Gut microbiota nutrition -our needs will change
The gut microbiome is a vital part of the human holobiont providing a virtuous cycle of health outcomes when we nourish it properly. There is much still to be learned about how we can nourish our gut microbiota but we do know that each of us is different and we are likely to benefit from a range of carbohydrates from a range of sources.
Sources of human gut microbiota nutrition
Our gut microbiota nutrition comes from four main sources [1, 2]:
Human breast milk
The things we eat and do not use directly for our metabolism
Gut mucus which we produce
Interactions between members of the gut microbiota
Those sources will contain complex carbohydrates, some proteins, and some protein components (peptides). However, carbohydrates are the most important and have been referred to as microbiota-accessible carbohydrates (MAC) [1]. We’ll concentrate on those in this discussion.
MAC diversity and microbiome resilience
It’s likely no surprise that many of the MAC reaching our gut microbiome come from plants we eat. It may be more surprising to learn that dietary animal meats, human breast milk, mucus secreted by our bodies, and substances produced by members of our microbiota themselves also contain many carbohydrates. The differences between those and what we tend to think of as plant-based carbohydrates lies in the former’s increased complexity and diversity.
“The fact that our microbiota nutrition contains things other than what we eat, means that a source of continuous microbiota nutrition is available when our food supplies run low”
It has been estimated that carbohydrates (referred to in literature as glycans) are the most structurally diverse major class of molecules in nature [4]. Such large diversity of MAC structure results in larger diversity of gut microbiota. As we have seen before, microbiota diversity tends to be associated with good human health.
The fact that our microbiota nutrition contains things other than what we eat, means that a source of continuous microbiota nutrition is available when our food supplies run low. When dietary carbohydrates are in short supply or when their composition changes, our microbiota can still rely upon mucus we produce and the substances they produce within themselves, at least for a time. This in turn means that our gut microbiome is more likely to maintain its functional resilience.
Back to those sources of gut microbiome nutrition
“Most carbohydrates in human breast milk are too complex to be directly turned into energy by the baby but they do establish and feed the baby’s gut microbiota.”
Human breast milk
This is one of the most amazing things I’ve discovered. It appears that breast-feeding mothers provide complex MAC specifically to establish and develop the new-born gut microbiota [1, 2].
In other words, whilst human breast milk contains hundreds of different types of carbohydrates, only a fraction is readily absorbed and metabolised by the newborn to support its growth. Most carbohydrates in human breast milk are too complex to be directly turned into energy by the baby but they are MAC to feed the baby’s gut microbiota.
The things we eat and do not use directly for our metabolism
We consume many different plant (e.g., starches) and animal-derived (e.g., cartilage and muscle) dietary MAC. Fermentation of those provides energy for our microbiota and transforms these MAC into things like short chain fatty acids (SCFA), which serve as beneficial nutrients for our bodies [2].
Certain plant-based carbohydrates are bound up in things like plant cell structures and cannot be absorbed by us or fermented by our microbiota. They tend to be loosely described as dietary fibre and they are simply excreted by us in our stool.
Gut mucus which we produce
In addition to dietary MAC, some members of our gut microbiota can ferment components of the mucus secreted in our intestines and cells discarded from our intestinal walls. The composition of MAC from mucus and intestinal cells are different, thereby representing additional nutritional diversity and its ensuing health benefits.
Interactions between members of the gut microbiota
Members of our microbiota interact with each other in complex food chains. For example, different microbes ferment the MAC from plants, animals and mucus in the lower intestine, thereby nourishing themselves and creating a range of breakdown products. Other microbes then further ferment those breakdown products, and so on until finally things like SCFA and vitamins are produced and may be used by our bodies [2].
A virtuous cycle
Consuming a diet high in MAC throughout our lives has been shown to increase microbiota diversity and increase the production of microbiota metabolites that are protective against so-called modern-life chronic diseases ((e.g., obesity, type-2 diabetes, heart disease, poly-cystic ovarian syndrome, hypertension, dementia, cancer, and non-alcoholic fatty liver disease). We are essentially feeding our microbiota, which in turn give back things like beneficial SCFA and vitamins that we wouldn’t otherwise have access to.
When we replace diverse natural sources of MAC with bioavailable high starch and processed food (potatoes, rice, bread, pastries, pasta, etc.), our microbiota diversity and production of protective microbiota metabolites are both decreased, and we are more likely to get sick.
Human gut microbiome variability
There are four important types of gut microbiota variability affected by nutrition worth considering because they may alter the way we manage our health.
Between individuals
Along the length of our gut
Short-term associated with nutrition
Long-term lifetime changes
Differences between individuals
We know that a healthy gut microbiome function can be achieved by everyone but the way that we achieve that appears to be different for each of us. Therefore, we should each understand our own gut health, short-term changes with diet, and longer-term changes as we explore our own well-lived lives.
Variation within the gut
Our intestine can be thought of as a fermentation vessel in which our microbiota feed themselves, replicate, and produce the components of our gut microbiome that ultimately provide a healthy functional outcome. As far as we know, no member of our gut microbiota can ferment all the types of MAC in the human intestine. Individual members of the microbiota target a just a sub-set of all the MAC present.
The MACs which benefit our microbiota tend to increase in number and diversity towards the lower part of our intestine. For example. the mucus in our intestine tends to be quite thin close to our stomach and increases in thickness towards the lower intestine. All of this translates into more and greater diversity of MAC from upper to lower intestine and therefore greater numbers and diversity of microbiota towards the lower intestine [2]
This insight can be especially important for people suffering from gut inflammation or leaky gut and in which their healthy distribution of gut microbiota may be out of kilter.
Short-term nutritional changes
Our gut microbiota can quickly adapt to changes in our diet [2]. This can affect microbiota diversity and microbiome function for better or for worse. My diet of processed food led to heart disease and I’m now trying to halt the disease progress by eating natural, diverse, and nutrient-dense food.
“Irrespective of life-stage, the composition of our microbiota, and the functionality of our microbiome, always appears to be highly influenced by MAC.”
Lifetime changes
The gut microbiota evolves from infant to adult (its highest level of diversity [6]) to old age and may be especially affected at life’s most sensitive stages of human development, such as infancy, adolescence, and old age.
Irrespective of life-stage, the composition of our microbiota, and the functionality of our microbiome, always appears to be highly influenced by MAC. Awareness of these sensitive periods, especially earlier in life, can help us to develop and maintain a healthy microbiome. This is especially important to avoid the harmful effects of accumulated diet-related chronic disease later in life.
Infancy
The infant microbiota may be influenced by a range of environmental factors, including birth mode, prematurity, birth location, maternal diet, pet ownership, illness, antibiotic use, and exposure to human breast milk.
As we’ve seen, exposure to human breast milk starts the process of feeding and developing a healthy infant microbiota. Thereafter more MAC become available to the infant microbiota after weaning and as the diet becomes richer in plant and animal nutrition. If a fully omnivorous diet is achieved, post weaning, the infant microbiota diversity and density will stabilize by age two or three years [2].
Evidence suggests that early-life influence on our microbiota may affect health and behaviour later in life.
Adoloscence
The adolescent body undergoes rapid and substantial changes including hormonal fluctuations, and physical development, especially in the brain. Such dramatic changes coincide with independence from parents, changes in social interaction, sleep patterns, and exposure to intoxicants.
Ageing
Ageing is a slow process associated with changes in organ physiology, including the gut, that affect maintenance of good health. This is often accompanied by the accumulated impacts of disease over a lifetime. Insulin resistance, chronic inflammation and their accompanying so-called chronic diseases (e.g., obesity, type-2 diabetes, heart disease, poly-cystic ovarian syndrome, hypertension, dementia, cancer, and non-alcoholic fatty liver disease) are more likely to manifest later in life, and accelerate the ageing process. The negative effects of poor diet and nutrition are likely, therefore, to be visible in older individuals.
“In order to maintain a healthy relationship with our microbiome, each of us may need to adopt a diet that is nutritionally unique and may change with environmental exposures at different stages of our lives”
What’s worth remembering?
A few themes emerge when considering microbiota nutrition and variability. Firstly, the composition of our microbiota and likely responsiveness to the things we eat varies greatly between each of us.
Secondly, maximum benefit from carbohydrates as nutrition for our gut microbiota can only be achieved when we consider all possible sources. Human breast milk, dietary plants and animal meats, human mucus and microbiota metabolites all contain a rich and diverse supply of nutritional MAC.
Finally, we are barely scratching the surface of what we understand about how changes in our microbiota affect our microbiome function and how what we eat is likely affect us throughout our lifetime.
In order to maintain a healthy relationship with our microbiome, each of us may need to adopt a diet that is nutritionally unique and may change with environmental exposures at different stages of our lives. My approach to healthy nutrition means that I avoid processed components and eat a range of natural plant- and meat-derived, nutrient-dense foods. That seems to work for me at this stage in my life.
References
Sonnenburg, E.D. and Sonnenburg, J.L. (2014) Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates. Cell Metabolism, 20, 779-786
Koropatkin, N., et al (2021) How glycan metabolism shapes the human gut microbiota. Nat Rev Microbiol 10, 323–335. https://doi.org/10.1038/nrmicro2746
Wang et al (2019) “We are What we Eat”; How Diet Impacts the Human Gut Microbiota in Adulthood. In Azcarate-Peril, M.A. et al, editors. How Fermented Foods Feed a Healthy Gut Microbiota: A Nutrition Continuum. Springer, pp. 259-284
Varki, A. (2017) Biological Role of Glycans. Glycobiology, 27, 3–49. https://doi.org/10.1093/glycob/cww086
Zeng, X., et al (2022) Gut bacterial nutrient preferences quantified in vivo. doi: https://doi.org/10.1101/2022.01.25.477736
Cryan, J, et al (2019) The Microbiota-Gut-Brain Axis. Physiol Rev 99: 1877–2013; doi:10.1152/physrev.00018.2018