similarities between germ-free mice and ketogenic humans

similarities between germ-free mice and ketogenic humans

tracing a chain of ideas

Sometimes the assumptions that scientists start with about what is “good”, “healthy”, or “normal” can cause them to interpret results in a completely different way than someone starting with different assumptions would have. Then, the resulting conclusions become the assumptions in the next round of interpretation, leading to a chain of logic in which one questionable assumption leads to another.

We recently read a paper in which the authors made a series of logical steps, and it became almost comical to us how at each step we would have interpreted their results in an opposite way than they did.

When the results of their experiment are looked at from our perspective, it suggests an intriguing hypothesis:

Maybe some of the health benefits a ketogenic diet are due, not just to the diet being low in digestible carbohydrate and thus leading to ketosis, but also to being low in indigestible fiber and thus starving certain gut bacteria.

Or, to phrase the same hypothesis differently, maybe one mechanism by which a glycolytic or high-fiber diet causes health problems is that it feeds harmful gut bacteria, and the presence of those bacteria causes the health problems.

If that hypothesis were true, it would imply that if you are eating a low-carb diet, then including a lot of low-carb vegetables would feed these hypothesized harmful gut bacteria and reduce some of the potential health benefits of a low-carb diet.

in brief

The purpose of this article is two-fold:

  • First, to compare the authors' interpretations of the observations to ours, given what we know about the metabolic effects of ketogenic diets.

    We draw attention to the fact that the metabolism of germ-free mice is strikingly similar to that of ketogenic dieters. This similarity holds at the whole-body level in terms of behaviour and physical characteristics, as well as the level of mitochondrial energetics. We show that these characteristics appear to be beneficial.

  • Second, to raise the following questions:

    Are some of the benefits of a ketogenic diet mediated by starving gut bacteria, and if so, does eating fiber (i.e. low-carb vegetables) reduce some of the health benefits of a keto diet? Would eating a carbohydrate- and fiber- free diet confer some keto-like benefits even in the absence of ketosis?

the end of the chain

It all started when we saw the following statement on the Wikipedia page about butyrate :

"Butyrates are important as food for cells lining the mammalian colon (colonocytes). Without butyrates for energy, colon cells undergo autophagy (self digestion) and die.[1] Short-chain fatty acids, which include butyrate, are produced by beneficial colonic bacteria (probiotics) that feed on, or ferment prebiotics, which are plant products that contain adequate amounts of dietary fiber."

The topic of butyrate is exciting to some scientists, because they have the idea that eating indigestible fiber is good for human health. Epidemiological studies have found correlations between high fiber intake and relatively less disease. However, randomised controlled trials have repeatedly failed to confirm the hypotheses that the fiber intake was actually protective. [1]. Therefore when a new idea comes up that might explain how eating fiber would be good for human health, scientists still hoping for such evidence latch onto it. Butyrate is an example of such a candidate mechanism for how eating fiber would be good for human health.

To us, since we think that eating fiber is useless (at best) for health, the statement above poses a challenge and a mystery. Almost the only source of butyrate in the human body is, as the wikipedia page explains in the excerpt above, from gut bacteria digesting fiber that you ate. (There's also some butyrate in butter, presumably made the same way in cows.)

If butyrate is necessary for the health and even the survival of colon cells, wouldn't that mean that a low-fiber diet — such as an all-meat diet — would be very unhealthy? Amber hasn't eaten any significant amount of indigestible fiber in more than four years; does this mean that her colon cells have died off?

So we set out to investigate what led to that statement on wikipedia. Our investigation ultimately led to an intriguing hypothesis about a candidate mechanism to explain some of the health benefits of a keto diet.

The paper referenced as "[1]" on the wikipedia page is Donohoe-2011-“The Microbiome and Butyrate Regulate Energy Metabolism and Autophagy in the Mammalian Colon”. We read it with interest.

The authors of this paper performed a good experiment, made precise measurements, got interesting results, and clearly reported their results. But when it came to interpretation, they started with some assumptions we don't think are warranted, and therefore produced a chain of reasoning that eventually led them and their readers, such as the authors of the wikipedia page, to conclusions that are opposite from ours.

similarities between germ-free mice and ketogenic dieters

If you have followed the debates about low-carb diets conferring a metabolic advantage (demonstrated by their superior performance as weight loss diets [2], [3]) then the above description of germ-free mice should sound familiar. Compared to low-fat dieters, ketogenic dieters tend to be leaner (i.e. have a higher ratio of muscle to body fat), and have lower insulin and blood glucose levels. This can happen despite similar caloric intake. Their liver glycogen levels are also lower; ketogenesis may depend on low glycogen levels [4].

However, the germ-free mice are not ketogenic, presumably because they are consuming regular, glucose-plentiful diets. In fact they are less ketogenic than the conventional mice, as measured by beta-hydroxybutyrate in the blood.

So what is the cause of the similarity in metabolism between germ-free mice and ketogenic humans?

There is one other important way in which the germ-free mice were different from the conventional mice. They had lower NADH/NAD+ ratios and ATP levels (per mitochondrion) in their colon cells, but not in the liver, heart, or kidneys. Note that the heart, liver and kidneys favour fat metabolism, even in glycolytic (non-ketogenic) dieters [5].

The authors took this to be further evidence that the mice were in a state of energy deprivation, even though by all accounts they appeared to be using substantially more energy. They even previously mentioned this in connection with the reduced fatness:

"[Germ-free] mice exhibit increased locomotor activity. Therefore, the increased food consumption and decreased body fat of germ-free mice may simply be due to increased energy expenditure." — from Donohoe-2011

However, it is a mistake to assume that lower NADH/NAD+ ratios and ATP levels per mitochondrion corresponds to less cellular energy. In fact, it is likely to be the opposite.

mitochondrial energetics is the commonality

There are three other conditions we know of that reduce the NADH/NAD+ ratio: calorie restriction [6], ketogenic diets [7], and the diabetes drug metformin [8]. Ketogenic diets share mechanisms with caloric restriction. Indeed, it seems likely that benefits of calorie restriction come from the activation of ketone bodies [9].

When you use fat and ketones for fuel instead of glucose, you produce fewer free radicals through reducing the NADH/NAD+ ratio [6]. This is probably the main mechanism by which it achieves the neuroprotection we mentioned in a recent post. Similarly, the reduction of the NADH/NAD+ ratio is probably one of the mechanisms by which calorie restriction can increase lifespan [5].

Calorie restriction also preserves ATP production, but it does this by increasing the number of mitochondria to match or exceed the lower ATP yield per mitochondrion [10], [11]. There is preliminary evidence that a ketogenic diet also increases mitochondrial number [12], [13]. So the idea of Donohoe et al. — that total ATP production is compromised because the NADH/NAD+ ratio in the individual mitochondrion has lowered ATP output per mitochondrion — seems unwarranted. Instead, there is likely to be a compensatory increase in mitochondrial number. That would be consistent with the fact that the mice appear to have more energy, not less. Ketogenic dieters have also been measured to have more energy expenditure than low-fat dieters [14].

So, a reduction of NADH/NAD+ ratio is associated with health benefits, and proposed longevity mechanisms. As you might now suspect, previous studies have shown that germ-free animals have increased lifespans [15]. (They also show decreased anxiety [16] and increased bone mass [17]. Once again, to us this sounds like a better kind of mouse to be!)

fiber-free for better health?

Given this observation — that some of the benefits of ketogenic diets are present in mice that don't have gut bacteria which process dietary fiber, even though the mice are not in ketosis — it raises the following questions:

  1. Could the starvation of gut bacteria be a part of the mechanism of the benefits of ketogenic diets?
  2. Since butyrate restores the mitochondrial working of the cells to be like the conventional controls (which, from our perspective, is a worse physiological state), could fiber be actually counter-productive to a ketogenic diet?
  3. In analogy to the way the putative benefits of fiber may simply be that they displace refined carbohydrates in the diet, could the reason probiotics can lead to improved health be not because they are beneficial, but because they push out more harmful strains [18]?
  4. Could a diet free of carb and fiber (i.e. one extremely low in plants) have benefits independent of its tendency to be ketogenic?

We don't have enough evidence to settle these questions, but they are interesting hypotheses that come directly from the results of this study.

in sum

  • Contrary to the conclusions of the authors and Wikipedia editors that butyrate is necessary for cell energy, we interpret the results as showing improved cellular energy in the absence of butyrate.
  • We now have another source for making hypotheses about potentially important cellular metabolism. Before we learned about germ-free mice, we could already use mechanisms discovered from caloric restriction and compare them to mechanisms of ketogenic diets. Now we can compare and contrast mechanisms from caloric restriction, ketogenic diets, and germ-free animals.
  • This raises some interesting (perhaps even provocative) questions about the health effects of dietary fiber and gut flora on human health.



Evidence type: review

Carla S Coffin, MD FRCPC and Eldon A Shaffer, MD FRCPC
Can J Gastroenterol. 2006 April; 20(4): 255–256.

(emphasis ours)

"A recent pooled analysis of 13 prospective cohort studies (6) found that dietary fibre was not associated with a reduced risk of colorectal cancer after adjusting for other dietary risk factors. The Cochrane collaboration (7) systematically reviewed five studies of over 4000 subjects for the effect of dietary fibre on the incidence or recurrence of colorectal adenomas and incidence of colorectal cancer over a two-to four-year period. The population included all subjects that had adenomatous polyps but no history of colorectal cancer or a documented ‘clean colon’ at baseline with follow-up colonoscopy. Study interventions included soluble and insoluble dietary fibre or a comprehensive dietary intervention with high fibre whole food sources. The combined data showed no outcome difference between the intervention and control groups in the number of subjects with at least one adenoma or a new diagnosis of colorectal cancer. The Cochrane reviewers (7) concluded that there was no evidence from randomized controlled trials to suggest that increased dietary fibre intake would reduce the incidence or recurrence of adenomatous polyps.

"Widespread popular media advertisements have purported the benefits of soluble fibre in lowering the risk of atherosclerotic coronary artery disease, mainly by modifying the main coronary artery disease risk factors (ie, dyslipidemia, diabetes and obesity). As for diabetes, high fibre diets slow the postprandial rise in blood glucose and thus, improve glycemic control (8). In dyslipidemic patients, pundits have proposed that psyllium lowers serum cholesterol by binding bile acids in the intestinal lumen resulting in decreased absorption and increased fecal excretion. The ensuing bile acid depletion increases hepatic demand for the de novo synthesis of bile acids from cholesterol. Investigating this mechanism, Van Rosendaal et al (9) found that fibre administration had no effect and certainly did not lower serum cholesterol. Similarly, an earlier study (10) comparing the effect of wheat bran on serum cholesterol of hyperlipidemic and normolipidemic controls showed no change in total cholesterol or ratio of low density lipoprotein to high density lipoprotein cholesterol. Another trial (11) of intensive dietary advice regarding fat, cereal fibre and fish intake on diet and mortality of men with a recent history of myocardial infarction did not find any substantial long-term benefit. The authors admitted to limitations of dietary data in the study (ie, only short-term period of advice and limited number of questions), but there was no evidence to guide decisions about value of dietary advice to increase fish or cereal fibre by people with coronary disease. We await the results of three Cochrane protocols undertaken to review the evidence of dietary fibre in fruits and vegetables, wholegrain cereals or high-fat, low fibre dietary intervention in the prevention of coronary heart disease (12–14). Any conclusions regarding the effectiveness of fibre for the prevention of heart disease appear premature."


"In one of the first randomized, placebo-controlled trials of the role of bran in patients with [diverticular disease] (17), the authors concluded that dietary fibre supplements do nothing more than relieve constipation, and the impression that fibre helps [diverticular disease] is “simply a manifestation of western civilization’s obsession with the need for frequent defecation”. Recent systematic reviews (18,19) of the role of dietary fibre and [diverticular disease] (both asymptomatic diverticulosis and symptomatic diverticulitis) conclude that most of the positive evidence of the effects of fibre supplementation in treating or preventing disease is from retrospective analyses with inherent limitations and high risk of bias."


"Systematic reviews have shown that the treatment of IBS patients with fibre is controversial. One recent meta-analysis of 17 randomized controlled trials (20) quantified the effectiveness of different types of fibre. The reviewers found that fibre was only marginally effective in terms of global symptom improvement or constipation and there was no effect in IBS related abdominal pain. Fibre has a role in treating constipation but its value for IBS, pain and diarrhea is controversial. Any effectivenss of fibre in the long-term management of IBS remains questionable. Clinically, bran is no better than placebo in the relief of the overall symptoms of IBS, and is possibly worse than a normal diet for some symptoms."


Evidence type: review of randomised controlled trials in humans.

Hession M, Rolland C, Kulkarni U, Wise A, Broom J.
Obes Rev. 2009 Jan;10(1):36-50. doi: 10.1111/j.1467-789X.2008.00518.x. Epub 2008 Aug 11.


There are few studies comparing the effects of low-carbohydrate/high-protein diets with low-fat/high-carbohydrate diets for obesity and cardiovascular disease risk. This systematic review focuses on randomized controlled trials of low-carbohydrate diets compared with low-fat/low-calorie diets. Studies conducted in adult populations with mean or median body mass index of > or =28 kg m(-2) were included. Thirteen electronic databases were searched and randomized controlled trials from January 2000 to March 2007 were evaluated. Trials were included if they lasted at least 6 months and assessed the weight-loss effects of low-carbohydrate diets against low-fat/low-calorie diets. For each study, data were abstracted and checked by two researchers prior to electronic data entry. The computer program Review Manager 4.2.2 was used for the data analysis. Thirteen articles met the inclusion criteria. There were significant differences between the groups for weight, high-density lipoprotein cholesterol, triacylglycerols and systolic blood pressure, favouring the low-carbohydrate diet. There was a higher attrition rate in the low-fat compared with the low-carbohydrate groups suggesting a patient preference for a low-carbohydrate/high-protein approach as opposed to the Public Health preference of a low-fat/high-carbohydrate diet. Evidence from this systematic review demonstrates that low-carbohydrate/high-protein diets are more effective at 6 months and are as effective, if not more, as low-fat diets in reducing weight and cardiovascular disease risk up to 1 year. More evidence and longer-term studies are needed to assess the long-term cardiovascular benefits from the weight loss achieved using these diets."


Evidence type: review of randomised controlled trials in humans.

Although this analysis is not peer-reveiwed, it is thorough, appears to be accurate, and does not omit any counter-evidence as far as we are aware.
Kris Gunnars
October 15, 2013
Authority Nutrition

(emphasis ours)

"In this article, I have analyzed the data from 23 of these studies comparing low-carb and low-fat diets.

"All of the studies are randomized controlled trials, the gold standard of science. All are published in respected, peer-reviewed journals.

"The majority of studies achieved statistically significant differences in weight loss (always in favor of low-carb). There are several other factors that are worth noting:

  • The low-carb groups often lost 2-3 times as much weight as the low-fat groups. In a few instances there was no significant difference.
  • In most cases, calories were restricted in the low-fat groups, while the low-carb groups could eat as much as they wanted.
  • When both groups restricted calories, the low-carb dieters still lost more weight (7, 13, 19), although it was not always significant (8, 18, 20).
  • There was only one study where the low-fat group lost more weight (23) although the difference was small (0.5 kg – 1.1 lb) and not statistically significant.
  • In several of the studies, weight loss was greatest in the beginning. Then people start regaining the weight over time as they abandon the diet.
  • When the researchers looked at abdominal fat (the unhealthy visceral fat) directly, low-carb diets had a clear advantage (5, 7, 19).

Evidence type: review of experiments

McGarry JD, Foster DW.
Arch Intern Med. 1977 Apr;137(4):495-501.


A two-site, bihormonal concept for the control of ketone body production is proposed. Thus, ketosis is viewed as the result of increased mobilization of free fatty acids from adipose tissue (site 1) to the liver (site 2), coupled with simultaneous enhancement of the liver's capacity to convert these substrates into acetoacetic and beta-hydroxybutyric acids. The former event is believed to be triggered by a fall in plasma insulin levels while the latter is considered to be effected primarily by the concomitant glucagon excess characteristic of the ketotic state. Although the precise mechanism whereby elevation of the circulating [glucagon]:[insulin] ratio stimulates hepatic ketogenic potential is not known, activation of the carnitine acyltransferase reaction, the first step in the oxidation of fatty acids, is an essential feature. Two prerequisites for this metabolic adaptation in liver appear to be an elevation in its carnitine content and depletion of its glycogen stores. Despite present limitations the model (evolved mainly from rat studies) provides a framework for the description of various types of clinical ketosis in biochemical terms and may be useful for future studies."


Evidence type: authority

El Bacha, T., Luz, M. & Da Poian, A. (2010)
Nature Education 3(9):8

"[M]any different cells do oxidize fatty acids for ATP production. Between meals, cardiac muscle cells meet 90% of their ATP demands by oxidizing fatty acids. Although these proportions may fall to about 60% depending on the nutritional status and the intensity of contractions, fatty acids may be considered the major fuel consumed by cardiac muscle. ... Other organs that use primarily fatty acid oxidation are the kidney and the liver."


Evidence type: controlled non-human animal experiments

Su-Ju Lin, Ethan Ford, Marcia Haigis, Greg Liszt, and Leonard Guarente.
Genes Dev. 2004 January 1; 18(1): 12–16.

"Our studies show that a switch to oxidative metabolism during CR increases the NAD/NADH ratio by decreasing NADH levels. NADH is a competitive inhibitor of Sir2, implying that a reduction in this dinucleotide activates Sir2 to extend the life span in CR. Indeed, overexpression of the NADH dehydrogenase specifically lowers NADH levels and extends the life span, providing strong support for this hypothesis. Regulation of the life span by NADH is also consistent with the earlier finding that electron transport is required for longevity during CR (Lin et al. 2002). The NAD/NADH ratio reflects the intracellular redox state and is a readout of metabolic activity. Our findings suggest that this ratio can serve a critical regulatory function, namely, the determination of the life span of yeast mother cells. It remains to be seen whether this ratio will serve related regulatory functions in higher organisms."


Evidence type: controlled non-human animal experiments

Marwan Maalouf, Patrick G. Sullivan, Laurie Davis, Do Young Kim, and Jong M. Rho Neuroscience.
2007 March 2; 145(1): 256–264.

"[W]e demonstrate that ketones reduce glutamate-induced free radical formation by increasing the NAD+/NADH ratio and enhancing mitochondrial respiration in neocortical neurons. This mechanism may, in part, contribute to the neuroprotective activity of ketones by restoring normal bioenergetic function in the face of oxidative stress."


Evidence type: controlled non-human animal experiment

Paul W Caton, Nanda K Nayuni, Julius Kieswich, Noorafza Q Khan, Muhammed M Yaqoob and Roger Corder
J Endocrinol April 1, 2010 205 97-106

(emphasis ours)

"Results Metformin increases SIRT1 in db/db mice

Systemic activation of SIRT1 with the activator SRT1720 is reported to lower blood glucose and improve insulin sensitivity in Zucker rats and diet-induced obese mice in part through inhibition of hepatic gluconeogenesis (Milne et al. 2007). Therefore, we investigated whether metformin inhibited gluconeogenesis through changes in hepatic SIRT1. Eight-week-old db/db or control (db/m) mice were administered metformin (250 mg/kg per day; 7 days). Levels of SIRT1 protein, activity and NAD+/NADH ratio were significantly increased in metformin-treated db/db mice compared with the controls and untreated db/db mice (Fig. 1A, C and D). Despite increased protein levels, Sirt1 mRNA levels were unchanged following metformin treatment (Fig. 1B). Levels of SIRT1 protein and activity as well as NAD+/NADH levels were unchanged between the control and untreated mice (Fig. 1A–C). Metformin had no effect on SIRT1 in control mice (data not shown). Furthermore, incubation of HepG2 cells with metformin (2 mM) also resulted in increased levels of SIRT1 protein and activity and NAD+/NADH ratio (Fig. 1E–G). This indicates that increasing SIRT1 protein and activity could be a key mechanism by which metformin inhibits gluconeogenic gene expression."


Evidence type: review of experiments

Marwan A. Maalouf, Jong M. Rho, and Mark P. Mattson
Brain Res Rev. 2009 March; 59(2): 293–315.

"Calorie restriction and the ketogenic diet share two characteristics: reduced carbohydrate intake and a compensatory rise in ketone bodies. The neuroprotective effects of reduced carbohydrate per se are being investigated by several research groups (Mattson et al. 2003; Ingram et al. 2006). We have evaluated the possibility that ketone bodies might mediate the neuroprotective effects of calorie restriction and of the ketogenic diet. An expanding body of evidence indicates that ketone bodies are indeed neuroprotective and that the underlying mechanisms are similar to those associated with calorie restriction - specifically at the mitochondrial level."


Evidence type: review of clinical reports

G. López-Lluch, N. Hunt, B. Jones, M. Zhu, H. Jamieson, S. Hilmer, M. V. Cascajo, J. Allard, D. K. Ingram, P. Navas, and R. de Cabo
Proc Natl Acad Sci U S A. 2006 February 7; 103(6): 1768–1773.

"[M]itochondria under CR conditions show less oxygen consumption, reduce membrane potential, and generate less reactive oxygen species than controls, but remarkably they are able to maintain their critical ATP production. In effect, CR can induce a peroxisome proliferation-activated receptor coactivator 1α-dependent increase in mitochondria capable of efficient and balanced bioenergetics to reduce oxidative stress and attenuate age-dependent endogenous oxidative damage."


Evidence type: review of controlled experiments

Marwan A. Maalouf, Jong M. Rho, and Mark P. Mattson
Brain Res Rev. 2009 March; 59(2): 293–315.

(emphasis ours)

"Slowing of brain aging in calorie-restricted animals was originally believed to result from reduced metabolic activity and, hence, decreased production of reactive oxygen species, a natural byproduct of oxidative metabolism (Wolf 2006). Several studies revealed that calorie restriction was associated with energy conservation (Gonzales-Pacheco et al. 1993; Santos-Pintos et al. 2001) and that mitochondria isolated from calorie-restricted animals produced less ATP than those from controls fed ad libitum, a finding compatible with increased UCP activity (Sreekumar et al. 2002; Drew et al. 2003). However, separate investigations in rodents have suggested that, when adjusted for body weight, metabolic rate does not decrease with calorie restriction (Masoro et al. 1982; McCarter et al. 1985; Masoro 1993). More importantly, calorie restriction prevents the age-related decline in oxidative metabolism in muscle (Hepple et al. 2005; Baker et al. 2006). These data are supported by recent studies indicating that, in contrast to isolated mitochondria, ATP synthesis in intact myocytes and in vivo does not decrease following calorie restriction (Lopez-Lluch et al. 2006; Zangarelli et al. 2006). Additional support is provided by the finding that, in yeast, oxidative metabolism increases with calorie restriction (Lin et al. 2002). […] Although the effects of calorie restriction on ATP generation might appear to contradict those on uncoupling proteins, this discrepancy can be explained by the fact that calorie restriction also promotes mitochondrial biogenesis, thereby enhancing total metabolic output per cell while decreasing mitochondrial production of reactive oxygen species (Diano et al. 2003; Nisoli et al. 2005; Civitarese et al. 2007)."


Evidence type: in vitro non-human animal experiment

Bough KJ, Wetherington J, Hassel B, Pare JF, Gawryluk JW, Greene JG, Shaw R, Smith Y, Geiger JD, Dingledine RJ.
Ann Neurol. 2006 Aug;60(2):223-35.

"OBJECTIVE The full anticonvulsant effect of the ketogenic diet (KD) can require weeks to develop in rats, suggesting that altered gene expression is involved. The KD typically is used in pediatric epilepsies, but is effective also in adolescents and adults. Our goal was to use microarray and complementary technologies in adolescent rats to understand its anticonvulsant effect.

METHODS Microarrays were used to define patterns of gene expression in the hippocampus of rats fed a KD or control diet for 3 weeks. Hippocampi from control- and KD-fed rats were also compared for the number of mitochondrial profiles in electron micrographs, the levels of selected energy metabolites and enzyme activities, and the effect of low glucose on synaptic transmission.

RESULTS Most striking was a coordinated upregulation of all (n = 34) differentially regulated transcripts encoding energy metabolism enzymes and 39 of 42 transcripts encoding mitochondrial proteins, which was accompanied by an increased number of mitochondrial profiles, a higher phosphocreatine/creatine ratio, elevated glutamate levels, and decreased glycogen levels. Consistent with increased energy reserves, synaptic transmission in hippocampal slices from KD-fed animals was resistant to low glucose.

CONCLUSION These data show that a calorie-restricted KD enhances brain metabolism. We propose an anticonvulsant mechanism of the KD involving mitochondrial biogenesis leading to enhanced alternative energy stores."


Evidence type: controlled non-human animal experiments

Srivastava S, Kashiwaya Y, King MT, Baxa U, Tam J, Niu G, Chen X, Clarke K, Veech RL.
FASEB J. 2012 June; 26(6): 2351–2362.

(Emphasis ours)


"We measured the effects of a diet in which d-β-hydroxybutyrate-(R)-1,3 butanediol monoester [ketone ester (KE)] replaced equicaloric amounts of carbohydrate on 8-wk-old male C57BL/6J mice. Diets contained equal amounts of fat, protein, and micronutrients. The KE group was fed ad libitum, whereas the control (Ctrl) mice were pair-fed to the KE group. Blood d-β-hydroxybutyrate levels in the KE group were 3-5 times those reported with high-fat ketogenic diets. Voluntary food intake was reduced dose dependently with the KE diet. Feeding the KE diet for up to 1 mo increased the number of mitochondria and doubled the electron transport chain proteins, uncoupling protein 1, and mitochondrial biogenesis-regulating proteins in the interscapular brown adipose tissue (IBAT). [18F]-Fluorodeoxyglucose uptake in IBAT of the KE group was twice that in IBAT of the Ctrl group. Plasma leptin levels of the KE group were more than 2-fold those of the Ctrl group and were associated with increased sympathetic nervous system activity to IBAT. The KE group exhibited 14% greater resting energy expenditure, but the total energy expenditure measured over a 24-h period or body weights was not different. The quantitative insulin-sensitivity check index was 73% higher in the KE group. These results identify KE as a potential antiobesity supplement."


Evidence type: randomised controlled clinical trial

Cara B. Ebbeling, PhD; Janis F. Swain, MS, RD; Henry A. Feldman, PhD; William W. Wong, PhD; David L. Hachey, PhD; Erica Garcia-Lago, BA; David S. Ludwig, MD, PhD
JAMA. 2012;307(24):2627-2634. doi:10.1001/jama.2012.6607.

"The results of our study challenge the notion that a calorie is a calorie from a metabolic perspective. During isocaloric feeding following weight loss, REE was 67 kcal/d higher with the very low-carbohydrate diet compared with the low-fat diet. TEE differed by approximately 300 kcal/d between these 2 diets, an effect corresponding with the amount of energy typically expended in 1 hour of moderate-intensity physical activity."


Evidence type: review of non-human animal experiments

H A Gordon and L Pesti.
Bacteriol Rev. 1971 December; 35(4): 390–429.

"Two attempts have been made to construct life tables and to determine lesions at natural death in germ-free and conventional animals. One study (105) was conducted in genetically closely linked Swiss Webster mice and included over 300 germ-free and the same number of conventional controls which were introduced into the colony at the age of 12 months (to eliminate the effect of early losses). At natural death, the ages of the mice were (means and standard errors in days 19; females, are given): germ-free males, 723 681 i 12; conventional males, 480 i 10; females, 516 i 10. This pattern of survival rates seemed to continue throughout the course of the experi- ment. In the second study (335), approximately 50 germ-free and the same number of conven- tional ICR mice were introduced into the colony after weaning. At natural death, the age of the mice was (using the same mode of expression): germ-free males, 556 i 43; females, 535 + 46; 41; females, 547 ± conventional males, 536 45. In the first trimester of life, the survival rate was essentially the same in the germ-free and conventional control groups. In the middle third, the germ-free mice displayed an increased survival rate (e.g., 40% cumulative mortality was reached for the combined group of germ-free males and females only at the age of approximately 580 days, whereas for the conventional controls this value was approximately 410 days). Increased mortality of the germ-free group at more advanced age resulted in the similarity of mean ages between the opposing animal groups when all animals participating in the study were considered."


Evidence type: controlled non-human animal experiment

Rochellys Diaz Heijtz, Shugui Wang, Farhana Anuar, Yu Qian, Britta Björkholm, Annika Samuelsson, Martin L. Hibberd, Hans Forssberg, and Sven Pettersson
Proc Natl Acad Sci U S A. 2011 February 15; 108(7): 3047–3052.

"Microbial colonization of mammals is an evolution-driven process that modulate host physiology, many of which are associated with immunity and nutrient intake. Here, we report that colonization by gut microbiota impacts mammalian brain development and subsequent adult behavior. Using measures of motor activity and anxiety-like behavior, we demonstrate that germ free (GF) mice display increased motor activity and reduced anxiety, compared with specific pathogen free (SPF) mice with a normal gut microbiota. This behavioral phenotype is associated with altered expression of genes known to be involved in second messenger pathways and synaptic long-term potentiation in brain regions implicated in motor control and anxiety-like behavior. GF mice exposed to gut microbiota early in life display similar characteristics as SPF mice, including reduced expression of PSD-95 and synaptophysin in the striatum. Hence, our results suggest that the microbial colonization process initiates signaling mechanisms that affect neuronal circuits involved in motor control and anxiety behavior."


Evidence type: controlled non-human animal experiment

Sjögren K, Engdahl C, Henning P, Lerner UH, Tremaroli V, Lagerquist MK, Bäckhed F, Ohlsson C.
J Bone Miner Res. 2012 Jun;27(6):1357-67. doi: 10.1002/jbmr.1588.


The gut microbiota modulates host metabolism and development of immune status. Here we show that the gut microbiota is also a major regulator of bone mass in mice. Germ-free (GF) mice exhibit increased bone mass associated with reduced number of osteoclasts per bone surface compared with conventionally raised (CONV-R) mice. Colonization of GF mice with a normal gut microbiota normalizes bone mass. Furthermore, GF mice have decreased frequency of CD4(+) T cells and CD11b(+) /GR 1 osteoclast precursor cells in bone marrow, which could be normalized by colonization. GF mice exhibited reduced expression of inflammatory cytokines in bone and bone marrow compared with CONV-R mice. In summary, the gut microbiota regulates bone mass in mice, and we provide evidence for a mechanism involving altered immune status in bone and thereby affected osteoclast-mediated bone resorption. Further studies are required to evaluate the gut microbiota as a novel therapeutic target for osteoporosis."


Evidence type: review of experiments and hypotheses

Parvez S, Malik KA, Ah Kang S, Kim HY.
J Appl Microbiol. 2006 Jun;100(6):1171-85.

(emphasis ours)


Probiotics are usually defined as microbial food supplements with beneficial effects on the consumers. Most probiotics fall into the group of organisms' known as lactic acid-producing bacteria and are normally consumed in the form of yogurt, fermented milks or other fermented foods. Some of the beneficial effect of lactic acid bacteria consumption include: (i) improving intestinal tract health; (ii) enhancing the immune system, synthesizing and enhancing the bioavailability of nutrients; (iii) reducing symptoms of lactose intolerance, decreasing the prevalence of allergy in susceptible individuals; and (iv) reducing risk of certain cancers. The mechanisms by which probiotics exert their effects are largely unknown, but may involve modifying gut pH, antagonizing pathogens through production of antimicrobial compounds, competing for pathogen binding and receptor sites as well as for available nutrients and growth factors, stimulating immunomodulatory cells, and producing lactase. Selection criteria, efficacy, food and supplement sources and safety issues around probiotics are reviewed. Recent scientific investigation has supported the important role of probiotics as a part of a healthy diet for human as well as for animals and may be an avenue to provide a safe, cost effective, and 'natural' approach that adds a barrier against microbial infection. This paper presents a review of probiotics in health maintenance and disease prevention."


  1. Excellent.

    Will add a precis of this and some of those studies to my collection of stuff about the BS of fiber:


    The way I see it, fiber is only good on a junk food diet - it helps get the crap back OUTTA your system, and displaces otherwise more harmful refined carbohydrates.

  2. This:


    Also in the ketogenic diet talk.

    1. That's an interesting connection. There is much to learn about the modulation of food by microbiota.

      "Cellular tubers, leaves, and fruits" are fibrous, though, so that hypothesis is another one that seeks to explain why fiber carbs are less detrimental than non-fiber carbs. I agree that they are, but I'm still not convinced they are better than none at all.

  3. So then my next thought is "what about butter"? Since it contains butyrate, should we consider it in terms of gut biota and energy?

    1. Good question. Butyrate appears to be able to be used ketogenically, but not when it is absorbed directly. That is, is can be antiketogenic or ketogenic, and I don't know which it would be in the context of a low carb diet. Also, I've read that butter is about 3% butyrate, and I don't know if that is enough to make a big difference at a typical rate of eating it.

  4. mitochondrion -- singular
    mitochondria -- plural

  5. Very nice dissection of the Donohoe paper.
    I guess RS is the fiber of choice at the moment. I see that in the latest discussion on FTA it is claimed that:
    (1) "on a low carb diet, colonocytes are fueled by blood glucose and this puts them at a disadvantage for normal apoptosis and in a ‘high-risk’ environment for colo-rectal cancer. Study: link to ncbi.nlm.nih.gov"
    and at the same time:
    (2) the old canard of a lack of glucose leading to mucin deficiency (supposedly leading to esophageal or colorectal cancer) is once again restated.
    So apparently on LC there's enough glucose to lead to cancer, and not enough glucose which also leads to cancer!

    1. Yar, my take on the RS hullaballoo is this:

      "“To review the problem for low carbers: Sorry low carbers, your microbiome is just not that into you, by Jeff Leach”

      I think Leach is doing great things, this article isn’t one of them.

      The headline act is touting stuff about “low carb” but then it’s mostly about fiber and resistant starch? Both of which you can get plenty of on LC – the question in the end is, should you…?

      I think the whole RS thing is interesting, also far and away a healthier option than the average refined carb diet, but the evidence that you’re better off with it as opposed to not eating starch at all is simply not compelling."

      As I said, I think RS as your main carbohydrate intake is better than a "normal" diet, but the touted benefits are typically plenty available without it at all.

      It's interesting on face value, but when you look at the laundry list of stuff RS is supposed to do for you in a lightly sarcastic response:

      "systemic immunity response, colon cancer risk factors, resistance to disease, colonic and plasma SCFA, glucose response, blood pressure regulation, insulin response, mineral absorption, leptin regulation, and decrease pathogens"

      These are all rather nebulous outcomes one would think, every single one of them are well known to occur on a ketogenic/zero carb regime also - well except maybe for the colonic SCFA thing, but as discussed elsewhere I don't find that to be a particularly convincing argument - just because I *can* make fat outta my arse doesn't necessarily mean I should.

  6. Reading this gives me some context to Ash's posts on FTA.

    The whole 'RS Roadshow' I have been putting on is not aimed at ketogenic dieters or to sway a person to eat a particular way. It is more about a missing nutrient in the SAD and Paleo Diet. BILLIONS are spent (wasted) annually by people trying to influence gut microbes, with the holy grail being bifidobacteria. A gut full of bifido should give us bionic guts and health outcomes associated with better intestinal influence. Most people on a Western diet have very little bifido, and in it's place are pathogens that often overgrow into the small intestine. An increase in bifidobacteria will not occur by eating yogurt containing bifidobacteria, but it will occur if you eat lots of a specific fiber type that is favored by bacteria that produce butyrate.

    I would NEVER come to a website like this and try to convince you all your way of eating is wrong. Why you would come to FTA, which is clearly not a ketogenic-friendly place and point out the flaws in supplementing with RS to increase gut health is beyond me. If you are just prostelytizing for a ketogenic diet, that's cool, but why the need?

    If someone could show me a study or even anecdotal evidence that increasing probiotic strains of bacteria, decreasing pathogenic, and eating to favor butyrate producing bacteria on a diet OTHER than ketogenic, I would be very interested.

    In the article above, my only critique is the off-hand use of the term 'fiber'. One thing we have spent months on at FTA is the worthlessness of the term 'fiber'. It is an outdated term. I agree wholeheartedly that no one needs to go out of their way to get more 'fiber'. Fiber has become a marketing ploy to make crap food appear healthy.

    What is needed is a breakdown of fiber types other than soluble and insoluble, which are meaningless. We need to know about prebiotic fiber, fermentable fiber, butyrogenic fiber, bulking fiber, non-fermentable fiber--that sort of thing. And also, the US RDAs for fiber are meaningless without a breakdown of how fiber is handled in the body. 20g/day of wheat chaff does not compare in any way to 10g RS + 10g Pectin or Psyllium....but I digress. This is things people who are on non-ketogenic diets worry about.

    Hope I didn't offend anyone...not my intention.
    Tatertot from FTA

    1. Hi, Tim.

      No offence taken here.

      Those are very good points about the narrowness of our current use of pre/probiotics, and the vagueness of the term fiber.

      My intention is not to proselytise (though of course this site is aimed to educate about the benefits of ketosis). I'm just offering a different interpretation of some observations.

      I agree that in some ways the concerns of ketogenic dieters are independent of the concerns of glycolytic dieters.

      I am glad different people are exploring different avenues. We can all learn from each other.

      To me, the "fiber" angle is an interesting part of this post, but I'm even more interested in the NADH/NAD+ ratio angle.

      It's a coincidence that RN and I posted around the same time (although the topic is getting hotter and hotter and more likely to coincide).

    2. Nah man, I'm not proselytes... prozylet.. prolystell.. telling anyone *how* to eat, note that I spoke about the "sorry low carbers" article which I've seen pop up a bunch of times and take issue with, therefore even though I'm not mentioning a ketogenic diet specifically, my input IS topical.

      I go to FTA because I dig Richard and his ravings, and whilst I we lean different directions on diet, we're both on the same train.

      The rest of my points are that I'm NOT putting the poo poo on RS, I'm simply saying that RS is a probably a good idea on a "normal" diet - but the touted benefits aren't really anything more than what I'd get simply by avoiding the "neolithic agents of disease" - which I think we all agree with.

      All in all you're doing great work, hopefully my snarky input will only help you to improve. :)

    3. "Why you would come to FTA, which is clearly not a ketogenic-friendly place and point out the flaws in supplementing with RS to increase gut health is beyond me."

      Tim/tatertot, FTA was ketogenic-friendly up until a few months ago. In fact, RN was quite vicious against anyone who disagreed with the keto diet. Now FTA is vicious and bullying against low-carb.

      The current spate will continue until RN decides that the fad he's currently pushing, potato starch as Life Source, isn't getting him enough attention.

      As RN has gotten more and more bored, FTA has turned into a lousy source for diet info. I think that's why RN is taking the blog back to its original anti-government role.

    4. Let's not argue about Richard's motivations. I like to assume people are sincere unless there is strong evidence otherwise.

  7. I tried a ketogenic diet. I had been VLC for nearly a year, then went full keto. Hated it! Maybe I didn't allow enough time to fully adapt, but I found I couldn't do any exertion without massive muscle cramps and soreness--lifting and bodyweight exercises were out of the question! Brain fog was immense. I tried for about 8 weeks at zero - 20g carbs/day. I was finally so sore after trying to do a few pullups, that I caved in and went back to regular LC diet. Soreness went away almost immediately.

    I have always been intrigued by a keto diet and keto athletes especially -- maybe some of us are just better adapted to a keto diet.

    I have a couple great papers on the fatty acid metabolism pathways of resistant starch, but as I recall Butyrate produced by co-feeders of RS is oxidized to CO2 (as 2 acetyl CoA) and this butyrate is also partially metabolized to β-hydroxy-butyric acid (BHBA) and yields 1 NADH for metabolism to 3 ATP while BHBA is oxidized peripherally. I'll try to find the papers and link them here if anyone is interested--we sent them to Peter at Hyperlipid nearly 6 months ago but he has been silent thus far. It seemed to me a real smoking gun for damage done to colonocytes when starved of exogenous food source.

    1. One thing that I think can help a lot when you are troubleshooting ketosis and keto-adaptation is to measure serum BOHB. You can never really be sure if you are in deep ketosis otherwise. Also if you are having muscle cramps, then taking electrolytes for a while could be the key.

      Papers are always welcome. I'm not sure I would respond within 6 months either, though — my queue is already immense, and I really ought to be working on my thesis this morning… ☺

  8. I am currently trying the RS/psylium/soil based organism thing. If it is good for you, the dose is probably too high. I just can't believe flatulence is a positive marker for health.
    Anyway, I learned recently that much of the reason for my gut problems is sulfur. Due to 23&me I found out I likely don't make as much of the enzyme as other people. Based on that info, I found molybdenum to be the closest thing to a miracle pill that I have ever seen. I started on Tatertot's protocol because I figured it would help me rebuild my gut flora. It is certainly helping me do that.
    There seem to be a few folks on the 23&me forums finding the thread on sulfur sensitivities and figuring out this is the cause of their problems. I don't know how to assess the situation- I know I have gone through FODMAPS, various probiotics, avoided histamines, ate fermented foods, and even tried some of Ray Peat's stuff. I didn't think very highly of fiber and am not particularly sure of it now, though I don't mind feeding my gut bacteria if they behave nicely and keep me happy.
    What if a lot of the IBS out there is really sulfur sensitivity and not any of this other stuff? I'd like to see people check on this possibility, but I don't want to just add to the general noise level.

    1. Hi, August. I have also looked into these kinds of explanations; I am heterozygous for an unfavourable MTHFR mutation, and one of my sons is homozygous.

      However, for me, many of the supplements that are supposed to be beneficial in such a case actually worsen my mood, including the sulfur donor SAMe. Insofar as I have tried giving them to my son, they have worsened his symptoms, too. Molybdenum didn't hurt, but I didn't notice it helping, either.

      I agree that there is no reason to be against gut bacteria if they aren't causing problems. I'm sure I still have plenty of life in my intestines!

      Good luck finding more answers.

  9. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435786/ - "Stopping or reducing dietary fiber intake reduces constipation and its associated symptoms"

    1. I did an extraction of that study and some others in the link in the first comment posted here.

  10. Some thoughts - less ATP because more uncoupling?
    And, "fibre" can be produced endogenously as mucus. Metformin stimulates this - does ketosis???

    1. Hi.

      Uncoupling is involved, I don't yet understand how.

      I hadn't heard about the mucin-metformin connection. That's very interesting. Metformin is fascinating, because it seems to get to a deeper level of cause than previous drugs, thus avoiding many of their side-effects.

      While chasing this lead you gave me, I found the following paper: Influence of antibiotics on intestinal mucin in healthy subjects.. The abstract includes these sentences:

      "To determine the effect on microbial breakdown of intestinal mucin healthy volunteers were treated orally with ten different antibiotics. The most pronounced effects were seen after administration of bacitracin, clindamycin or vancomycin: the electrophoretic mucin pattern in faeces changed from a normal conventional pattern to a specific pattern similar to that found in germ-free rats."

      It is not open access, so I will clarify that a bit for interested readers without subscriptions:

      "It is a well-established fact that mucin produced in the gastrointestinal tract is of great importance for the organism. Mucin has several functions in the body, being involved in both physiological and patho- physiological conditions. In earlier studies we have shown that germ-free animals excrete high amounts of water-soluble hexosamines (components of mucin) in faeces which produce a typical electrophoretic band pattern after staining with Schiff's reagent, a reagent for glyco- proteins and mucopolysaccharides (1, 2). This faecal glycoprotein pattern is identical to the pattern present in the colon and does not seem to be affected by different types of rat food (2). In recent studies germ-free rats receiving total parenteral nutrition showed exactly the same electrophoretic band pattern as rats eating ordinary rat food (unpublished results). Conventional animals, which excrete ex- tremely low amounts of hexosamines, and healthy humans lack this band pattern, indicating a break- down of the mucin (1-3).

      "The clinical implications of our findings are far from clear. An increasing amount of undegraded mucin on the mucosal cells could slow the rate of passage of drugs such as tetracycline (10), and limit the cholesterol absorption in the intestine by surface mucin binding of cholesterol (11 ). Increasing amounts of mucin could also affect 1he intestinal micro- climate, causing changes in pH and resulting in disturbed absorption of weak electrolytes and also drugs (12). A thicker mucin layer could also enhance host resistance to bacterial infection by binding mucin and organisms into aggregates. On the other hand, mucin can act as a culture medium for certain human pathogens (13, 14)."

      Casts more doubt on the idea that low carb dieters would have a deficit of mucous.

    2. It looks like Metformin mimics carb restriction in multiple ways (and maybe this is why it's so benign; its effects are diffused across many pathways, to a specific end-point). I don't see why this goblet cell mucin effect wouldn't be an example of this.
      Put yourself in the position of Mother Nature, Eve O'Looshin. You are designing an animal that can survive going hungry and remain fit to reproduce. You don't want all the symbiotic microbes to die off between meals, especially those you'd rather pass on to offspring. So you design things so the endogenous carbohydrate supply increases as the exogenous one declines, in a way that favours the microbes that have most survival value and culls the rest.
      It seems from the Metformin study that the mechanisms needed for this adaptation do exist, but any such hypothesis will need someone to verify that it's happening and quantify the species affected.

  11. This fascinates because I have been slowly reducing my vegetable intake over the last few years. Despite being low carb for a decade, it wasn't until I went vigilantly gluten-free that I realized the state of my intestinal health. I felt a "healing glow" in my belly for six months, my arthritis improved (and continues to do so) and all kinds of things announced themselves as gut-unfriendly. One of them was fiber.

    Low fiber is also advocated by the Fiber Menace author on his website. I have been following his recommends and things work as described. At this point, I'm down to leafy greens only.

    1. Hi, Pamela.

      I have many internet acquaintances who saw further improvements in health over "just" VLC when ditching vegetables (as did I), so I'm sympathetic to that view. Arthritis and asthma are among the common anecdotally reported improved conditions, which is interesting because (IMO) we have only vague notions about what causes them.

  12. Amber, thanks for a great post and a very interesting hypothesis! I'm already keto, so I'm going to try and reduce my vegetable intake and see what happens.

    1. Thanks for the encouragement. Let us know what happens!


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