The gut microbiota
The gut and in particular the colon, supports a complex habitat comprised of trillions of microbes. While the environment plays a role in shaping this ecosystem, diet plays a significant role in microbial composition, which in turn can induce metabolic shifts in the host.[2, 3] The total genome of the microbiota inhabiting the digestive tract contains 150 times more genes than the host, thus being able to code for many processes and functions undeveloped in the human genome.
The microbiota ferment undigested food fragments. Fermentation of dietary fibres found in plant foods result in the production of short chain fatty acids (SCFA) which not only provide an energy source for the colonocytes but also are thought to be involved in regulation of many metabolic processes. Butyrate, a SCFA, seems to be of particular importance for the maintenance of bowel health and prevention of colorectal cancer. Resistant starch is a dietary fibre component which promotes butyrate production and populations with high resistant starch diets have low risk of diet related bowel diseases.
Dysbiosis occurs when there is an imbalance in the gut flora. Dysbiosis has been implicated in coeliac disease, type 1 diabetes, inflammatory bowel diseases, allergies, asthma, atherosclerosis, hypertension, heart failure, chronic kidney disease, obesity, type 2 diabetes, anxiety, depression and autism.
The microbiota and cardiovascular disease
Trimethylamine-N-oxide (TMAO) has been identified as an independent risk factor for cardiovascular disease and atherosclerosis.[8, 9] TMAO is produced in-vivo by the microbiota from consumption of choline, phosphatidylcholine and carnitine, products found in animal tissues.[8, 10] Given the established mechanisms for production of TMAO in the colon, modulations of the gut microbiome through dietary intervention and changes in dietary fibre intake have the potential to alter circulating TMAO concentrations. Low carbohydrate diets have been shown to increase TMAO,  while plant-based diets reduce TMAO due to restriction of substrate for production. The low rates of CVD noted in those following plant-based dietary patterns may be mediated by the microbiota and related to low TMAO concentrations.
The Nutrition Prescription
Research consistently shows the benefits of plant-based foods such as fruits, vegetables, whole-grains and legumes for the health of the microbiota.
The microbiota require adequate ‘food’ to eat. These fibres, from fruits, vegetables, whole grains and legumes lead to higher richness and diversity of the gut microbiota, with high abundances of known beneficial bacteria. This promotes a healthy balance of organisms, therefore preventing and reversing dysbiosis. In addition, plant polyphenols have various health benefits, and interactions with the microbiota can modify bioavailability and activity. Given the polyphenols are contained within varieties of plant-based foods, a wide variety and diversity of foods should be chosen.
Whole food plant-based diets provide an abundance of dietary fibre. Eating a wide variety of whole foods promotes a diverse microbiome.
Include sources of resistant starch as part of a plant-based diet. These include oats, other whole grains (particularly rye), root vegetables (particularly potatoes) and pasta. For cooked products, cooling after cooking results in retrogradation of the starch and increases resistant starch content.
Medical supervision of diet change
People with signs and symptoms of poor gut health should always consult their general practitioner or specialist for diagnosis, treatment and supervision of diet change.
There is emerging evidence that physical activity plays an important role in maintaining the health of the microbiota, with aerobic exercise shown to promote greater diversity and increased short chain fatty acid production. In addition to a whole food plant based diet, regular physical activity is recommended for optimal gut health.
Video overview from NutritionFacts.org
Run time: 5 minutes
Q: How long does it take for the microbiota to adapt to a WFPB diet?
A: Research has shown the microbiota are capable of adapting to new dietary patterns very quickly, within a matter of days. Subjects who were switched to a plant based diet rich in fruits, vegetables, whole grains and legumes showed increases in bacterial abundances of beneficial bacteria, particularly those related to short chain fatty acid secretion, within a five day period. These changes, however, may take some time to become stable, with long term dietary changes inducing further significant and beneficial changes.
Q: What if eating more fibre results in bloating and gas?
A: This is a common question when people first contemplate switching to a whole food plant-based diet. Please see our answer here.
Visconti A, Le Roy CI, Rosa F, et al. Interplay between the human gut microbiome and host metabolism. Nature Communications. 2019;10(1):4505. doi:10.1038/s41467-019-12476-z
Voreades N, Kozil A, Weir TL. Diet and the development of the human intestinal microbiome. Front Microbiol. 2014;5. doi:10.3389/fmicb.2014.00494
Goodrich JK, Waters JL, Poole AC, et al. Human Genetics Shape the Gut Microbiome. Cell. 2014;159(4):789-799. doi:10.1016/j.cell.2014.09.053
A human gut microbial gene catalogue established by metagenomic sequencing | Nature. Accessed September 28, 2020.
Bird AR, Conlon MA, Christophersen CT, Topping DL. Resistant starch, large bowel fermentation and a broader perspective of prebiotics and probiotics. Benef Microbes. 2010;1(4):423-431. doi:10.3920/BM2010.0041
Abell GCJ, Cooke CM, Bennett CN, Conlon MA, McOrist AL. Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch. FEMS Microbiol Ecol. 2008;66(3):505-515. doi:10.1111/j.1574-6941.2008.00527.x
Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microbial Ecology in Health & Disease. 2015;26(0). doi:10.3402/mehd.v26.26191
Wang Z, Klipfell E, Bennett BJ, et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature. 2011;472(7341):57-63. doi:10.1038/nature09922
Wang Z, Tang WHW, Buffa JA, et al. Prognostic value of choline and betaine depends on intestinal microbiota-generated metabolite trimethylamine-N-oxide. Eur Heart J. 2014;35(14):904-910. doi:10.1093/eurheartj/ehu002
Brown JM, Hazen SL. Metaorganismal nutrient metabolism as a basis of cardiovascular disease. Curr Opin Lipidol. 2014;25(1):48-53. doi:10.1097/MOL.0000000000000036
Al-Waiz M, Mikov M, Mitchell SC, Smith RL. The exogenous origin of trimethylamine in the mouse. Metabolism. 1992;41(2):135-136. doi:10.1016/0026-0495(92)90140-6
Genoni A, Christophersen CT, Lo J, et al. Long-term Paleolithic diet is associated with lower resistant starch intake, different gut microbiota composition and increased serum TMAO concentrations. Eur J Nutr. 2020;59(5):1845-1858. doi:10.1007/s00394-019-02036-y
Tomova A, Bukovsky I, Rembert E, et al. The Effects of Vegetarian and Vegan Diets on Gut Microbiota. Front Nutr. 2019;6. doi:10.3389/fnut.2019.00047
Glick-Bauer M, Yeh M-C. The health advantage of a vegan diet: exploring the gut microbiota connection. Nutrients. 2014;6(11):4822-4838. doi:10.3390/nu6114822
Heiman ML, Greenway FL. A healthy gastrointestinal microbiome is dependent on dietary diversity. Molecular Metabolism. 2016;5(5):317-320. doi:10.1016/j.molmet.2016.02.005
Tuohy KM, Conterno L, Gasperotti M, Viola R. Up-regulating the Human Intestinal Microbiome Using Whole Plant Foods, Polyphenols, and/or Fiber. J Agric Food Chem. 2012;60(36):8776-8782. doi:10.1021/jf2053959
Lockyer S, Nugent AP. Health effects of resistant starch. Nutrition Bulletin. 2017;42(1):10-41. doi:10.1111/nbu.12244
Chen J, Guo Y, Gui Y, Xu D. Physical exercise, gut, gut microbiota, and atherosclerotic cardiovascular diseases. Lipids in Health and Disease. 2018;17(1):17. doi:10.1186/s12944-017-0653-9
David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559-563. doi:10.1038/nature12820
Zhang Q, Ma G, Greenfield H, et al. The association between dietary protein intake and bone mass accretion in pubertal girls with low calcium intakes. British Journal of Nutrition. 2010;103(5):714-723. doi:10.1017/S0007114509992303