Obesity: Lose Weight by Fixing Bacteria in Colon 
By Walter Sorochan Emeritus Professor San Diego State University

Posted March 02, 2016, Updated November 24, 2021. The information presented here is for informative and educational purposes only and is not intended as curative or prescriptive advice. The statements of this web-site have not been evaluated by the United States Food and Drug Administration (FDA). Nothing stated here should be considered as medical advice for dealing with a given problem, or to diagnose / treat / prevent / cure any disease. Work in progress.

Cut calories if you want to lose body weight. Others have suggested counting calories, exercise, special diet foods, and even sweating off excess pounds. But none of these have been very effective in helping obese persons lose weight for long periods of time. Furthermore, we have an epidemic of obesity that medical science is unable to solve. Professor Tim Spector, a leading genetics expert at King’s College London, claims that everything we know and have been told about diets and losing body weight is wrong!  Spector: Gut bacteria eat food left-over fiber 2015 Naish: Everything known about diets is wrong 2015

This article deals with the new information linking colon bacteria with food and obesity and suggestions on losing body weight with the help of bacteria in the colon [lower intestine]. 

Today in 2016, there is a lot of interest about a link between the food we eat, bacteria in the large intestine and obesity. For example, Kimberly Snyder, a Los Angeles-based nutritionist whose clients include the actresses Drew Barrymore and Hilary Duff, raves about the benefits of good bacterial balance for staying thin.  There is a major shift in thinking about what causes obesity. 

two-different-sized-womenBad bacteria thrive on a junk food diet!  Spector: Gut bacteria eat food left-over fiber 2015  Heighton: Junk food kills gut bacteria 2015  Naish: Everything known about diets is wrong 2015   Intestinal bacteria may help determine whether we are lean or obese. Wallis: Gut Bacteria Help Make Us Fat and Thin 201 This means that the food we eat determines the kind of bacteria that thrive in the colon.

Supporting this idea is a new theory about what really makes us fat — which could revolutionize our approach to weight loss. Professor Tim Spector, a leading genetics expert at King’s College London, believes it’s the bacteria in our gut. He has found that the type and variety of our gut bugs have an astonishing influence on many aspects of our health.  Microbes are not only essential to how we digest food. They also control the calories we absorb and provide vital enzymes and vitamins, as well as keeping our immune system healthy. Research shows that bacteria are likely to be responsible for much of our obesity epidemic. The root of the problem may be our modern diet and its effect on our gut bacteria. Spector: Gut bacteria eat food left-over fiber 2015  Naish: Everything known about diets is wrong 2015

bacterium-christensenella-minuta-in-twins-and-miceIf bacteria in the gut create toxins that can make us fat, could beneficial bacteria have the opposite effect? Professor Spector’s team experimented with a microbe called Christensenella, which is associated with being lean. When they transplanted it into mice, it prevented them getting fat — despite their being on high-fat diets.  The illustration on the right summarizes the research done on this microbe.  While this works well on lab mice, in humans the answer is not as simple as just giving the bacteria Christensenella to everyone. Other factors complicate matters significantly, such as the mix of bugs already in individual people’s stomachs [the mice’s guts were germ-free before the experiments], and the question of whether a person’s individual genes are friendly to Christensenella." Some humans who have this microbe appear to be protected against obesity but, unfortunately, many do not,’" says Professor Spector.  Naish: Everything known about diets is wrong 2015

Kind bacteria in gut making us obese

Although the information about bacteria that are linked to obesity are preliminary at this time, obesity is associated with changes in the relative abundance of two dominant bacteria:   Turnbaugh: gut bacteria link to obesity 2007 DiBaise: Microbacteria Causing obesity 2012

Bacteroidetes --- obese persons have fewer of this bacteria. These Bacteria increase in number with weight loss. 

Firmicutes --- obese persons have more of this bacteria. Obese eat less but are able to get more energy from the food they eat than lean persons; hence obese store this energy and gain more weight within 10 to 14 days. A class of bacteria found in Firmicutes, Mollicutes [ that lack a cell wall ] increase dramatically in obese persons when eating a low fat, sugar rich CHO Western diet.

Archaea [ methane-producing ] --- bacteria have been found to be present in greater abundance in obese humans than in lean individuals.  DiBaise: Microbacteria Causing obesity 2012  Turnbaugh: Obesity linked to gut bacteria 2008

The composition of the gut microbiota has been shown to differ in lean and obese humans and animals and to change rapidly in response to dietary factors. The gut microbiota may also influence the development of conditions characterized by low-level inflammation, such as obesity and type 2 diabetes, through systemic exposure to bacteria in the lower intestinal. Together, these data suggest that modification of the gut microbiota may be a relevant therapeutic avenue for obesity and other metabolic disorders.  Ley: Human gut microbes link obesity 2006   DiBaise: Microbacteria Causing obesity 2012 

Exercise is important to gut bacteria. The study of lab rats by Professor Tim Spector showed that those exercising on a wheel produced twice as much of the fatty acid butyrate in their guts compared with sedentary rats. Butyrate is produced by our gut microbes and has a broad range of beneficial effects on the immune system.  Exercise stimulates microbes to produce more of it.  Naish: Everything known about diets is wrong 2015

A study published this year in Science magazine found that mice without a protein known as toll-like receptor 5 (TLR5) in their gut gain excessive weight and develop full-blown diabetes and fatty liver disease when fed a high-fat diet.  "If we think of the gut flora as a community, TLR5 is like a neighborhood police force that can keep the houligans in check. Without TLR5, bad bacteria can get out of control. In the study authors found that these bad bacteria caused a low-grade inflammation in the mice, which caused them to eat more and develop insulin resistance. They also found that treating these mice with strong antibiotics [enough to kill most of the bacteria in the gut] reduced their metabolic abnormalities. But the most interesting part of this study is what happened when the researchers transferred the gut flora from the TLR5-deficient overweight mice into the guts of skinny mice: the skinny mice immediately started eating more and eventually developed the same metabolic abnormalities the overweight mice had. In other words, obesity and diabetes were “transferred” from one group of mice to the other simply by changing their gut flora."  Kresser: healthy gut key to weight loss 2010

To read how one person and his gut bacteria reacted to eating a MacDonald hamburger for 10 days

How modern life screws up our gut and makes us fat and diabetic, go to: Kresser: healthy gut key to weight loss 2010

What all of this research suggests is that healthy gut bacteria is crucial to maintaining normal weight and metabolism. Unfortunately, several features of the modern lifestyle directly contribute to unhealthy gut flora:

  • Antibiotics and other medications like birth control and NSAIDs [asperins, anti-acids]
  • Diets high in refined carbohydrates, sugar and processed foods
  • Diets low in fermentable fibers
  • Dietary toxins like wheat and industrial seed oils that cause leaky gut
  • Chronic stress
  • Chronic infections

We also know that infants that aren’t breast-fed and are born to mothers with bad gut flora are more likely to develop unhealthy gut bacteria, and that these  early differences in gut flora may predict overweight and obesity in the future.

Suggestions for Getting rid of obesity:  The suggestions below are based on the evidence and assumption that bacteria do play a major role in causing obesity.  The suggested steps below are intended as a guide. If you do try to follow these steps, you may need to deal with several steps at the same time. Reason: each person may have a different kind of colon bacteria and different numbers. You may need to experiment with these suggestions.

Focusing on colon bacteria does not diminish the impact of lifestyle, stress environmental toxins and other factors that may cause obesity.

Try losing body weight by trying to fix the bacteria in your colon.  This approach requires time, patience and giving up the comfort foods that feed the bad bacteria.  You should be under the guidance of an informed therapist.

Step 1:  Work with an informed therapist:  Losing body weight can cause major changes in your metabolism and how your body responds to weight lose.  Your therapist needs to monitor your weight lose.  If your doctor is not informed about digestive disorders such as leaky gut, then you need to find one who is informed.

Step 2:  Stop creating excess toxins in your body: This is a very next important step! Stop creating more toxins to a body already overburdened with toxins. For example, ingesting aspirin, non-steroidal anti-inflammatory drugs (NSAIDs), skin creams, laxatives, birth control pills, cough medicines, and antibiotics. You may also need to stop other prescription medications but consult with your medical doctor before doing so. Change the toxic environment that you may be living with, such as radiation, Electro Magnetic Forces, lead and mercury, chlorinated and fluoridated water and auto pollution. These are environments that create toxins that destroy good and bad bacteria in the gut. When toxins destroy good bacteria, a vacuum is created; allowing the bad bacteria usually rush in and suppress the good bacteria. You need to minimize the toxins in your body and give your liver a chance to get rid of them. Drink lots of water to help the liver and kidney flush out these toxins out of your body.  The body needs time to all of this.  Detoxifying your body begins to destabilize the bacteria in the colon.

Step 3:  Destabilize the existing bacteria in the colon:  If you do not cause a little bit of chaos and instability in the colon, then the bad bacteria will continue to suppress the good bacteria and make it difficult to bring about change.  You can safely destabilize the colon in two basic ways.  One way is to begin eating fermented food like sauerkraut or dill pickles along with your regular diet over several days.  To help the fermented sauerkraut, you can eat foods that have good live bacteria like cottage cheese or yogurt.  Do so over several days.  Avoid eating sweets like puddings, pies and ice-cream, soft drinks and processed foods that are full of white sugar or corn syrup.  This is a step to prepare your colon for a big change.

Step 4:  Inoculate good bacteria: You can do this with probiotic bacteria for three to five consecutive days or longer. Check your body for a change in previous symptoms like change in bowel movement, bloating and flatulence [gas]. Keep in mind that many probiotics on sale do not work because the bacteria are dead, the bacteria are too few in number or the bacteria are of the wrong kind. You should take probiotics in between meals so these are not partially or totally destroyed by digestive enzymes.  Look for a probiotic that has Firmicutes, and Mollicutes as well as other bacteria.  For more information about probiotics

Step 5:  Cultivate the new probiotic bacteria: You need to feed your baby probiotics with good food so the young bacteria may grow and repopulate the colon. Avoid eating the bad foods for these feed the bad bacteria and will retard the growth of good bacteria. Eat the good foods continuously for three to five or more days. Good food allows the good bacteria to multiply and suppress the bad bacteria. This takes time and patience.

You will know if the good bacteria are winning the colon war. How? By monitoring how you feel: has bloating and joint pain subsided? Has there been a change in your bowel movement as well as change from constipation or diarrhea? Your natural body 'feeling' sensors are more accurate than any blood or urine test.

Step 6:  Stabilize the probiotic bacteria: This is a must; and it is usually overlooked. You do this by eating a constant and consistent diet to feed the good bacteria and starve the bad guys. Good bacteria need time to increase in population and become dominant in the colon. Also, you should consider ingesting some herbs that help this healing process. How long a time? Well, everyone is different but the answer is in the next step.

Step 7:  Maintenance of healthy gut: This is the missing key for most persons trying to fix a digestive disorder. Once you have established a normal functioning gut with good bacteria, good diet and feeling good, then you have to evolve two other essential supporting habits: First, you need to continue to eat good foods and avoid the bad foods. Even having a sugar desert once a week can jump start starving bad bacteria to become aggressive and explode in number and ruin your effort to change the bacteria in your colon. Avoid bad foods, even an ice cream cone that feels good and 'comforting'. Secondly, there are many scientists who advocate taking a probiotic pill every day as a maintenance precaution, although this is an option. You should expect to occasionally eat a bad food that disrupts the normal balance of bacteria in the colon. Taking a probiotic pill every day ensures that the good bacteria will help restore and regulate the colon in spite of you letting your guard down.

Preventing a digestive disorder like leaky gut and obesity is something you have to work on every day. Just as the phrase "once an alcoholic, always an alcoholic!" And so once you have been obese, you can always become one again!

Consult with your informed therapist before trying to lose body weight.


DiBaise John K, Daniel N Frank and Ruchi Mathur, "Impact of the Gut Microbiota on the Development of Obesity: Current Concepts," Am J Gastroenterol Suppl, 2012, 1:22–27.   DiBaise: Microbacteria Causing obesity 2012

Heighton Luke, "Junk food kills bacteria that protect against obesity, heart disease and cancer, study finds," The Telegraph, May 10, 2015. Heighton: Junk food kills gut bacteria 2015

Kresser Chris, "A healthy gut is the hidden key to weight loss," Chris Kresser LET'S TAKE BACK YOUR HEALTH, October 29, 2010.  Kresser: healthy gut key to weight loss 2010

Ley Ruth E., Peter J. Turnbaugh, Samuel Klein & Jeffrey I. Gordon, "Microbial ecology: Human gut microbes associated with obesity," Nature, December 21,2006 444, 1022-1023.   Ley: Human gut microbes link obesity 2006

Ley Ruth E. and others, "Obesity alters gut microbial ecology," PNAS Physics Portal Physics.org., June 14, 2005.   Ley: Obesity alters colon bacteria 2005

Naish John, "Everything you think you know about diets is WRONG: Counting calories is a total waste of time, it’s bacteria in your gut that make you fat and finally, cheese, alcohol and chocolate can all help," Daily Mail, May 12, 2015.   Naish: Everything known about diets is wrong 2015

O'Hara, A. M. and Shanahan, F., "The gut flora as a forgotten organ," EMBO Reports, 2006, 7 (7): 688–693.  O'Hara: Unraveling gut flora as organ 2006

Ridaura, Vanessa K.; et al. (2013). "Gut microbiota from twins discordant for obesity modulate metabolism in mice". Science, 2013, 341 (6150).   Ridaura: Obesity in mice 2013

Spector Tim, "Why the GI diet might be a waste of time, but dark chocolate and microbes could be key to being a healthy weight," Independent, November 27, 2015.  Spector: Gut bacteria eat food left-over fiber 2015 [ Author of book: The Diet Myth ]

Subramanian Sathish,1,2Laura V. Blanton,1,2Steven A. Frese,3Mark Charbonneau,1,2David A. Mills,3and Jeffrey I. Gordon, "Cultivating Healthy Growth and Nutrition through the Gut Microbiota," Cell161, March 26, 2015.   Subramanian: Healthy nutrition in gut 2015

Turnbaugh, Peter J.; et al., "An obesity-associated gut microbiome with increased capacity for energy harvest," Nature, January 2007, 444 (7122): 1027–131.   Turnbaugh: gut bacteria link to obesity 2007

Turnbaugh Peter J., Fredrik Bäckhed, Lucinda Fulton, Jeffrey I. Gordon, "Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome," Cell Host & Microbe, April 17, 2008, Volume 3, Issue 4, Pages 213–223.  Turnbaugh: Obesity linked to gut bacteria 2008

Wallis Claudia, "How Gut Bacteria Help Make Us Fat and Thin," Scientific American, June 1, 2014.  Wallis: Gut Bacteria Help Make Us Fat and Thin 2014

Yong Ed, "The Most Heritable Gut Bacterium is… Wait, What is That?," National Geographic, November 06, 2014.   Yong: Bacteria, heredity & obesity 2014  

Zeevi David and others, "Personalized Nutrition by Prediction of Glycemic Responses," The Cell, November 19, 2015, Volume 163, Issue 5, p1079–1094.   Zeevi: Personalized nutrition 2015