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Do lean and obese people have different gut bacteria?

October 10, 2016 by Deana Ferreri, Ph.D.

Health Concerns: Overweight and Obesity

You may have heard of a study described something somewhat like this: Gut bacteria from obese mice were transferred to lean mice, and the lean mice started to gain weight.  Several studies have found variability in the microbiomes between lean and obese people. It may sound like a change to the bacterial species populating the gut could be a magic pill that sparks weight loss, but it’s not so magical; for each of us, the profile of the gut microbiome is primarily a result of what we eat.

Research on the microbiome is abundant but relatively new, and there is not yet a definition of a “healthy” gut microbiome.  There is much variability between individuals and geographical areas, and even, there is a great deal of variation between healthy Westerners, as was found from the Human Microbiome Project.1,2

Is there a “lean” microbiome and an “obese” microbiome?

The vast majority of our gut bacteria fall into two phyla: Firmicutes and Bacteroidetes. Mice also have primarily these two phyla.  Mice who are genetically engineered to be obese have more Firmicutes and fewer Bacteroidetes compared to their lean counterparts.4 Similarly, mice who are fed a Western diet and consequently become obese also have a higher Firmicutes to Bacteroidetes ratio compared to mice given a control diet.  When microbiota of obese mice are transferred to germ-free mice (mice with no gut microbiota), the mice gain weight.  When Western diet-fed obese mice are switched to a standard diet and lose weight, their Firmicutes to Bacteroidetes ratio decreases.  From these mouse studies, it seems straightforward: a high Firmicutes to Bacteroidetes ratio and obesity go hand in hand.3,5

So should obese people take a probiotic with lots of Bacteroidetes and no Firmicutes? Not so fast – it’s not that simple.

Following these mouse studies, several studies reported that obese humans also had a higher Firmicutes to Bacteroidetes ratio compared to lean humans.  However, other studies – including much larger studies utilizing data from the Human Microbiome Project – found no such difference in ratio between lean and obese humans.6,7

These studies uncovered another interesting difference though: obese humans have a less rich, less diverse microbiome; leaner people have more microbes and a greater variety of them.7-9  This difference was not only observed for obesity; low microbial content and diversity has also been associated with insulin resistance and inflammatory markers.10,11  Also the microbiota of a hunter-gatherer population who have not been exposed to processed foods or antibiotics was also found to be much more diverse than the microbiota of Americans.12

A microbiome of greater microbial content and diversity is likely a healthier microbiome.13

To build a rich, diverse microbiome, we need to feed ourselves – and our resident microbes – a health-promoting diet.  The microbial profile in the gut is malleable; each of us can alter our own microbiome.

Feeding the microbiome a high-fiber diet

The nutrients that are provided to the gut microbiome from our food determine which bacterial species thrive and which don’t.  The relatively low microbial diversity in Western populations compared to traditional hunter-gatherer and rural agrarian populations is thought to be driven by a diet low in plant fibers.  The amount and variety of plant polysaccharides (e.g. fiber and resistant starch) is the primary determinant of the composition and function of the microbiome.13

One benefit of fiber-rich foods for the microbiome is that they help to preserve the protective mucin layer over the cells of the colon.  Without adequate plant fibers, bacteria that eat the type of polysaccharides that make up the mucin layer thrive. As a result the colon wall is more vulnerable to harmful bacteria and the barrier between the gastrointestinal tract and the rest of the body is compromised.14

Also, the gut microbiome affects more than just gut health.  The microbiome produces vitamins, protects us against pathogenic microorganisms, benefits our immune system, and facilitates energy extraction from food.  These organisms also metabolize plant polysaccharides (such as fiber and resistant starch) into short-chain fatty acids: butyrate is an energy source for intestinal epithelial cells and may protect against carcinogenic changes in these cells; propionate acts as a signaling molecule in the colon wall; and acetate modulates gene expression in the gastrointestinal tract and also in other tissues.13,15

Some of the health effects of the microbiome may be due to the products of microbial fermentation, which are then absorbed into bloodstream and travel to different parts of the body.

Healthy diet, friendly microbial fermentation products

The gut microbiota metabolizes plant fiber into short-chain fatty acids such as butyrate and propionate.  Butyrate is an energy source for intestinal epithelial cells, and also helps to protect against carcinogenic changes.15  Propionate is used for glucose production in the intestinal epithelium, and based on studies in mice it is thought that the activation of intestinal glucose production genes by propionate signals to the brain, helping to improve insulin sensitivity throughout the body and reduce appetite.16  This may underlie the connection between a healthy microbiome and healthier body weight.  Fiber-rich plant foods provide the fuel for bacteria that produce short-chain fatty acids.

Poor diet, unfriendly microbial fermentation products

TMAO is an example of how a poor diet leads to an unhealthy microbiome, which produces unhealthy fermentation products.13  TMAO is produced from carnitine, an amino acid that is abundant in animal products, especially red meat; there is little or no carnitine in plant foods. TMAO (trimethylamine-N-oxide) is a pro-inflammatory molecule linked to cardiovascular risk.  The gut bacteria of people who eat more animal foods drive greater production of TMAO compared to those that eat little or no animal foods.  TMAO has been found to contribute to atherosclerotic plaque development by slowing the removal of cholesterol from the arterial wall in mice. In humans a combination of high carnitine and high TMAO was associated with increased likelihood of cardiovascular disease or cardiovascular events (heart attack and stroke).  This research suggests that regularly eating carnitine-containing foods (such as red meat) facilitates the growth of gut bacteria that more readily convert carnitine into TMAO, which is heart disease-promoting.17-19

The gut microbiome is one more way diet affects human health.

When you make a switch to a more healthful, fiber-rich diet (or the other way around), your microbiome responds quickly (within a few days),20 and maintaining that diet day to day keeps the favorable species going.  Long-term favorable dietary patterns are linked to favorable microbial patterns.21

In summary, the message people received from the early mouse studies was that there is a magical microbiota profile that can keep us from gaining weight, but it appears the evidence points toward what it always has – a healthy, high-fiber, plant-rich diet. 


  1. Yong E: There Is No 'Healthy' Microbiome. In The New York Times, November 1, 2014. []

  2. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature 2012, 486:207-214.

  3. Turnbaugh PJ, Backhed F, Fulton L, Gordon JI. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 2008, 3:213-223.

  4. Ley RE, Backhed F, Turnbaugh P, et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 2005, 102:11070-11075.

  5. Turnbaugh PJ, Ley RE, Mahowald MA, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444:1027-1031.

  6. Sze MA, Schloss PD. Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome. MBio 2016,7.

  7. Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS One 2014, 9:e84689.

  8. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484.

  9. Beaumont M, Goodrich JK, Jackson MA, et al. Heritable components of the human fecal microbiome are associated with visceral fat. Genome Biol 2016, 17:189.

  10. Le Chatelier E, Nielsen T, Qin J, et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013, 500:541-546.

  11. Cotillard A, Kennedy SP, Kong LC, et al. Dietary intervention impact on gut microbial gene richness. Nature 2013, 500:585-588.

  12. Yatsunenko T, Rey FE, Manary MJ, et al. Human gut microbiome viewed across age and geography. Nature 2012, 486:222-227.

  13. Sonnenburg JL, Backhed F. Diet-microbiota interactions as moderators of human metabolism. Nature 2016, 535:56-64.

  14. Sonnenburg ED, Sonnenburg JL. Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metab 2014, 20:779-786.

  15. Hamer HM, Jonkers D, Venema K, et al. Review article: the role of butyrate on colonic function. Aliment Pharmacol Ther 2008, 27:104-119.

  16. De Vadder F, Kovatcheva-Datchary P, Goncalves D, et al. Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell 2014, 156:84-96.

  17. Koeth RA, Wang Z, Levison BS, et al. Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 2013.

  18. Wang Z, Klipfell E, Bennett BJ, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 2011, 472:57-63.

  19. Woolston C. Red meat + wrong bacteria = bad news for hearts. In Nature, 2013 []

  20. David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014, 505:559-563.

  21. Wu GD, Chen J, Hoffmann C, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011, 334:105-108.

Deana Ferreri, Ph.D., after finishing a B.S. in biomedical engineering, researched endothelial cell biology leading to a doctorate in biomedical science in 2008. While studying the cardiovascular system, Deana became interested in nutrition and lifestyle approaches to heart disease prevention. After graduating, she aimed to use her background in science to educate people about the powerful effects of food on health. Deana has been writing science-based content for and assisting Dr. Fuhrman with literature research since 2009.


Comments (0):



10/20/2016 01:22 PM

So what about the use of Probiotics and Prebiotics? If someone is eating primarily a WFPB diet that includes fermented items like kraut, pickles, kombucha, as well as plenty of fiber (oats, beans, etc) and greens, without (or minimal) processed food, meat, dairy and added oil, then is taking a supplement necessary? And how do you know if the supplement is helping or not?

This comment was last edited on 10/20/2016 01:23 PM

Dr. Ferreri replies:

10/20/2016 04:49 PM

Since high-fiber foods act as prebiotics, probiotic supplements are generally not necessary unless someone has digestive issues or has had gut bacteria depleted (due to antibiotics for example).  Dr. Fuhrman explains here:

In most cases, a probiotic "working" would be related to improving gastrointestinal discomfort. If you are just curious about your microbiome profile or whether a supplement makes noticable changes, there are companies that will analyze your microbiome and give you some info on diversity and the phyla that are present. 

This reply was last edited on 10/20/2016 04:49 PM