Microbes are microscopic non-human creatures that inhabit virtually every part of our body. What they lack in size, they make up in numbers. There are trillions of them and their ecosystem is made up of bacteria, fungi, viruses, archaea, prokaryotes and eukaryotes. There is a symbiotic relationship and the result is mutual benefit for both the host and the microbiome.


We have more bacterial cells in our body than humans.
Our human genes are about 23,000 while the genes of bacterial origin range between 2-3 million.
Our gut contains the largest share of microbes in our body.
The gut has its nervous system called the Enteric Nervous System.
75-80% of our immune system resides in the gut and the microbes are responsible for their development in the early years.
Hormones produced by the microbes in our gut influence our eating behaviour.
They affect the thermoregulation of their hosts.
They assist in digestion, govern your appetite, control your metabolism and influence your mood.
Help maintain ph levels of the body.
Prevent gastric complications.


Diet and Nutrition play a role from the time we are an infant. Human breast milk, which is made of living white blood cells, immunoglobulins, and oligosaccharides is not recognized by the infant, rather they are metabolized by the gut bacteria (especially from the genus, Bifidobacterium) to produce SCFA which then acts as fuel and energy for the body.

In contrast, children who are fed formula suffer from changes in the expression of their genes that are a part of their immune system and are more susceptible to pathogenic attacks. In fact they are 8 times more likely to develop cancer in comparison to their counterparts who are breast fed for 6 months.



The term "YOU ARE WHAT YOU EAT" needs to be modified to read "YOU ARE WHAT YOU DIGEST, ASSIMILATE, ABSORB, AND METABOLIZE" and that is largely a function of our microbial community.

The 3 major macronutrients - Carbohydrates, Fats, and Proteins are the building blocks of energy in the human body and they all provide us with different microbiota-accessible nutrients. The amount and type of a particular nutrient decides which population of bacteria will grow generating different metabolites which can have a positive or negative influence on the gut epithelium and mucosal immune system.

Two things dictate the health of our gut and microbiome



Your microbiome composition can change within 24 hours based on what you eat even for a short time.

 Dairy and Processed foods (processed meat, processed high-fibre vegetables, packaged foods like chips, biscuits, etc) support gut microbes that increase blood sugar, and cholesterol, leading to inflammation and finally to a higher risk of cardiac disease and type 2 diabetes.

A diverse diet from high-fibre vegetables and fruits, nuts and seeds, whole grains and limited organic animal foods like fish and eggs are linked to a lower risk of chronic diseases.

Minimally process plant foods are the best foods for the gut microbiome and protect us against chronic and metabolic diseases Vegetarian microbiome are more suitable for starch digestion and meat eaters have microbes more suitable for bile digestion which although can be beneficial are also much more inflammatory.



Gut metabolites in a high protein diet shift to protein fermentation disturbing gut mucosal homeostasis.
Animal protein have low fermentable filers so lead to the growth of low beneficial bacteria, thus quantity should be limited.
Excessive red meat tends to increase levels of TMAO (a proatherogenic) and that increases the risk of cardiovascular disease.
Higher amounts lead to gut inflammation and colorectal cancer. Plant protein-whey, pea protein help increase good bacteria.
Organic meat, especially Chicken, is better for the growth of the species Akkermansia Muciniphila which helps protect the gut mucosal barner.
Too high a protein level increases insulin-like growth factor 1(IGF-1) levels which leads to increased risk for cancer diabetes and mortality rates.
A HIGH PROTEIN AND HIGH FIBRE DIET should go hand in hand to reduce transit time (due to the fiber) and any harmful effects from protein metabolism are minimized.


The harmful fats are saturated in larger quantities and trans fat in any quantity as they increase the risk of cardiovascular disease. They promote bacteria associated with inflammation and metabolic disorders. For example Bacons sausages, cheese, chips, microwave popcorn, frozen pizza, deep fried foods.

Mono-poly saturated fats help alleviate the risk of chronic disease. These promote the growth of bacteria that reduce inflammation. For example: avocado, walnuts, almonds olive, pumpkin, and sesame seeds, and fatty fish.


Resistance starch, oligosaccharides, and no starch polysaccharides come from plants and feed beneficial bacteria in the gut like Bifidobacterial and Lactobacilli. These increase diversity in the gut microbiome

Bacteria break these finer down to produce SCFAs-butyrate, acetate, and propionate.

SCFAs can reduce inflammation, improve insulin sensitivity, and gut barrier function, and regulate appetite and metabolism, SCFA can alter gene expression by inhibiting histone deacetylase (epigenetic alteration).

SCFA reduces pH and may help to reduce disease-causing bacteria eg Enterobacteriaceae like E. coli and Salmonella.

However, too much SCFA can have some negative consequences as well which is why IBS patients are given low FODMAP diets (these reduce SCFA production)

Examples of such foods include beans, green bananas, legumes, oats, blueberries, cabbage, broccoli, figs, leeks, white onions, and whole-grain rice.


A diet high in sugar can lead to an overgrowth of harmful bacteria in the gut because sugar is a source of fuel for these bacteria

High sugar intake can also lead to insulin resistance and metabolic disorders which cause dysbiosis

It can also cause the overgrowth of the pathogenic fungus, eg Candida.


Vitamin A and Zinc are crucial for the growth of beneficial bacteria.

Vitamin D regulates the immune system and helps maintain gut barrier integrity

Iron is also required for certain essential bacteria to grow Excessive from can however lead to the growth of harmful bacteria.


Winters N. Kelley JH. The Metabolic Approach to Cancer. White River Junction, VT: Chelsea Green Publishing, 2017

Enders G. Gut: The Inside Story of Our Body's Most Underrated Organ. Vancouver, BC: Greystone Books: 2015

DeSalle R. Perkins S. Welcome to the Microbiome: Getting to Know the Trillions of Bacteria and Other Microbes In, On, and Around You. New Haven, CT: Yale University Press. 2015.

Yong EI Contain Multitudes: The Microbes Within Us and a Grander View of Life. New York, NY: Ecco: 2016

Dona A. Arvaanitoyannis 1. Health Risks of Genetically Modified Foods Crit Rev Food Sci Nutr 2009.49(2):164-175. doi: 10.1080/10408390701855993 PMID: 18989835

Nakayama A, Full Body Systems, Functional Nutrition Alliance, Graduated 2023

Singh, RK, Chang, H.W., Yan. D. Lee. KM. Ucmak. D. Wong, K. Abrouk. M. Farahnik, B. Nakamura, M. Zhu, TH. Bhutani, T. & Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health. AMA Journal of Ethics, 10(7), 1-8

Singh, R.K. Chang, HW, Yan, D. Lee, K.M. Ucmak, D. Wong, K, Abrouk, M. Farahnik, B. Nakamura. M. Zhu, T.H. Bhutani, T. & Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health Journal of Translational Medicine, 15/1), 73. doi: 10.1186/512957-017-1175-y

Frame. LA Costa, E, & Jackson, SA (zozol Cument explorations of nutrition and the gut microbiome a comprehensive evaluation of the review literature Nutrition Reviews, 78101 798-812 doi: 10.1093/nutrit/nuz106

Zhang, Pizozzi influence of Foods and Nutrition on the Gut Microbiome and Implications for intestinal Health International Journal of Molecular Sciences 23/17) 9588. doi: 10.3390/jms23179588. PMID 36076980. PMCID: PMC9455721

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