Tag Archives: microbiome

Mind Your Microbes: Gut Health | The Paleo Diet

I have a gut feeling that things are about to become much more interesting in the science world.1, 2, 3 As researchers continue to discover more and more exciting news about just how our microbiomes can uniquely identify us, change our food cravings, and alter our health, we must continually realize the importance of keeping a ‘healthy gut’.4 While this phrase has become increasingly popular in the mainstream world of health, many still do not realize exactly is meant by having ‘good gut health’. Perhaps more troubling – they have no idea how to obtain it. A Paleo diet will be the single best thing you can do for your gut, by avoiding Western foods which have been proven to alter gut bacteria in a negative fashion.5, 6

Mind Your Microbes: Gut Health |  The Paleo Diet

Bischoff, Stephan C. “‘Gut Health’: A New Objective in Medicine?” BMC Medicine 9 (2011): 24. PMC. Web. 20 May 2015.

By adding in foods that help to promote gut health (fermented choices like sauerkraut) you will be moving things in the right direction.7, 8 Poor gut health is correlated with a multitude of negative symptoms and conditions, including a lifetime of antibiotic treatments (which have increasingly been shown to be detrimental to the microbiome), and is often the most common problem experienced by anyone with poor health. 9, 10, 11, 12

For over a decade, researchers have known that the gut microflora is a major part of metabolic activities that result in salvage of energy and absorbable nutrients.13 Researchers have also known that the microbiota plays a crucial role as a source of infection and environmental insult and also in protection against disease and maintenance of gut function.14 Since this is scientific information, the general public remained largely unaware of it – even as we became fatter, sicker and more likely to receive a host of antibiotic treatments.15, 16, 17

Mind Your Microbes: Gut Health | The Paleo Diet

Bischoff, Stephan C. “‘Gut Health’: A New Objective in Medicine?” BMC Medicine 9 (2011): 24. PMC. Web. 20 May 2015.

Sadly, it has taken illness, poor health and chronic pain for many to discover a Paleo diet. But this doesn’t have to be the case. Preventative – rather than reactive – measures are ideal when looking to maintain one’s health in the long term.18 Since your microbiome is a unique fingerprint, you want it to be in the best shape possible.19, 20, 21 Researchers at Harvard recently even warned that people may be able to be identified by their microbiome fingerprint (which has possible data privacy implications).22 Fast food has been shown to worsen the balance of good bacteria to bad bacteria in the gut, and also increases the likelihood of obesity.23, 24 These are all good reasons to adopt a Paleo diet and ‘mind your microbes’ – as the saying goes.

Mind Your Microbes: Gut Health | The Paleo Diet

Hoffmann, Christian et al. “Archaea and Fungi of the Human Gut Microbiome: Correlations with Diet and Bacterial Residents.” Ed. Chongle Pan. PLoS ONE 8.6 (2013): e66019. PMC. Web. 20 May 2015.

Lastly, many are unaware that they themselves carry more bacterial cells than human cells – meaning that bacteria literally run our lives.25, 26, 27 This is one of the biggest reasons to really focus on improving your own gut’s health – and in turn – adopt a better diet. Western diets have poor implications and results for the human microbiome – it is a bad idea to continue to eat that way.28, 29, 30 Instead, focus on a nutrient dense, anti-inflammatory Paleo Diet – and make your bacteria happy.



[1] Cummings JH, Antoine JM, Azpiroz F, et al. PASSCLAIM–gut health and immunity. Eur J Nutr. 2004;43 Suppl 2:II118-II173.

[2] Choct M. Managing gut health through nutrition. Br Poult Sci. 2009;50(1):9-15.

[3] Bischoff SC. ‘Gut health’: a new objective in medicine?. BMC Med. 2011;9:24.

[4] Available at: //www.sciencedaily.com/releases/2015/05/150511162914.htm. Accessed May 16, 2015.

[5] 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.

[6] Martinez-medina M, Denizot J, Dreux N, et al. Western diet induces dysbiosis with increased E coli in CEABAC10 mice, alters host barrier function favouring AIEC colonisation. Gut. 2014;63(1):116-24.

[7] Selhub EM, Logan AC, Bested AC. Fermented foods, microbiota, and mental health: ancient practice meets nutritional psychiatry. J Physiol Anthropol. 2014;33:2.

[8] Van hylckama vlieg JE, Veiga P, Zhang C, Derrien M, Zhao L. Impact of microbial transformation of food on health – from fermented foods to fermentation in the gastro-intestinal tract. Curr Opin Biotechnol. 2011;22(2):211-9.

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

[10] Kelder T, Stroeve JH, Bijlsma S, Radonjic M, Roeselers G. Correlation network analysis reveals relationships between diet-induced changes in human gut microbiota and metabolic health. Nutr Diabetes. 2014;4:e122.

[11] Hoffmann C, Dollive S, Grunberg S, et al. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS ONE. 2013;8(6):e66019.

[12] Catanzaro R, Anzalone M, Calabrese F, et al. The gut microbiota and its correlations with the central nervous system disorders. Panminerva Med. 2015;57(3):127-43.

[13] Guarner F, Malagelada JR. Gut flora in health and disease. Lancet. 2003;361(9356):512-9.

[14] Tuohy KM, Probert HM, Smejkal CW, Gibson GR. Using probiotics and prebiotics to improve gut health. Drug Discov Today. 2003;8(15):692-700.

[15] Rocca WA, Petersen RC, Knopman DS, et al. Trends in the incidence and prevalence of Alzheimer’s disease, dementia, and cognitive impairment in the United States. Alzheimers Dement. 2011;7(1):80-93.

[16] Roth J, Qiang X, Marbán SL, Redelt H, Lowell BC. The obesity pandemic: where have we been and where are we going?. Obes Res. 2004;12 Suppl 2:88S-101S.

[17] Available at: //www.ncbi.nlm.nih.gov/pubmedhealth/behindtheheadlines/news/2014-10-10-antibiotic-resistance-continues-to-rise-/. Accessed May 16, 2015.

[18] Maciosek MV, Coffield AB, Flottemesch TJ, Edwards NM, Solberg LI. Greater use of preventive services in U.S. health care could save lives at little or no cost. Health Aff (Millwood). 2010;29(9):1656-60.

[19] Franzosa EA, Huang K, Meadow JF, et al. Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci USA. 2015;

[20] Gillevet P, Sikaroodi M, Keshavarzian A, Mutlu EA. Quantitative assessment of the human gut microbiome using multitag pyrosequencing. Chem Biodivers. 2010;7(5):1065-75.

[21] Albenberg LG, Lewis JD, Wu GD. Food and the gut microbiota in inflammatory bowel diseases: a critical connection. Curr Opin Gastroenterol. 2012;28(4):314-20.

[22] Available at: //www.sciencedaily.com/releases/2015/05/150511162914.htm. Accessed May 16, 2015.

[23] Available at: //www.ibtimes.com/what-good-gut-bacteria-fast-food-kills-natural-allies-worsens-obesity-other-health-1916714. Accessed May 16, 2015.

[24] Slavin J. Fiber and prebiotics: mechanisms and health benefits. Nutrients. 2013;5(4):1417-35.

[25] Available at: //www.scientificamerican.com/article/strange-but-true-humans-carry-more-bacterial-cells-than-human-ones/. Accessed May 16, 2015.

[26] O’hara AM, Shanahan F. The gut flora as a forgotten organ. EMBO Rep. 2006;7(7):688-93.

[27] 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.

[28] Myles IA. Fast food fever: reviewing the impacts of the Western diet on immunity. Nutr J. 2014;13:61.

[29] Poutahidis T, Kleinewietfeld M, Smillie C, et al. Microbial reprogramming inhibits Western diet-associated obesity. PLoS ONE. 2013;8(7):e68596.

[30] Wong JM, Esfahani A, Singh N, et al. Gut microbiota, diet, and heart disease. J AOAC Int. 2012;95(1):24-30.

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.

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