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A Unified Theory on Obesity – Part II

In Part I of this series I discussed various facets of the leptin story vis a vis obesity physiology. This second part is going to be a similar discussion on gut microbiota. There will be significant overlap between Parts I and II, which should serve to further the unified narrative.

The gut microbiota and obesity field began in earnest in 2006 when Ley et al. reported the differences in bacterial superkingdoms between lean and obese mice [1]. Specifically, the obese mice (genetically obese, leptin deficient, ob/ob) had fewer Bacteroidetes, and more Firmicutes, than did lean (wild-type). A similar pattern was found in humans during weight loss, of increased Bacteroidetes and decreased Firmicutes while overall diversity was maintained.

Figure 1: Ley et al. (2006)

This group followed up with the publication of the now famous microbiota transplant experiment, showing that germ-free mice given a floral transplant from obese mice became fatter than counterparts receiving gut flora from lean mice [2]. The purpose of this experiment was to show a causational link between the gut floral phenotype and obesity, and on that level was a failure.

The experiment had several methodological problems, one being that the obese donor mice had a monogenetic cause of obesity, of which a causational link to gut flora had not been demonstrated*. Another problem was that the region of the intestine targeted for transplant was the caecum, below the primary absorptive section of the small intestine. With a hypothesis centered on energy harvest, to ignore the microbiome of the primary absorption section for the microbiome of a tertiary or quaternary absorption section is strange.

Figure 2: Turnbaugh et al. (2006)

The failure, however, is in the results themselves. They were able to show an increase in absorbable calories in the “obese microbiota” transplant subjects, which correlated to increased weight and adiposity, but these effects were minor.






Figure 3: Latham et al. (2009) [3]

They did not produce anything close in magnitude to genetic obesity, or even diet induced obesity, from these bacterial transplants.





From these humble roots, a highly funded and influential research field was spawned.

I became aware of this science from the popular press around 2010, as well as the ushering in of the probiotics industry on its heels. When I followed up on it in graduate school, however, red flags became apparent. Firstly, I had trouble finding someone that could explain a mechanistic link between the presence of certain bacteria and obesity.

Most of the talks I saw, articles I read, and conversations I had were centered on the presentation of the microbiome sequence and simultaneously observed macro effects. It was initially suggested that greater dietary energy harvest via fermentation of difficult to digest polysaccharides caused the obesity, but the data show only a minor caloric gain (Figure 2 above).

Another question that I couldn’t find a good answer to was about the area of intestine targeted for microbiome sequencing. Much of the research looked in the large intestine, where large populations of short chain fatty acid producing bacteria reside and harvest calories from fibers. Some of the sequencing is of fecal samples, some of dissected large or small intestine, and some of endoscopy aspirants (mostly in human studies) in the duodenum. These different sections of the intestine have distinct morphology, function, and resulting titers and diversities of bacteria from each other. This is not to say that sequence data from the large intestine cannot be compared to sequence data from other sections. The point is that if the mechanism causing the obesity has to do with the primary dietary absorptive section of the small intestine (duodenum), then that should be focused on. If it’s thought to be the caecum, where fermentation of fibers occurs, that should be the focus.

Figure 4: Gastrointestinal Histology








It seems like the microbiome field is stuck perpetually in discovery science, rather than asking hypothesis driven questions. The decision of what and where to sequence seems to be out of convenience and lab tradition rather than an experimental reason. With the differences in location of sample collection and quality of sequencing (deep sequencing, ultra-deep sequencing, etc.) it is essentially impossible to compare apples to apples microbiota results between groups.

On the topic of mechanism, there is only one that I consider demonstrated as causal, and it is conspicuously absent from much of the microbiome conversation. Lipopolysaccharide (LPS), or endotoxin, is a bacterial glycolipid component in the cell wall of gram-negative bacteria. Metabolic endotoxemia from high-fat diet, or exogenously from injection, can cause obesity and insulin resistance [4]. Metabolic endotoxemia is controlled, at least in part, by changes in gut microbiota [5], even in genetic obesity*. Deficiency of the co-receptor of the so-called LPS receptor TLR4, CD14, confers resistance to diet-induced obesity and insulin resistance [4]. Dietary fat both influences the microbiota towards LPS-producing and permeability increasing bacteria with or without obesity [6]. Some gut bacteria require certain fatty acids as growth factors [7]. Likewise, the dietary fatty acid profile influences that of the bacteria themselves, presumably changing their physiology [8].

More importantly, dietary fat increases postprandial endotoxemia [9], particularly so with saturated fat [10]. This endotoxin transport is conducted through the fatty acid absorption and subsequent chylomicron production and secretion process. Saturated fats encourage lipoprotein production more than other types of fats. The complexing of LPS with lipoproteins may be an immune action, as it results in greater excretion in bile [11]. In fact, triglyceride-rich lipoproteins are preventative of septic death in rats [12]. As explained in my review of “Saturated fatty acids activate TLR-mediated proinflammatory signaling pathways,” both transport of LPS and receptor binding and signaling is facilitated by the lipid raft stabilization properties of SFA [13], whereas PUFA destabilize lipid rafts.

Has there been a clinical treatment example of reducing endotoxemia for obesity treatment? I think that there may have been, and that will be the topic of Part III.


* At the time of the Ley et al. publication there was no known connection between leptin deficiency and subsequent gut floral changes, and whether this was involved in genetic obesity. This connection is explored later in the article.

Metabolic endotoxemia – Chronic circulating plasma lipopolysaccharide levels of ~12-58 pg/mL, or 10-15 times lower than during acute sepsis.

Chylomicrons were collected from animals fed corn oil and milk as fat sources.



[1]      Ley RE, Turnbaugh PJ, Klein S, Gordon JI. Human gut microbes associated with obesity. Nature 2006;444:1022–3. doi:10.1038/nature4441021a.

[2]      Turnbaugh PJ, Ley RE, Mahowald M a, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006;444:1027–31. doi:10.1038/nature05414.

[3]      Latham JR, Pathirathna S, Jagodic MM, Choe WJ, Levin ME, Nelson MT, et al. Selective T-Type Calcium Channel Blockade Alleviates Hyperalgesia in ob / ob Mice. Diabetes 2009;58:2656–2665. doi:10.2337/db08-1763.

[4]      Cani PD, Amar J, Iglesias MA, Poggi M, Knauf C, Bastelica D, et al. Metabolic Endotoxemia Initiates Obesity and Insulin Resistance. Diabetes 2007;56:1761–72. doi:10.2337/db06-1491.P.D.C.

[5]      Cani PD, Bibiloni R, Knauf C, Neyrinck AM, Delzenne NM. Changes in gut microbiota control metabolic diet–induced obesity and diabetes in mice. Diabetes 2008;57:1470–81. doi:10.2337/db07-1403.Additional.

[6]      Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen YY, et al. High-Fat Diet Determines the Composition of the Murine Gut Microbiome Independently of Obesity. Gastroenterology 2009;137:1716–1724.e2. doi:10.1053/j.gastro.2009.08.042.

[7]      Partanen L, Marttinen N, Alatossava T. Fats and fatty acids as growth factors for Lactobacillus delbrueckii. Syst Appl Microbiol 2001;24:500–6. doi:10.1078/0723-2020-00078.

[8]      Kankaanpää P, Yang B, Kallio H, Isolauri E, Salminen S, Kankaanpa P. Effects of polyunsaturated fatty acids in growth medium on lipid composition and on physicochemical surface properties of Lactobacilli. Appl Environ Microbiol 2004;70:129–36. doi:10.1128/AEM.70.1.129.

[9]      Harte AL, Varma MC, Tripathi G, Mcgee KC, Al-Daghri NM, Al-Attas OS, et al. High fat intake leads to acute postprandial exposure to circulating endotoxin in type 2 diabetic subjects. Diabetes Care 2012;35:375–82. doi:10.2337/dc11-1593.

[10]    Mani V, Hollis JH, Gabler NK. Dietary oil composition differentially modulates intestinal endotoxin transport and postprandial endotoxemia. Nutr Metab (Lond) 2013;10:1–9. doi:10.1186/1743-7075-10-6.

[11]    Read TE, Harris HW, Grunfeld C, Feingold KR, Calhoun MC, Kane JP, et al. Chylomicrons enhance endotoxin excretion in bile. Infect Immun 1993;61:3496–502.

[12]    Read TE, Grunfeld C, Kumwenda ZL, Calhoun MC, Kane JP, Feingold KR, et al. Triglyceride-rich Lipoproteins Prevent Septic Death in Rats. J Exp Med 1995;182:267–72.

[13]    Huang S, Rutkowsky JM, Snodgrass RG, Ono-Moore KD, Schneider D a, Newman JW, et al. Saturated fatty acids activate TLR-mediated proinflammatory signaling pathways. J Lipid Res 2012;53:2002–13. doi:10.1194/jlr.D029546.


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