You’ll never walk alone – What is the microbiome?
Previously I wrote that “I now eat for my body and my gut microbiome”. Here I try to describe the microbiome and how it works. The composition of the human microbiome is unique to every one of us, but irrespective of this we each benefit from vital core beneficial functions. We must remember its need for nourishment because without our microbiome, we just wouldn’t exist.
Throughout this paper I use the terms microorganism and microbe (at least its adjective, microbial) interchangeably to mean a very small living thing (organism) not seen by the naked eye. I use the term macroorganism to mean an organism that we can see with our eyes.
Evolutionary perspective
Microorganisms are on and in every living thing that we can see on earth. For most of the first 2.5 billion years, life on earth consisted only of single-celled organisms. The first multi-cellular organisms (e.g., plants and animals of a sort we might recognise) evolved into this microbial world, hosting large communities of microorganisms on and in their bodies1. Our current view is that microbial communities are everywhere, and play a critical role in plant, animal and human health [2] to the extent that we cannot live without them.
“Microbiota consist of all living microorganisms that form a microbiome…”
What is the microbiome?
The term microbiome is used to describe the community of microorganisms (microbiota) and the structural elements, cell transformation products (metabolites), signaling molecules, and surrounding environmental conditions that have evolved within every environment (e.g., soil, lake, ocean), plant, and animal on earth [3]. I like to think of the microbiota existing in a soup of its own making, which can change depending on environmental circumstances. The scientists who defined the microbiome in this way describe it as containing microbiota and their “theatre of activity”[4] (what I describe as their soup).
There is a general tendency to conflate microbiota and bacteria, which understates the true diversity and value of the former. Microbiota consist of all living microorganisms that form a microbiome, and may include bacteria, archaea, fungi, algae and small protists. Viruses, phages, plasmids, prions, viroids, and free DNA are not living organisms, and are not part of the microbiota, but they are part of the soup which contribute to the microbiome.
Microbiota are essential for life on earth
Microbiota benefit all living plants and animals on earth. As an example, Ed Yong in his book does a marvelous job of summarising the beneficial symbiotic role of the human microbiota:
“They help to digest our food, releasing otherwise inaccessible nutrients. They produce vitamins and minerals that are missing from our diet. They break down toxins and hazardous chemicals. They protect us from disease by crowding out more dangerous microbes or killing them directly with antimicrobial chemicals. …They guide the construction of our bodies, releasing molecules and signals that steer the growth of our organs. They educate our immune system, teaching it to tell friend from foe. They affect the development of the nervous system, and perhaps even influence our behaviour. They contribute to our lives in profound and wide-ranging ways; no corner of our biology is untouched. If we ignore them, we are looking at our lives through a keyhole”
Sadly, microorganisms have traditionally been thought of as disease-causing agents. To the contrary, research has demonstrated that only a small proportion of microorganisms are associated with disease and that the great majority are essential for all other life on earth.
We are holobionts
Animals (including humans) and plants are not biologically autonomous. The symbiotic associations between microbiota and host are so integral and important that plants and animals are no longer described in biology as autonomous entities. Instead, every plant and animal is considered to be an organized biological unit. These biological units are referred to by the new-ish term holobiont [5].
Any new area of research can suffer from misrepresentation, and microbiome research is no exception. In a sincere attempt to help us understand this new field, microbiota and holobiont are often referred to as new organs and superorganisms, respectively. Use of such terms is inaccurate and risks missing the unique nature and incredible potential of holobionts[5].
Microbiome health and benefit to us
Microbiomes appear to work in ways that are very similar to other ecological communities in nature. Accordingly, a diverse environment can produce a diverse microbiota which through dynamic and complex interactions positively influences host physiology and health [2]. Typically, the greater the microbiota diversity, the healthier the host.
The good news is that we humans can provide a diverse environment for our microbiota. For example, our large intestine (colon) provides many different types of places (ecological niches) within its folds for our microbiota to live in and we can feed our microbiota with many different types of nutrition. Such a diverse environment results in a diverse microbiota with a large number and distribution of different species and strains. Greater microbiota diversity tends to be good for us because it creates microbiota redundancy and microbiome resilience.
“…our microbiome can withstand stress and maintain its functionality and benefit to us”
Redundancy means that if, for whatever reason, a particular beneficial member of the microbiota declines or is eliminated, its function can be assumed by other microorganisms. Microbiota redundancy confers microbiome resilience, meaning our microbiome can withstand stress and maintain its functionality and benefit to us. This scenario is analogous in team sports with a deep bench allowing for injured players to be substituted to ensure that the team’s winning ways are not affected.
If microbiota diversity is reduced, our microbiome function may be affected, causing disruption of the normal healthy balance between microbiota and host. Such disruptions can be caused in humans by use of broad-spectrum antibiotics and poor nutrition. However, disrupted microbiomes can be restored with proper nutrition[6].
Microbiome benefit to us
In exchange for unique places to live our microbiota provide us with a range of essential benefits, including protection against pathogens, nutrient production and recycling, beneficial fat storage, development and behaviour, and production of body heat [6].
“…we share a functional core microbiome, but not a core microbiota.”
What is worth remembering?
Our microbiome is an integral and vital component of our lives without which we would not exist. Over millions of years our bodies and microbiomes have developed together to form a biologically distinct holobiome which is mutually beneficial, robust, remarkably resistant to harm and capable of restoration with proper nutrition. Most fascinating of all, we are each the same and yet distinctly different from one another because “…we share a functional core microbiome, but not a core microbiota.”[2] We never walk alone and we are all, at a functional level, the same inside, ultimately.
References
Yong, E. (2016) I contain multitudes: The microbes within us and a grander view of life. New York: Harper Collins
Lozupone, C.A. et al (2012) Diversity, stability and resilience of the human gut microbiota. Nature, 489(7415), 220–230. doi:10.1038/nature11550
Berg, G. et al (2020) Microbiome definition re-visited: old concepts and new challenges. 8:103 https://doi.org/10.1186/s40168-020-00875-0
Whipps J, Lewis K, Cooke R. (1988) Mycoparasitism and plant disease control. In Burge M, editor. Fungi in biological control systems. Manchester University Press, pp. 161-187
Bordenstein, S. R., Theis, K.R. (2015) Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes. PLoS Biol, 13(8), e1002226. doi:10.1371/journal.pbio.1002226
Armet, A.M., et al (2022) Rethinking healthy eating in light of the gut microbiome. Cell Host & Microbe 30, 764-785, https://doi.org/10.1016/j.chom.2022.04.016