The Link Between Obesity and the Microbiome – Causes and Cures

Print Friendly, PDF & Email
Winterize Your Immune System: The Power of Probiotics to Fortify Immune Strength

Prebiotics help gut fermentation to take place; probiotics stimulate the growth of helpful bacteria

(Updated June 1st, 2021)

In April of 2016, the Lancet published a long-awaited report on world obesity, which was based on 19.2 million people studied from 1975 to 2014. The exponential increase in obesity that they reported is alarming; the authors predict that by 2025, 18 percent of men and 21 per cent of women will be clinically obese across the globe.

Currently in Canada, 60 per cent of adults and 30 per cent of children are obese. This situation has the potential to crash healthcare systems because obesity effectively doubles health care costs and increases the risk of death from Covid-19 and various other illnesses.

When the Human Genome Project was completed in 2003, and only 20K to 25K genes were discovered (about the same as a banana), it became evident that we are not complex machines ourselves. Instead, each one of us is a complex superorganism functioning symbiotically with trillions of microbes resident inside us, each with their own DNA and their own genes. In other words, our survival and the well-being of all our organs and systems, and especially our development from zygote to adulthood, depends entirely on these microbes!

Our 25,000 genes won’t be much use to us if we don’t cooperate with bugs that reside inside of us, collectively known as our microbiome. The dance and hormonal communication chatter of these beneficial bacteria work to run our very lives. So instead of finding a human gene that may turn diseases on or off as scientists had hoped, they found bacteria, viruses, and other microorganisms of far greater importance in orchestrating health and disease.

The most amazing discovery surrounding the disease-microbe connection is its relation to obesity. As microbiome researchers C. Heintz and W. Mair put it: You are what you host!

How Industry Works to Fatten You Up

Obesity is ultimately commercially fuelled; somebody profits from it. Research published in the Lancet has shown that the food industry uses the same strategies to bypass unwanted regulation as the tobacco industry used to. Obese people themselves don’t really understand why this condition is happening to them. This is especially true of the working poor who rely on cheap food, which is highly processed and mostly devoid of nutritional quality and laced with artificially toxic taste enhancers.

In this scenario, the resident microbiome gets starved first, and then the body develops systemic illnesses. Ironically, a healthy diet (i.e. fresh and rich in nutrients for both the microbiome and ourselves) costs a person only about $1.50 more per day than a junk food diet, resulting in an annual increase of $550 per person in their food budget.

Two important events occurred in 2016, in addition to the Lancet review of world obesity. They are of utmost importance to dealing meaningfully with the obesity epidemic.

1. On March 16, 2016, the DARK Act was defeated in the U.S. DARK is the popular acronym given to the proposed legislation: Deny Americans the Right to Know. Monsanto, DuPont, and Dow Chemical had originally drafted this Act and lobbied hard to get it passed by Congress, but the Senate refused to ratify it. If passed, it would have made labelling of genetically modified (GM) foods “voluntary”, not “mandatory,” and thereby would have also wiped out the mandatory labelling legislation which went into effect July 1 in Vermont, and a little later also in other U.S. states.

The DARK Act represented the food industry’s attempt to stop popular opposition to GM foods (about 90 per cent of the public opposes GM foods in the U.S. and 97 per cent in Canada) once and for all, successfully making everybody into force-fed customers.

Genetically modified (GM) foods depend on pesticides to grow. And it turns out that those pesticides, as well as the GM foods themselves, are key factors in making people obese – especially the mass of low-income people who cannot easily afford organic, pesticide-free foods.

The pesticide Roundup is in fact patented as an antibiotic, and the abuse of antibiotics has turned out to be a main cause of the obesity epidemic. This condition can be traced to the medical overuse of antibiotics for humans, as well as widespread overuse in agriculture (pesticides and herbicides for plants and regular antibiotics for food-producing animals). Roundup is also a primary factor in the development of antibiotic resistance, thereby endangering people who desperately need them in certain situations. (We now have pathogens resistant to Vancomycin, the antibiotic of last resort, and super-deadly C. difficile can no longer be treated by any antibiotic drug, but only with stool implants from a person with a healthy microbiome.)

2. In June 2016, the European Union decided against renewing Monsanto’s license for Roundup, basing its decision on a petition signed by two million Europeans, as well as the 2015 independent report by the International Agency for Research in Cancer with the World Health Organization. Together, the petition and the report declared Roundup a probable carcinogen. The number of countries refusing to grow, sell, or import GM foods in Europe has now risen to 19. The campaign to stop Roundup in the EU was led by Pavel Poc, the vice-chair of the EU parliament’s Environment Committee.

Also in June in the U.S., a 420-page report was published by the National Academy of Sciences (NAS) claiming that GM crops are safe and that there is no evidence showing harm to human health. This is the usual propaganda – a claim that there is no evidence in such “controversial” matters invariably means that the existing evidence was ignored. It is worth reading an analysis of this bizarre NAS report by Food and Water Watch (founded by Maude Barlow who runs Council of Canadians), an analysis that exhaustively documents the underlying skullduggery.

Causes of Obesity

ENVIRONMENTAL TOXINS – Many years ago, environmental medicine expert, Dr. Jozef Krop of Mississauga, admitted a patient to a Toronto hospital. This patient was in a state of life-threatening obesity, so Krop placed her on a regime of medically supervised basic fluids only. But instead of losing weight, she gained some 10 pounds in the first week! A thorough investigation conducted by the hospital and Dr. Krop revealed that the floor-cleaning detergent used in those days contained potent neurotoxins and allergens. When exposed, the patient’s body reacted by retaining even more water than before. (She subsequently recovered to her normal weight, after her home environment was purged of hazardous chemicals.)

American Academy of Environmental Medicine physician, Dr. Sherry Rogers, coined the phrase: “The solution to pollution is dilution.” Indeed, much obesity is actually the result of water retention as the body attempts, on the cellular level, to protect itself against toxic substances. Much research has been done on how to identify environmental toxins, and as a result, new methods of detoxification have been developed that are measurably effective. Now, thanks to the human microbiome research, we also understand the way that toxins do their work and how our resident microbiome tries to defend its host.

ANTIBIOTICS – The most significant cause of obesity is the use of antibiotics, especially early in life, which interferes with the beneficial microbiome bacteria. In the U.S., 69 per cent of children have had at least one course of antibiotics by the age of one year. It can take a year for the microbiome to recover from a single course of antibiotics. Doctors hand them out like candy without doing cultures for specificity first (something that you can demand they do).

Most frequently used is the broad-spectrum amoxicillin – which not only wipes out any offending pathogens, but also kills off all beneficial gut bacteria. If a child’s food is high in fats loaded with more antibiotics (used in animal farming to increase weight at slaughter), as well as processed foods which tend to include many toxins used as preservatives and even chlorine to ensure longer shelf life, as well as vegetables and fruit loaded with pesticides and herbicides but little fibre – well, there is your obesity recipe in broad strokes. Insulin resistance and diabetes may follow, and fatty liver disease has been diagnosed even in preschoolers. In this context, neither increased exercise nor reducing calories will do much good because any possible gains cannot last unless the influx of dietary toxins stops.

As Martin Blaser explains in Missing Microbes, we are treated by the food industry like farm animals – made obese through antibiotics. What we do to our food-producing animals we do to ourselves.

Following the World Health Organization’s announcement of a world-wide irreversible antibiotic crisis, Health Canada has taken some small steps towards ending the use of antibiotics in food producing animals. Furthermore, the American Medical Association is calling for a total ban of antibiotics in food production (see

Pesticides, Birth Control Pills, Stress

Persistent organic pollutants (POPs), such as DDT, continue to be used in various parts of the world where they contaminate the foods grown in those areas (e.g. DDT-sprayed rice from India). These POPS have long been known to promote obesity and trigger diseases like arthritis and cancer. Also on the list of obesity-promoting, carcinogenic chemicals are synthetic sweeteners such as aspartame and sucralose, birth control pills, and synthetic hormone replacement medications.

Most importantly, psychiatric drugs, and those used to treat the highly questionable diagnosis of hyperactivity in children, are known to cause obesity as a side effect. Microbiome research shows that diminished microbial diversity can also induce mental health problems. Therefore, improving the quality of a hyperactive kid’s diet is more likely to calm him down than a toxic drug.

The microbiome is also highly sensitive to the toxic impact of the stress hormone cortisol. Chronic stress, including insufficient sleep, or repeated acute stress, will raise cortisol levels such as to kill beneficial bacteria. As well, PTSD has been shown to be causative in the development of obesity.

The process by which our resident gut bacteria are rendered helpless to protect us is through inflammation, specifically through innate immune receptors and sensors called inflammasomes, which respond to enemies – pathogens and stress. (They initiate a cascade of activity measurable by C-Reactive Protein testing.) Their purpose is to raise the alarm and call the immune system to action. A deficiency in inflammasomes is caused by a deficiency in beneficial mircobiome bacteria, which are key communicators in this process.

However, one thing is certain: the microbiome population needs its own food to thrive and thereby sustain us. That’s where the famous prebiotics and dietary fibre come in because they allow for the all-important gut fermentation process to take place. Probiotics stimulate the growth of helpful bacteria. Probiotics, which most of us know about, cannot colonize a gut unless the resident helpful bacteria get their pre-biotic diet first. The two important pre-biotics are known as Inulin and Oligosaccharides. Good health food stores carry these as supplements, or you can use food sources of prebiotics such as raw garlic, bananas, dandelions, raw honey, asparagus, unpasteurized apple cider vinegar, and more.


Losing weight and keeping it off can only be achieved with the cooperation of the microbiome. Prebiotic inulin and oligosaccharides, along with probiotics containing the full spectrum of Bifidobacteria and Lactobacillus, are the most essential supplements needed to reduce weight and keep it off. In extreme cases, studies show that a fecal transplant from a slim person to an obese one can jumpstart the weight normalization process. Rectal implants of pre- and probiotics in a saline solution have also been used successfully to achieve re-colonization of the GI tract with beneficial bacteria, especially after a long course of antibiotics.

Of course, to achieve optimal weight, a person must avoid processed foods, artificial sweeteners, and allergenic foods (often gluten-containing). Further, any meat and dairy products, as well as most vegetables and fruits, have to be certified organic (free of pesticides, herbicides, and antibiotics). One’s diet should also contain a lot more raw foods.

Given that our water supply is contaminated with prescription drugs (which are not fully metabolized in the body and therefore excreted in the urine), it is worth considering the purchase of water purification devices. For example, APF Water technology is now available in GE refrigerators. These filters remove 94 per cent of the residues of the top five prescription drugs, as well as chlorine, etc., from the water. Also, taking high doses of Vitamin C (to bowel tolerance level) is essential because it removes toxic substances without compromising the microbiome.

Exercise and stress reduction measures are equally important. The aim is to enter into a dialogue with one’s body and become mindful of what feels right. Let your gut feeling guide you.

Editor’s note: As a supplementary article to this one, Helke Ferrie has written a “Success Story” about her own recovery from obesity – what caused it and what cured it. That article has been posted on Vitality’s website under the title: “How I Overcame Obesity – More Than Once.”


All research involving the human microbiome is available on the internet for free. The sources listed below are all from open access research.

Basic current facts on obesity:

  • Trends in adult body-mass index in 200 countries from 1975 to 2014: a pooled analysis of 1,698 population-based measurement studies with 19.2 million participants. Authors: NCD Risk Factor Collaboration; Lancet vol. 387, April 2, 2016
  • United European Gastroenterology Report on childhood obesity in 46 countries in Europe, May 2016, available on Google for free download. Summary in The Guardian, May 31, 2016, by Tim Radford
  • J. Naukkarinen et al. Identical twins with significant weight differences shed light on the phenomenon of metabolically health obesity, Diabetologia 2013
  • R. Unger et al. Gluttony, sloth and the metabolic syndrome: a roadmap to lipotoxicity. Trends in Endocrinology and Metabolism March 9, 2010
  • M. Falchi et al. Low copy number of the salivary amylase gene predisposes to obesity. Nature Genetics, 2014
  • Report on annual meeting of American Society for Microbiology May 30, 2010 on ScienceDaily website, May 31, 2010

Recommended Resources:

  • Martin Blaser’s 2014 book Missing Mircobes is the single best source on more details all of this information.
  • G. E. Mullin, Integrative Gasteroenterology
  • G.E. Mullin, The Gut Balance Revolution, Rodale, 2014. Excellent diet book by a professor of nutrition from Johns Hopkins Medical School
  • R. Dunn, The Wild Life in Our Bodies
  • talks “Meet Your Microbes” by Jonathan Eisen
  • J. D. Leach, Honor thy Symbionts, by Human Food Project, via Google or
  • is an excellent source for information GMO issues; see entry on the 2016 report on genetically engineered crops and the underlying conflicts of interests. Download via Google “The Non-GMO shopping guide”.
  • Go to for information on Monsanto and the issues discussed in this article. On how Roundup causes antibiotic resistance: April 29, 2015
  • An excellent source of information is
  • Highly recommended also is founded by Canada’s Maude Barlow who runs Council of Canadians
  • Dr. Mercola’s website is full of information on microbiome and disease/health issues. Specially recommended are his entries for June 13, 2016 and July 16, 2014
  • View the 2004 documentary Supersize Me, which amusingly has a blurb on the box stating: “This documentary is not affiliated with or endorsed by McDonald’s Corporation.”
  • S.A. Joyce et al. Regulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut. Proceedings of National Academy of Sciences, 2014
  • The information on the diet industry has known that diets don’t work long term comes from S. Aamodt’s article in The New York Times, May 6, 2016, entitled “Why you can’t lose weight on a diet”. Her findings on appetite control from neuroscience are undoubtedly valid, but strangely, she doesn’t seem to consider the research on the human microbiome.

The determinative role of the human microbiome in obesity:

  • See references provided for Vitality’s May 2016 feature by Helke Ferrie
  • M.Sanchez et al. Childhood Obesity: A role for gut bacteria? International Journal of Environmental Research and Public Health, December 23, 2014
  • M. Blaser, Missing Microbes – How Killing Bacteria Creates Modern Plagues, One World, 2014 (this is the most comprehensive, definitive introduction to all aspects of the human microbiome’s role in health and disease; chapter 13 and its sources is on obesity causes and treatments)
  • The expression “You are what you host” comes from C. Heintz & W. Mair, You are what you host: microbiome modulation of the aging process, Cell, Jan. 30, 2014. NOTE: this research describes the effect of the microbiome on aging,  not obesity.

Cost issues regarding obesity:

  • D-H., Kim, J. P. Leigh, Estimating the effect of wages on obesity, Journal of Occupational and Environmental Medicine, vol. 52 (5), 2010
  • T. Ostbye et al. Is overweight and class I obesity associated with increased health claims? Obesity, April 22 (4), 2014
  • R. Sturm, R. An, Obesity and Economic Environments, CA Cancer Journal for Clinicians, vol. 64 (5), Sept. 10, 2014
  • M. Rao et al, Do healthier foods and diet patterns cost more than less healthy options? A systematic review and meta analysis, BMJ Open, vol. 3 (12), December 2013

Obesity causes: antibiotics, pharmaceutical drugs, pollutants, stress:

  • See chapter 13 in Martin Blaser’s 2014 book Missing Microbes
  • L. M. Cox et al (including Martin Blaser), Altering the intestinal microbiota during critical developmental windows has lasting metabolic consequences, Cell, vol. 158, p. 705-721, Aug. 14, 2014
  • C. Bailey et al. Association of antibiotics in infancy with early childhood obesity, JAMA Pediatrics, vol. 168 (11), 2014
  • CBC news, Kelly Crowe, July 9, 2014. Health Canada’s quiet move to end use of antibiotics to fatten up animals
  • M-S. Gauthier et al. The metabolically healthy but obese phenotype is associated with lower plasma levels of persistent organic pollutants compared to the metabolically abnormal obese phenotype, Journal of Clinical Endocrinology & Metabolism, Feb. 2014
  • J. Lee, Child obesity is linked to chemicals in plastics, April 17, 2009
  • M. K. Skinner et al. Ancestral dichlorodiphenyltrichloroethane (DDT) exposure promotes epigenetic transgenerational inheritance of obesity. BMC Medicine vol. 11 (1), 2013
  • T.J. Maher et al. Possible neurological effects of Aspartame, a widely used food additive. Environmental Health Perspectives, vol. 75 p. 53-57, 1978
  • N.K. Jain et al. Sorbitol intolerance in adults. American Journal of Gastroenterology, vol. 80 (9) 1985
  • S. Basu et al. The Relationship of Sugar to Population-Level Diabetes Prevalence: An Econometric Analysis of Repeated Cross-Sectional Data, PLOS One, Feb 27, 2013
  • S.S. Schiffman, K. I. Rother. Sucralose, a synthetic organochlorine sweetener: Overview of biological issues, Journal of Toxicology and Environmental Health, vol. 16 (7), 2013
  • A. Alfano, Many psychiatric drugs have serious effects on body weight, Scientific American, July 2015. NOTE: for full information go to psychiatrists Dr. David Healey (, Mad in America (, and read the manufacturers’ inserts provided with psychiatric drug packaging.) Report on Endocrine Society’s 95th Annual Meeting, June 17, 2013, on ScienceDaily website: Short-Term antidepressant use, stress, high-fat diet linked to long-term weight gain.
  • A. Berenson et al. Changes in weight, total body fat, percent body fat, and central-to-peripheral fat ratio associated with injectable and oral contraceptive use, American Journal of Obstetrics and Gynecology, March 4, 2009
  • S. J. Melhorn et al. Meal patterns and hypothalamic NPY expression during chronic social stress and recovery, American Journal of Physiology, Sept. 1, 2010
  • L. D. Kubzansky et al. The weight of traumatic stress, JAMA Psychiatry, Nov. 20, 2013
  • E. van den Akker et al. Increased scalp hair cortisol concentrations in obese children, Journal of Clinical Endocrinology and Metabolism, Dec. 2013


  • A. Trompette et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nature Medicine, Jan. 6, 2014
  • Genetically Engineered Crops: Experiences and Prospectives, 2016 Report by Committee on Genetically Engineered Crops, Board on Agriculture and Natural Resources, Division on Earth and Life Sciences, National Academies of Sciences (Engineering and Medicine) available for free download from
  • The Organic Centre ( Bringing you the science behind organics – go to for the most up-to-date info on organic produce and the health effects of conventionally grown/raised foods Institute for Responsible Technology which has published books on the documented adverse health effects of GM foods
  • R. Moodie et al. Profits and pandemics: prevention of harmful effects of tobacco, alcohol, and ultra-processed food and drink industries, Lancet, vol. 381, No. 9867 February, 2013

Mechanism of action/pathophysiology of obesity:

  • A.J. Cox et al. Obesity, inflammation, and the gut microbiota. Lancet Diabetes, vol. 3 (3) July 22, 2014
  • T. Deng et al. Class II major histocompatibility complex plays an essential role in obesity-induced adipose inflammation, Cell Metabolism, vol. 17 (3) March 5, 2013
  • J. R. Marchesi et al. The gut microbiota and host health: a new clinical frontier, Gut, Sept. 2015
  • H. Guo et al. Inflammasomes: mechanism of action, role in disease, and therapeutics, Nature Medicine, June 29, 2015
  • M. Bawa, V.A. Saraswat, Gut-Liver Axis: Role of Inflammasomes, Journal of Clinical and Experimental Hepatology, vol. 3 (2) June 2013
  • E. Le Chatelier et al. Richness of human microbiome correlates with metabolic markers, Nature 500, pages 541–546, 29 August 2013
  • To understand the mechanism of action leading to obesity and how these can be reversed with the appropriate foods and pre- and probiotics and why the following Wikipedia entries are excellent sources: see entries on Pyroptosis, Prebiotics, Probiotics, Oligosaccharides, and Inulin

Helke Ferrie is a medical science writer with a master's degree in physical anthropology. Her specialty lies in investigative research into ethical issues in medicine and the politics of health. She started her investigative journalism career in the mid-1990s, looking at issues of medicine and environment. She has been a regular contributor to Vitality Magazine ever since. Helke has also authored books on various subjects including: "Ending Denial: The Lyme Disease Epidemic", "What Part of No! Don't They Understand: Rescuing Food and Medicine from Government Abuse", and "The Earth's Gift to Medicine".

Write a Comment

view all comments