The Four Lost Nutrients to Restore the Gut Microbiome

Our partner in health, the gut microbiome, has grown weak with ultra-processing of food. Fibers, Phenols, Good Fats, and Ferments can make it strong again. You will find tips at the end on how to add these microbiome friendly components back into your diet so you can reclaim your gut microbiome and health.

Self feeding

When we think about food, we tend to focus on the nutrients important for our health but less about the nutrients important for the health of our friends and partners in health, the microbes in our gut. Our microbes are unsung heroes that take undigested food and transform it into vital nutrients not always present in our diet alone.[1,2] 

Modern diets involving ultra-processing and low consumption of whole plant-based foods (e.g. whole grains, beans, nuts, seeds, fruits, and vegetables) have been starving our gut microbes; and in effect, starving ourselves of many nutrients that are critical for our metabolic, immune, and psychological health.[3] How could we have missed this important fact you might ask? What are the nutrients that feed our microbes? What are the nutrients they produce? Read on below!

Modern nutrition history

The story of modern nutrition begins over 100 years ago when science first discovered that food can be separated into different components that each have key metabolic roles in our body:  The macronutrients including carbohydrates (sugar and starchy foods), protein (lean portions of meat and beans) and fat (fatty portions of meat and nuts). And the micronutrients including vitamins (B’s, C, A, D, E, K) and minerals (potassium, magnesium, selenium, etc.).[4] 

With the discovery of these nutrients we could label and explain nutrient deficiencies like kwashiorkor (protein deficiency), beriberi (B1/thiamine deficiency), pellagra (B3/niacin deficiency), scurvy (C deficiency), rickets (D deficiency), and so on![4] 

Armed with this knowledge, we emphasized a balanced diet that contained certain portions of carbs, fats, and proteins and fortified foods like bread and baked goods with micronutrients that we may not have received enough of otherwise in the diet. This knowledge allowed for incredible advances forward in addressing nutritional disease.[4]

Rise of ultra-processing:

But at the same time nutrition took a turn for the adverse with the advent of modern processing techniques which with good intentions was aimed at maximizing shelf stability and minimizing cost of goods.[5] They replaced some traditional processing & preserving methods of brining and fermenting that historically augmented rather than diminished the nutritional quality of foods.[6]

Over time ultra-processed foods came to replace many of our whole foods (grains, beans, nuts, seeds, fruits, and vegetables).[7] Processing removed important nutrients like fibers and polyphenols (e.g white flour and rice).[8–10]  It also concentrated simple carbohydrates/sugars (e.g. sodas, juice, corn syrup) and less healthy types of fat (e.g. omega-6’s).[11,12]  

Processed foods delivered on the macro and micronutrient profiles that science defined as important to human health, but missed the key ingredients that feed our gut microbes.

Microbial awakening

The last 10 years has seen an awakening to the importance that microbes are playing in our diet and linked them to many chronic health conditions  (e.g. obesity,[13] diabetes,[13] autoimmune disease,[14] depression,[15] Alzheimer’s,[16] etc.).  We are recognizing just how important the gut microbes are and how cultivating them is critical for health. 

If grown right, they produce many nutrients that are well known to us like B vitamins, amino acids, and even neurotransmitters.[1,2] They also produce other molecules that are less commonly known like secondary bile acids and short chain fatty acids (e.g. butyrate).[17,18] Indeed our gut microbiomes are little factories that produce critical nutrients, many of which are simply not present in the diet!

Grow your garden

OK.  So with a little luck, perhaps I’ve intrigued you with the idea that gut microbes are important to health; but you might ask now, how do we grow them? The public health messaging of eating whole foods that are largely plant based, and embracing medically validated diets like the Mediterranean and Dash diets are all pointing in the right direction. They reintroduce the microbe-fueling nutrients that have largely been missing from our modern ultra-processed diets.[19,20] 

Yet adherence to public health’s and doctors’ good advice remains imperfect and the epidemic of metabolic, inflammatory, and neurologic disease continues to grow.[21] How do we fix this?

Just as the 19th century saw a flurry of research in the lab that decoded the macro and micronutrients of foods, we are now seeing a similar flurry of research around the nutrients made by our microbes and that are critical for health.[22,23] Butyrate, involved in preventing leaky gut, balancing the immune system, and regulating neurons may be one of the more important molecules produced by our microbiome. (See blog on butyrate) Understanding these processes allow us to shine the light more specifically on which foods to eat in greater abundance and to redesign processed foods that reincorporate these nutrients. 

We are coming to realize that the historical focus on whether too much carbohydrate or too much fat is the source of health problems may have been off base. Instead we need to focus on a healthy balance of the right types of carbohydrates (fibers vs. simple carbohydrates) and types of fats (omega-3’s vs. omega-6’s and saturated) (See Blog on Carbohydrates vs. Fat).[24]  

The four phonetic F’s of food

The fibers and healthy fats of plant-based foods both contain nutrients that healthy gut microbes thrive on. Many plant-based foods also have high polyphenols that serve to balance the gut microbiome. Fiber, healthy fats, and phenols are the so called phonetic F’s of food; but there is one more F to add, fermentation. Just as our microbes in the lower gut can take plant-based foods and transform them into vital nutrients, so too can microbes outside our bodies transform foods into those with greater nutrition.

Getting practical

So what foods to focus on you might ask?  Below are some specifics to consider: 

·  Fibers: steel cut oats, beans, brown rice, whole grain breads/pastas/crackers. Focus on the whole grain!

·  Phytonutrients: berries, apples, plums, purple cabbage. Eat the rainbow of fruits and vegetables!

·  Healthy Fats: fatty fish (salmon, tuna, sardines), fatty fruits and their oils (avocado and olive), tree nuts and their butters (almond, cashew, dark chocolate). Focus on omega-3’s!

· Ferments: Olives, pickles, sauerkraut, kimchi, kefir, yogurt, cheese, kombucha. Those in the refrigerated section are key!

In the end, let your healthy eating mantra be Fibers, Healthy Fats, Phytonturients, and Ferments! Your microbes will thank you, and your body will be healthier for it! (Link to an article on the four Phonetic F’s as they relate to mitochondrial health.)

More Articles & Resources

Please feel free to visit where you’ll find more practical food and microbiome digests to improve gut health and lift your whole self! Would love to hear your comments below too!

1. Chen Y, Xu J, Chen Y. Regulation of Neurotransmitters by the Gut Microbiota and Effects on Cognition in Neurological Disorders. Nutrients. 2021;13. doi:10.3390/nu13062099

2. Das P, Babaei P, Nielsen J. Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. BMC Genomics. 2019;20: 208.

3. Zinöcker MK, Lindseth IA. The Western Diet-Microbiome-Host Interaction and Its Role in Metabolic Disease. Nutrients. 2018;10. doi:10.3390/nu10030365

4. Mozaffarian D, Rosenberg I, Uauy R. History of modern nutrition science-implications for current research, dietary guidelines, and food policy. BMJ. 2018;361: k2392.

5. Augustin MA, Riley M, Stockmann R, Bennett L, Kahl A, Lockett T, et al. Role of food processing in food and nutrition security. Trends Food Sci Technol. 2016;56: 115–125.

6. Leeuwendaal NK, Stanton C, O’Toole PW, Beresford TP. Fermented Foods, Health and the Gut Microbiome. Nutrients. 2022;14. doi:10.3390/nu14071527

7. Chen X, Zhang Z, Yang H, Qiu P, Wang H, Wang F, et al. Consumption of ultra-processed foods and health outcomes: a systematic review of epidemiological studies. Nutr J. 2020;19: 86.

8. Babu PD, Subhasree R, Bhakyaraj R, Vidhyalakshmi R. Brown rice-beyond the color reviving a lost health food-a review. Magnesium. 2009;187: 67–72.

9. Slavin J. Why whole grains are protective: biological mechanisms. Proc Nutr Soc. 2003;62: 129–134.

10. Călinoiu LF, Vodnar DC. Whole Grains and Phenolic Acids: A Review on Bioactivity, Functionality, Health Benefits and Bioavailability. Nutrients. 2018;10. doi:10.3390/nu10111615

11. Martínez Steele E, Baraldi LG, Louzada ML da C, Moubarac J-C, Mozaffarian D, Monteiro CA. Ultra-processed foods and added sugars in the US diet: evidence from a nationally representative cross-sectional study. BMJ Open. 2016;6: e009892.

12. Hall KD, Ayuketah A, Brychta R, Cai H, Cassimatis T, Chen KY, et al. Ultra-Processed Diets Cause Excess Calorie Intake and Weight Gain: An Inpatient Randomized Controlled Trial of Ad Libitum Food Intake. Cell Metab. 2019;30: 67–77.e3.

13. Singer-Englar T, Barlow G, Mathur R. Obesity, diabetes, and the gut microbiome: an updated review. Expert Rev Gastroenterol Hepatol. 2019;13: 3–15.

14. Clemente JC, Manasson J, Scher JU. The role of the gut microbiome in systemic inflammatory disease. BMJ. 2018;360: j5145.

15. Barandouzi ZA, Starkweather AR, Henderson WA, Gyamfi A, Cong XS. Altered Composition of Gut Microbiota in Depression: A Systematic Review. Front Psychiatry. 2020;11: 541.

16. Chen C, Liao J, Xia Y, Liu X, Jones R, Haran J, et al. Gut microbiota regulate Alzheimer’s disease pathologies and cognitive disorders via PUFA-associated neuroinflammation. Gut. 2022. doi:10.1136/gutjnl-2021-326269

17. Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS. Bile acids and the gut microbiome. Curr Opin Gastroenterol. 2014;30: 332–338.

18. Sanna S, van Zuydam NR, Mahajan A, Kurilshikov A, Vich Vila A, Võsa U, et al. Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases. Nat Genet. 2019;51: 600–605.

19. Martini D. Health Benefits of Mediterranean Diet. Nutrients. 2019;11. doi:10.3390/nu11081802

20. Filippou CD, Tsioufis CP, Thomopoulos CG, Mihas CC, Dimitriadis KS, Sotiropoulou LI, et al. Dietary Approaches to Stop Hypertension (DASH) Diet and Blood Pressure Reduction in Adults with and without Hypertension: A Systematic Review and Meta-Analysis of Randomized Controlled Trials. Adv Nutr. 2020;11: 1150–1160.

21. Patino-Alonso MC, Recio-Rodríguez JI, Belio JFM, Colominas-Garrido R, Lema-Bartolomé J, Arranz AG, et al. Factors associated with adherence to the Mediterranean diet in the adult population. J Acad Nutr Diet. 2014;114: 583–589.

22. Mozaffarian D. Nutrition’s dark matter of polyphenols and health. Nature Food. 2021;2: 139–140.

23. Bland JS. The Dark Matter of Nutrition: Dietary Signals Beyond Traditional Nutrients. Integr Med . 2019;18: 12–15.

24. Hydes T, Alam U, Cuthbertson DJ. The Impact of Macronutrient Intake on Non-alcoholic Fatty Liver Disease (NAFLD): Too Much Fat, Too Much Carbohydrate, or Just Too Many Calories? Front Nutr. 2021;8: 640557.

3 responses to “The Four Lost Nutrients to Restore the Gut Microbiome”

  1. Look forward to your thoughts!

  2. Great article Chris! Do the bacteria from kombucha and yogurt get through our digestive system to the point that they are helpful or do they get destroyed by our digestive enzymes/acids? If you have any research to validate either way, I would appreciate it! I do eat fermented foods and incorporate it into my families bodies, but I want to make sure it is actually making it way to the areas of the digestive tract that are helpful for our bodies. Thank you for the blog!

    1. Thanks for the positive thoughts Kristin! There is evidence to suggest that lactic acid bacteria in yogurt survive the GI tract. There is less data on kombucha. Regardless their postbiotics including B vitamins, lactic acid, and acetic acid ma contribute to health.

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