Tag Archives: fermented foods

Your Microbiome and Obesity | The Paleo Diet

There has been a plethora of interest in the human microbiome as of late. In fact, barely a week ago, a new study was published, which showed that mice who drank water (laced with huger-suppressing bacteria) ate less, had lower body fat, and staved off diabetes – even when consuming a poor diet.1 This is just the latest of many potential breakthroughs made in the last few years in regards to the microbiome. Though this breakthrough is specific to obesity, there are many unique and diverse links made to the types of bacteria found within our gut.2, 3, 4, 5, 6, 7, 8

Your Microbiome and Obesity | The Paleo Diet

“The Role and Influence of Gut Microbiota in Pathogenesis and Management of Obesity and Metabolic …” Frontiers. N.p., n.d. Web. 31 Mar. 2015.

Interestingly, another recent study discussed the link between the lifestyles of indigenous populations, and their gut health.9 Researchers found the microbial populations among various hunter-gatherers were markedly similar – and drastically different than those who live a more modern way of life.10, 11, 12, 13 This supports the observation that human microbiomes are actively involved in health, and that subsequent changes from living more sanitized, industrialized lifestyles, has led to increased likelihood of autoimmune disorders.14, 15, 16 This is yet another way in which our Paleolithic ancestors had it right.17, 18

It has taken the scientific community some time to come around to the realization that obesity is correlated with an alteration in the gut microbiome.19, 20 Two classes of bacteria (bacteroides and firmacutes) are important here, with firmacutes bacteria being very prevalent in those whom are obese.21, 22, 23 But, it turns out not all the data supports firmacutes being the only factor. The main focus, instead, as far as mechanism goes, is the formation of increased amounts of metabolic endotoxins.24, 25 These metabolic endotoxins are more specifically, deoxycholic acid and lipopolysaccharides (LPS).26, 27

Your Microbiome and Obesity | The Paleo Diet

Schnorr, Stephanie L. et al. “Gut Microbiome of the Hadza Hunter-Gatherers.” Nature Communications 5 (2014): 3654. PMC. Web. 31 Mar. 2015.

A Paleo diet promotes improved gut health, whereas the Western diet is a large source of problems, for the microbiome.28, 29 Interestingly, we see the duality of evidence here, in that (observationally) hunter-gatherers display much better microbial profiles.30 But, we also have specific mechanistic evidence, which shows exactly how poor gut health translates into obesity. This is a clear-cut example that the Western diet (quite literally) makes us sick – and fat.

Your Microbiome and Obesity | The Paleo Diet

Brown, Kirsty et al. “Diet-Induced Dysbiosis of the Intestinal Microbiota and the Effects on Immunity and Disease.” Nutrients 4.8 (2012): 1095–1119. PMC. Web. 31 Mar. 2015.

So, what can one do, if looking to optimize their microbiome? Many will state that a probiotic is absolutely necessary, and there is no other way to improve your ratio of beneficial microbiota. This is simply not the case. Quite obviously, you should eat a nutrient-dense, protein and antioxidant packed diet. A Paleo diet is beneficial for a myriad of reasons, but including fermented foods (like sauerkraut) regularly, will result in a vastly improved ratio of good bacteria to bad bacteria. Without any extra supplementation required!

And, this improved ratio is a significant shield against obesity, as evidenced by salient scientific literature. This optimal ratio of specific types of microbes is simply something that a Western diet is not capable of achieving. If you needed one more reason to consume a delicious Paleo diet, the emerging link between gut health and obesity, is definitely one of the best reasons. Go home, enjoy a glass of kombucha or dig into a bowl of sauerkraut, and take comfort in the fact that you are helping to nurture your microbiome – so you may stay lean and healthy for a long time to come.


[1] Chen Z, Guo L, Zhang Y, et al. Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity. J Clin Invest. 2014;124(8):3391-406.

[2] Le chatelier E, Nielsen T, Qin J, et al. Richness of human gut microbiome correlates with metabolic markers. Nature. 2013;500(7464):541-6.

[3] Parekh PJ, Arusi E, Vinik AI, Johnson DA. The role and influence of gut microbiota in pathogenesis and management of obesity and metabolic syndrome. Front Endocrinol (Lausanne). 2014;5:47.

[4] Vrieze A, Van Nood E, Holleman F, Salojärvi J, Kootte RS, Bartelsman JF, et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology (2012) 143(4):913.

[5] Borody TJ, Khoruts A. Fecal microbiota transplantation and emerging applications. Nat Rev Gastroenterol Hepatol (2012) 9(2):88–96.

[6] Kadooka Y, Sato M, Imaizumi K, Ogawa A, Ikuyama K, Akai Y, et al. Regulation of abdominal adiposity by probiotics (Lactobacillus gasseri SBT2055) in adults with obese tendencies in a randomized controlled trial. Eur J Clin Nutr (2010) 64(6):636–43.

[7] Everard A, Lazarevic V, Derrien M, Girard M, Muccioli GG, Neyrinck AM, et al. Responses of gut microbiota and glucose and lipid metabolism to prebiotics in genetic obese and diet-induced leptin-resistant mice. Diabetes (2011) 60(11):2775–86.

[8] Romijn JA, Corssmit EP, Havekes LM, Pijl H. Gut-brain axis. Curr Opin Clin Nutr Metab Care. 2008;11(4):518-21.

[9] Obregon-tito AJ, Tito RY, Metcalf J, et al. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat Commun. 2015;6:6505.

[10] Brown K, Decoffe D, Molcan E, Gibson DL. Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients. 2012;4(8):1095-119.

[11] Eckburg P.B., Bik E.M., Bernstein C.N., Purdom E., Dethlefsen L., Sargent M., Gill S.R., Nelson K.E., Relman D.A. Diversity of the human intestinal microbial flora. Science. 2005;308:1635–1638.

[12] Proctor L.M. The human microbiome project in 2011 and beyond. Cell Host Microbe. 2011;10:287–291.

[13] Dethlefsen L., McFall-Ngai M., Relman D.A. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature. 2007;449:811–818.

[14] Campbell AW. Autoimmunity and the gut. Autoimmune Dis. 2014;2014:152428.

[15] Okada H, Kuhn C, Feillet H, Bach JF. The ‘hygiene hypothesis’ for autoimmune and allergic diseases: an update. Clin Exp Immunol. 2010;160(1):1-9.

[16] Konkel L. The environment within: exploring the role of the gut microbiome in health and disease. Environ Health Perspect. 2013;121(9):A276-81.

[17] Ley R.E., Hamady M., Lozupone C., Turnbaugh P.J., Ramey R.R., Bircher J.S., Schlegel M.L., Tucker T.A., Schrenzel M.D., Knight R., et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–1651.

[18] Tappenden K.A., Deutsch A.S. The physiological relevance of the intestinal microbiota—Contributions to human health. J. Am. Coll. Nutr. 2007;26:679S–683S.

[19] Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444(7122):1027-31.

[20] Tsai F, Coyle WJ. The microbiome and obesity: is obesity linked to our gut flora?. Curr Gastroenterol Rep. 2009;11(4):307-13.

[21] Abdallah ismail N, Ragab SH, Abd elbaky A, Shoeib AR, Alhosary Y, Fekry D. Frequency of Firmicutes and Bacteroidetes in gut microbiota in obese and normal weight Egyptian children and adults. Arch Med Sci. 2011;7(3):501-7.

[22] Kallus SJ, Brandt LJ. The intestinal microbiota and obesity. J Clin Gastroenterol. 2012;46(1):16-24.

[23] Bradlow HL. Obesity and the gut microbiome: pathophysiological aspects. Horm Mol Biol Clin Investig. 2014;17(1):53-61.

[24] Tilg H, Kaser A. Gut microbiome, obesity, and metabolic dysfunction. J Clin Invest. 2011;121(6):2126-32.

[25] Cani PD, Amar J, Iglesias MA, et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes. 2007;56(7):1761-72.

[26] Yoshimoto S, Loo TM, Atarashi K, et al. Obesity-induced gut microbial metabolite promotes liver cancer through senescence secretome. Nature. 2013;499(7456):97-101.

[27] Trøseid M, Nestvold TK, Rudi K, Thoresen H, Nielsen EW, Lappegård KT. Plasma lipopolysaccharide is closely associated with glycemic control and abdominal obesity: evidence from bariatric surgery. Diabetes Care. 2013;36(11):3627-32.

[28] Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1(6):6ra14.

[29] De filippo C, Cavalieri D, Di paola M, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA. 2010;107(33):14691-6.

[30] Schnorr SL, Candela M, Rampelli S, et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun. 2014;5:3654.

Fermented Foods and Gut Health

Fermented foods are highly beneficial to your health. However, the underlying practices regarding human consumption (the Paleolithic tradition of eating them) and the new scientific developments regarding just how these foods are bioactive – are two vastly underrepresented areas of knowledge. I hope to cover both areas and explain just why our ancestors instinctually sought out fermented foods, and what we now know about the exact scientific mechanisms that underlie their function in the human body, as well as the brain.

Firstly, our Paleolithic ancestors consumed honey, fruits or berries, and their juices, which were unknowingly subjected to natural microbial fermentation.1 It didn’t take salient scientific literature to suggest these fermented foods were optimal for their health.2 Fermented foods have mentally stimulating properties, analgesic properties, sedating properties, and many other positive functions.3 Interestingly, the shift away from traditional diets has been marked with not only changes in gut microflora, but also an increase in depression and negative mental health conditions.4

Fermented Foods for Gut Health

Hidaka, Brandon H. “Depression as a Disease of Modernity: Explanations for Increasing Prevalence.” Journal of Affective Disorders 140.3 (2012): 205–214. PMC. Web. 19 Dec. 2014.

As the authors of this study note, chronic diseases, which are growing in prevalence, largely arise from a mismatch of our microbiome, which did exceedingly well in past environments, and modern day living.5 Our modern world is overfed, malnourished, sedentary, sleeping less than ever, and socially isolated.6 This not only leads to depression, but to metabolic syndrome, as well – which furthers depression.7 How can fermented foods help to combat the modern pandemic of metabolic syndrome, obesity, and depression?

This is a good question, and one with many answers.8 Mechanistically, their role in the production of specific neurotransmitters is important, and one possible answer to the proposed question.9 As researchers have noted, micronutrients play a role in the synthesis of neurotransmitters.10 A Western diet provokes not only a systemic inflammatory state, but also an altered mood (via intestinal permeability) and can even interfere in microbe-to-brain signaling pathways.11, 12 In fact, researchers have even found metabolic syndrome in the brain.13

This study provided mechanistic evidence that dietary habits can interact with brain functions. Of course, another reason to consume a Paleo Diet rich in fermented foods, and lower in sugar, is the long-term detrimental effects of high-sugar diets on cognitive function.14

Fermented Foods for Gut Health | The Paleo Diet

Agrawal, Rahul, and Fernando Gomez-Pinilla. “‘Metabolic Syndrome’ in the Brain: Deficiency in Omega-3 Fatty Acid Exacerbates Dysfunctions in Insulin Receptor Signalling and Cognition.” The Journal of Physiology 590.Pt 10 (2012): 2485–2499. PMC.

Fermented Foods for Gut Health | The Paleo Diet

Kodl, Christopher T., and Elizabeth R. Seaquist. “Cognitive Dysfunction and Diabetes Mellitus.” Endocrine Reviews 29.4 (2008): 494–511. PMC. Web. 19 Dec. 2014.

Historically, traditional diets are correlated with lower levels of anxiety and depression. Plainly stated in one study’s conclusion, “those with better quality diets were less likely to be depressed, whereas a higher intake of processed and unhealthy foods was associated with increased anxiety.”15 What do almost all traditional diets have in common? They contain fermented foods. In fact, fermented foods and beverages can comprise anywhere between 5-40% of the human diet in some populations.16 In addition, important groups of gut bacteria, often considered markers of a healthy gut, are inversely associated with obesity.17, 18, 19

Fermented Foods for Gut Health | The Paleo Diet

“The Role and Influence of Gut Microbiota in Pathogenesis and Management of Obesity and Metabolic …” Frontiers. N.p., n.d. Web. 19 Dec. 2014.

Furthermore, in mice, the absence of toll-like receptor 5 alters the gut microbiota – leading to more food intake, insulin resistance, and obesity.20 Eating fermented foods helps to favorably effect the composition of the gut microbiota.21 In addition, epidemiological studies have shown that consumption of cabbage and sauerkraut is connected with a significant reduction of breast cancer occurrences.22

So, how did our Paleolithic ancestors know that fermented foods would be beneficial? This answer remains unclear, even though traditions were passed down from generation to generation. Fermentation of food increases beneficial flora, like lactic acid bacteria.23 While our ancestors likely didn’t know this, they still used fermented foods regularly, likely due to the anecdotal results they witnessed.24 Indigenous people have patterns of illness very different from Western civilization; yet, they rapidly develop diseases, once exposed to Western foods and lifestyles.25, 26

Fermented Foods for Gut Health | The Paleo Diet

Sandoval, Darleen A., and Randy J. Seeley. “The Microbes Made Me Eat It.” The Microbes Made Me Eat It. N.p., n.d. Web. 19 Dec. 2014.

Beneficial microbes in fermented foods can decrease anxiety, diminish perceptions of stress, and improve mental outlook.27 Brain derived neurotrophic factor (BDNF) can be increased via either probiotics, or fermented foods.28 BDNF is found in regions of the brain that control eating, drinking, and body weight; it likely contributes to the management of these functions.29 Stress is also known to alter gastrointestinal microflora.30 Probiotics and fermented foods can help to lower systemic inflammatory cytokines, decrease oxidative stress, improve nutritional status, and correct SIBO.31

In one study, researchers even linked gut microbes to autism.32 In their study, a probiotic was found to help. This brings us to the possible exciting conclusion that probiotics and large servings of fermented foods may provide therapeutic strategies for neurodevelopmental disorders.33

Fermented Foods for Gut Health | The Paleo Diet

Bercik P, Denou E, Collins J, et al. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology. 2011;141(2):599-609, 609.e1-3.

Interestingly, researchers have also found that propionic acid, which is a short-chain fatty acid produced by microbiota, can have negative effects on health and behavior. A number of inherited and acquired conditions, such as propionic/methylmalonic acidemia, biotinidase/holocarboxylase deficiency, ethanol/valproate exposure, and mitochondrial disorders, are all known to result from elevations of propionic acid and other short-chain fatty acids.34

The Western diet traditionally produces an unfavorable ratio of ‘good vs. bad’ gut flora.35 In addition, gut flora can help regulate fat storage.36 So not only are you more likely to have neurological problems, with a poor ratio of gut flora, but you are more likely to become obese.37 Hopefully all this information has driven home the fact that the Paleo Diet, which is anti-inflammatory, and rich in fermented foods, will deliver a positive ratio of healthy gut bacteria. It may seem like a small change, but it can make all the difference in the world, when it comes to your health.

Fermented Foods for Gut Health | The Paleo Diet

Bäckhed, Fredrik et al. “The Gut Microbiota as an Environmental Factor That Regulates Fat Storage.” Proceedings of the National Academy of Sciences of the United States of America 101.44 (2004): 15718–15723. PMC. Web. 19 Dec. 2014.

Fermented Foods for Gut Health | The Paleo Diet

Turnbaugh, Peter J. et al. “The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis.” Science translational medicine 1.6 (2009): 6ra14. PMC.


[1] Steinkraus KH: Comparison of fermented foods of the East and West. In Fish Fermentation Technology. Edited by Lee CH, Steinkraus KH, Reilly PJ. Tokyo: United Nations University Press; 1993:1-12.

[2] Steinkraus, K.H. (2002), Fermentations in World Food Processing. Comprehensive Reviews in Food Science and Food Safety, 1: 23–32.

[3] Park KY, Jeong JK, Lee YE, Daily JW. Health benefits of kimchi (Korean fermented vegetables) as a probiotic food. J Med Food. 2014;17(1):6-20.

[4] Hidaka BH. Depression as a disease of modernity: explanations for increasing prevalence. J Affect Disord. 2012;140(3):205-14.

[5] Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13(4):260-70.

[6] Spalding A, Kernan J, Lockette W. The metabolic syndrome: a modern plague spread by modern technology. J Clin Hypertens (Greenwich). 2009;11(12):755-60.

[7] Edwardson CL, Gorely T, Davies MJ, et al. Association of sedentary behaviour with metabolic syndrome: a meta-analysis. PLoS ONE. 2012;7(4):e34916.

[8] Swain MR, Anandharaj M, Ray RC, Parveen rani R. Fermented fruits and vegetables of Asia: a potential source of probiotics. Biotechnol Res Int. 2014;2014:250424.

[9] Rechenberg K, Humphries D. Nutritional interventions in depression and perinatal depression. Yale J Biol Med. 2013;86(2):127-37.

[10] Bourre JM. Effects of nutrients (in food) on the structure and function of the nervous system: update on dietary requirements for brain. Part 1: micronutrients. J Nutr Health Aging. 2006;10(5):377-85.

[11] André C, Dinel AL, Ferreira G, Layé S, Castanon N. Diet-induced obesity progressively alters cognition, anxiety-like behavior and lipopolysaccharide-induced depressive-like behavior: focus on brain indoleamine 2,3-dioxygenase activation. Brain Behav Immun. 2014;41:10-21.

[12] Sánchez-villegas A, Toledo E, De irala J, Ruiz-canela M, Pla-vidal J, Martínez-gonzález MA. Fast-food and commercial baked goods consumption and the risk of depression. Public Health Nutr. 2012;15(3):424-32.

[13] Agrawal R, Gomez-pinilla F. ‘Metabolic syndrome’ in the brain: deficiency in omega-3 fatty acid exacerbates dysfunctions in insulin receptor signalling and cognition. J Physiol (Lond). 2012;590(Pt 10):2485-99.

[14] Kodl CT, Seaquist ER. Cognitive dysfunction and diabetes mellitus. Endocr Rev. 2008;29(4):494-511.

[15] Jacka FN, Mykletun A, Berk M, Bjelland I, Tell GS. The association between habitual diet quality and the common mental disorders in community-dwelling adults: the Hordaland Health study. Psychosom Med. 2011;73(6):483-90.

[16] Borresen EC, Henderson AJ, Kumar A, Weir TL, Ryan EP. Fermented foods: patented approaches and formulations for nutritional supplementation and health promotion. Recent Pat Food Nutr Agric. 2012;4(2):134-40.

[17] Conterno L, Fava F, Viola R, Tuohy KM. Obesity and the gut microbiota: does up-regulating colonic fermentation protect against obesity and metabolic disease?. Genes Nutr. 2011;6(3):241-60.

[18] Flint HJ. Obesity and the gut microbiota. J Clin Gastroenterol. 2011;45 Suppl:S128-32.

[19] Parekh PJ, Arusi E, Vinik AI, Johnson DA. The role and influence of gut microbiota in pathogenesis and management of obesity and metabolic syndrome. Front Endocrinol (Lausanne). 2014;5:47.

[20] Sandoval DA, Seeley RJ. Medicine. The microbes made me eat it. Science. 2010;328(5975):179-80.

[21] Hemarajata P, Versalovic J. Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therap Adv Gastroenterol. 2013;6(1):39-51.

[22] Szaefer H, Licznerska B, Krajka-kuźniak V, Bartoszek A, Baer-dubowska W. Modulation of CYP1A1, CYP1A2 and CYP1B1 expression by cabbage juices and indoles in human breast cell lines. Nutr Cancer. 2012;64(6):879-88.

[23] Chelule PK, Mbongwa HP, Carries S, Gqaleni N. Lactic acid fermentation improves the quality of amahewu, a traditional South African maize-based porridge. Food Chem. 2010;122:656–661.

[24] Anukam KC, Reid G. African traditional fermented foods and probiotics. J Med Food. 2009;12(6):1177-84.

[25] Lipski E. Traditional non-Western diets. Nutr Clin Pract. 2010;25(6):585-93.

[26] Llaverias G, Danilo C, Wang Y, et al. A Western-type diet accelerates tumor progression in an autochthonous mouse model of prostate cancer. Am J Pathol. 2010;177(6):3180-91.

[27] Bested AC, Logan AC, Selhub EM. Intestinal microbiota, probiotics and mental health: from Metchnikoff to modern advances: part III – convergence toward clinical trials. Gut Pathog. 2013;5(1):4.

[28] Bercik P, Denou E, Collins J, et al. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology. 2011;141(2):599-609, 609.e1-3.

[29] Binder DK, Scharfman HE. Brain-derived neurotrophic factor. Growth Factors. 2004;22(3):123-31.

[30] Logan AC, Katzman M. Major depressive disorder: probiotics may be an adjuvant therapy. Med Hypotheses. 2005;64(3):533-8.

[31] Dinan TG, Stanton C, Cryan JF. Psychobiotics: a novel class of psychotropic. Biol Psychiatry. 2013;74(10):720-6.

[32] Gilbert JA, Krajmalnik-brown R, Porazinska DL, Weiss SJ, Knight R. Toward effective probiotics for autism and other neurodevelopmental disorders. Cell. 2013;155(7):1446-8.

[33] Parvez S, Malik KA, Ah kang S, Kim HY. Probiotics and their fermented food products are beneficial for health. J Appl Microbiol. 2006;100(6):1171-85.

[34] Macfabe DF. Short-chain fatty acid fermentation products of the gut microbiome: implications in autism spectrum disorders. Microb Ecol Health Dis. 2012;23

[35] Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med. 2009;1(6):6ra14.

[36] Bäckhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA. 2004;101(44):15718-23.

[37] Ley RE, Bäckhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA. 2005;102(31):11070-5.

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