meat, and ours is tasty too. Most people do not realize that most of our immune system about 60-70% is actually in our abdomen as a vast system of lymph networks referred to as GALT (gut associated lymphatic tissue).

Galt representation
GALT representation

Moreover, about 80% of plasma cells mainly immunoglobulin A (IgA)-bearing cells reside in GALT. We have more foreign DNA from bacteria and other symbiotic microorganisms in us than our own. In carnivores animals because of acidity most of the upper GI tract is sterile. When food reaches the colon, there can be no foreign invaders, and most of the already present species of colon microbiota are “nice” ones. When we eat meat the situation is different. The human gastrointestinal tract features the anatomical modifications consistent with an herbivorous diet with low acidity and long transit time, so the potential for the growth of aggressive strains of not symbiotic bacteria is real, and if they are present in the food they can colonize the intestinal lining and cause constant presence for our immune system. The reason for the so-called balance between probiotic and non-probiotic bacteria is because of this. We always have a big chunk of our microbiome that is not symbiotic with our bodies. Eating meat feeds a large chunk of this nonsymbiotic bacteria. High animal products and low fiber consumption are not just associated with an increase in transit time and constipation. They are also associated with the rise of the low level of chronic inflammation and the risk of colon cancer.

When we consume meat it will be sitting in our colon for a long time and because we are not adapted to eating meat and animal products in higher amounts that will have negative effects and that is just how it is. Taking probiotic supplements won’t change anything in real numbers because bacteria multiply very rapidly when there is an energy source. If bacteria eat meat and meat stays in our digestive tract for days the end result is inflammation. If we over-consume animal products at regular intervals we would have a bad microbiome in our colon and a chronic rise in inflammation.

Digestive System comparison, human vs carnivore
Digestive System comparison, human vs carnivore

One might wonder what happens in the digestive tract of real omnivorous species? Do real anatomical omnivores have a short or long colon and do they ferment fiber? Carnivore abdomen composition is more primitive than herbivorous adaptations with higher acidity to kill off dead meat bacteria. Therefore, one would expect an omnivore to be a carnivore that shows some adaptations of the gastrointestinal tract to an herbivorous diet. This is precisely the situation we found in the raccoons, the bears, and some members of the canine families. Bears, for example, are mainly herbivores with 70-80% of their diet consisting of plant foods. Because bears include significant amounts of meat in their diet, they must maintain the anatomical characteristics that allow them to capture and kill their prey. Therefore, bears have a maxillary structure, musculature, and dentition that allow them to apply the forces necessary to kill and dismember their prey even though most of their diet consists of plant foods. The most important adaptation to an herbivorous diet in bears is the modification of their teeth. The bears kept the incisors, the large canines, and the premolar shearers of a carnivore; but the molars were square with rounded cusps to crush and grind. They still have high acidity and high resistance filter and short colon. They cannot digest the fibrous vegetation and, therefore, are highly selective. Their diet is dominated mainly by aromatic herbs, tubers, and berries. Many scientists believe that the reason why bears hibernate is due to their primary food (succulent vegetation) are not available in the cold winters of the north. The small intestine is short (less than five times the length of the body) like that of pure carnivores, and the colon is simple, soft, and short.

Omnivore vs. Human representation
Omnivore vs. Human representation

There is also a entirely different mechanism that consumption of meat is associated with an increase in inflammation even if we do not count the toxins and pollution in meat and its effect on microbiome. This mechanism is natural and normal, and all of the carnivorous species had it, and the reason why this exists is because of the fact that even dead non-probiotic bacteria do count as toxins. These substances are known as endotoxins (Greek éndon within; cognate with Old Irish ind-), and the problem with them is that there are thermally (250C) and chemically stable and extremely toxic. Endotoxin is a complex lipopolysaccharide (LPS) found in the outer cell membrane of gram-negative bacteria (E.coli, Salmonella typhi, Shigella), typically waterborne. Bacteria shed endotoxin in large amounts upon cell death. Meaning, the bacteria can be dead or cooked for a long time, but their dead meat bacteria endotoxins are still there.

Related Posts

  1. acrylamide
  2. spoiled meat
  3. inflammation


Passages selected from a book: “Go Vegan? Review of Science: Part 1” [Milos Pokimica]

  1. Enterotypes of the human gut microbiome. doi: 10.1038/nature09944
  2. Intestinal floras of populations that have a high risk of colon cancer Appl Environ Microbiol. 1995 Sep; 61(9): 3202–3207.
  3. Up-regulating the human intestinal microbiome using whole plant foods, polyphenols, and/or fiber. doi: 10.1021/jf2053959
  4. Gut Microbiota and Inflammation doi: 10.3390/nu3060637
  5. Meat-loving microbes: do steak-eating bacteria promote atherosclerosis? doi: 10.1161/CIRCGENETICS.113.000213.
  6. Eggs as a dietary source for gut microbial production of trimethylamine-N-oxide. doi: 10.3945/ajcn.114.094458
  7. The health advantage of a vegan diet: exploring the gut microbiota connection. doi: 10.3390/nu6114822.
  8. Metabolic benefits of dietary prebiotics in human subjects: a systematic review of randomized controlled trials. doi: 10.1017/S0007114513003607

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GoVeganWay.com brings you reviews of the latest nutrition and health-related research. The information provided represents the personal opinion of the author and is not intended nor implied to be a substitute for professional medical advice, diagnosis, or treatment.  The information provided is for informational purposes only and is not intended to serve as a substitute for the consultation, diagnosis, and/or medical treatment of a qualified physician or healthcare provider.



In the event of a medical emergency, call a doctor or 911 immediately. GoVeganWay.com does not recommend or endorse any specific groups, organizations, tests, physicians, products, procedures, opinions, or other information that may be mentioned inside.

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October 21, 2021


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