Invisible Health
An introduction to the Microbiome
August 2022
by Dr. Jake Robinson
The microbiome can be defined as the entire collection of microbes (bacteria, algae, archaea, fungi, protozoa, and viruses) in a given environment, and its ecological theatre of activity. In the scientific realm, we tend to separate the microbiome into the environmental microbiome and the human (or animal) microbiome; but, really, both interact with each other in a constant flux of activity.
Often when we think about the climate crisis, we think about big weather events outside the context of cities like London. However, it is important to look at the whole range of effects that the climate crisis has, including its effects on the soil that nourishes us. There are microscopic organisms living in the soil, which help regulate its health. Healthy soil is nourishing soil which helps create vast biodiversity. This makes soil foundational to the entire workings of our planet, including climate regulation. For example, the Amazon Rainforest contributes to the regulation of global rainfall and climate regulation (source).
Given how important the environmental microbiome is both to human health and planetary regulation, it is important that we begin to include it in the context of cities and urbanisation. Focusing on the microbiome can help those who create our cities understand how to protect us from further disruption of our planet in a tangible, focused, and realistic manner. This is especially important, as cities continue to be significant human habitats.
The more we understand the microbiome, the more we can play a role in including their fruition in cities, we do not have to make a choice between cities and healing. Urbanisation typically involves the loss of native macro-biodiversity (e.g., plants and animals). This loss of macro-biodiversity is linked to a loss of complex microbial communities (e.g., fungi and bacteria), which, in turn, can negatively impact the health-promoting microbes residing in and on human bodies (i.e., the human microbiome).
“A single teaspoon of soil would likely contain between 10,000 and 50,000 different microbial species. There are approximately one trillion different microbial species in our planet’s natural environments. This is ten times as many species as there are stars in the Milky Way.”
The Microbiome
An explainer
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The environmental microbiome refers to the microbial communities that reside in the soil, the water, the plants, and the air (also known as the ‘aerobiome’). In terms of diversity, the soil is one of the densest habitats on Earth. A single teaspoon of soil would likely contain between 10,000 and 50,000 different microbial species. There are approximately one trillion different microbial species in our planet’s natural environments. This is ten times as many species as there are stars in the Milky Way. Each environment has its own unique microbiome. The environmental microbes play vital roles in the functioning of our ecosystems.
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The human microbiome is the collection of microbial species that live in and on our bodies. Each body site has its own unique microbial community. For example, the microbiome of our armpits is distinct from the microbiome of our mouths or guts. The gut microbiome is the densest microbial habitat in the human body, with trillions of bacteria, viruses, fungi, and others calling it their home. The genes in our microbiome outnumber our own ‘human’ genes by 150 to 1, and if we could extract the microbes from a single person’s gut and line them up, they could circle the Earth 2.5 times. The microbes in our bodies play essential roles in maintaining our health and ‘homeostasis’ by regulating our immune system, digesting our foods, and providing chemicals to keep our cells and organs in a healthy state.
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We are protected by two nested layers of biodiversity––the microbes in our guts, skin, and airways, and the microbes from the natural environments surrounding us. The microbes that live in our bodies are supplemented by the microbes in the environment and the microbes in our foods. Humans emit a million biological particles every hour, including a considerable portion of microbes. We each have our own signature microbial clouds that follow us around. There are approximately a million microbial cells in a single cubic metre of air, and people can inhale a whopping 100 million bacteria each day. In essence, the microbes in and on our bodies and the microbes in the environment are constantly being exchanged. Some environmental microbes are fleeting visitors, and some are long-term residents in our bodies.
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The loss of microbial diversity associated with urban areas underpins the so-called “biodiversity hypothesis” which proposes a link between two global megatrends: 1) biodiversity loss and 2) a rapid increase in noncommunicable diseases (NCDs; e.g., diabetes, inflammatory bowel disease, and mental health problems).
A growing number of studies support the biodiversity hypothesis. Evidence shows that the microbiomes associated with urban areas and urban lifestyles are suboptimal for health and well-being. The evidence spans different levels of empirical study, including human population-level studies, human cohort studies, and many animal model studies. Collectively, these studies support calls to conserve and restore biodiversity in our urban areas to enhance human health. This has the crucial co-benefit of supporting the other organisms who share the land with us.
Exposure to diverse microbial communities is considered important to human health and well-being because different microbes play different functional roles in our bodies. Maximising the number of species can also maximise the number of functional roles that are fulfilled. Microbial diversity is also important for proper immune function. Studies have shown that rural aerobiomes shift immune function away from adverse allergic responses compared to urban aerobiomes.
“The microbes that live in our bodies are supplemented by the microbes in the environment and the microbes in our foods. Humans emit a million biological particles every hour, including a considerable portion of microbes. We each have our own signature microbial clouds that follow us around. There are approximately a million microbial cells in a single cubic metre of air, and people can inhale a whopping 100 million bacteria each day. In essence, the microbes in and on our bodies and the microbes in the environment are constantly being exchanged.”
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In general, a diverse environmental microbiome is good for the human microbiome. So, what makes the environmental microbiome more diverse?
Vegetation and soil are key sources of airborne microbes—microbes that we are constantly exposed to because we inhale them with every breath we take. Exposure to diverse airborne microbes depends on the vegetation complexity in urban environments (i.e., the richness and diversity of species, and structural diversity). For example, a mixed species and multi-layered natural space (e.g., a woodland) is more favourable than a monoculture habitat (e.g., a sports field). This means that increasing the diversity of plant species and their structural complexity will likely increase the diversity of microbes in the air that humans are exposed to (which, as we now know, is considered a good thing).
Exposure to diverse communities of microbes in the urban air also depends on vertical stratification: microbial species diversity decreases as altitude increases. This makes sense because the soil is one of the most biodiverse habitats on the planet. However, despite this vertical stratification, the air at all human body heights (up to 2 metres) is still more diverse in green spaces with greater vegetation diversity/complexity than monoculture habitats like sports fields or amenity grasslands. Therefore, even though the aerobiome is not as rich and diverse as the soil microbiome, it is more diverse in areas with great vegetation diversity and complexity.
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Interestingly, preliminary results also show that the relative abundance of pathogenic microbes (the few that can cause human diseases) significantly decreases when more trees and plants are present in the urban environment.
All of this suggests that, if we increase the number of plant species and structural diversity (i.e., different shapes and sizes) in our urban areas, we will be exposed to a greater variety of beneficial microbes and to a reduced level of pathogens in the air. Therefore, ecological restoration can be viewed as a public health intervention. This means that bringing biodiversity into our cities is not only aesthetically pleasing and good for wildlife, but it is good for human health too.
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Land disturbed by human activities has been shown to harbour significantly higher levels of opportunistic pathogens.
When we restore ecosystems, specialist microbes begin to form stronger connections, robust interactions, and resilient communities. Some become keystone species or ‘core groups’. This means many other species depend upon their presence in the ecosystem (i.e., these core species/groups have a disproportionately large effect on the ecosystem relative to their abundance). As this ecological complexity builds up, the opportunist pathogens become outcompeted. This is one reason why we must restore our urban ecosystems. Noteworthy, in addition to paying attention to the plants, we must pay more attention to the soil. The health of the soil directly influences the health of the plants.
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Pollution is another important factor to consider when assessing the health and integrity of the microbial ecosystem in cities.
Air pollutants, such as noxious gases and particulate matter, interact with the microbes on plants and in the air. It has been suggested that air pollution can interact with the microbiome of tree pollen.
When this happens, the genes in the pollen switch to make the pollen more allergenic. This means that pollution could increase the allergenicity of tree pollen, which makes humans more susceptible to allergic diseases—another reason why we need to eliminate pollution from our urban environments.
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Given that we can spend as much as 80 to 90% of our time indoors in urban settings, it is important to at least briefly discuss the indoor microbiome in cities.
A dense urban environment can prevent the transfer of diverse microbes from natural environments to indoor environments. Indoor environments can also harbour a higher relative abundance of pathogens than outdoor environments.
This means that we need to increase the natural habitats surrounding our buildings, increase the natural features inside our buildings, and consider bio-integrated architecture whereby building materials can be colonised by and support living entities. A recent study showed that indoor gardening can enhance the skin microbiome and stimulate proper immune functioning.
We should also consider designing our indoor environments with appropriate light and ventilation to improve the air quality.
“Air pollutants, such as noxious gases and particulate matter, interact with the microbes on plants and in the air. It has been suggested that air pollution can interact with the microbiome of tree pollen. When this happens, the genes in the pollen switch to make the pollen more allergenic.”
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If we are to live in mutualistic symbiosis with Nature, we need to start using Nature-based knowledges to align our thinking with them. This starts with thinking about time in a different way. Industrialised nations prioritise the “now” rather than thinking in generations, centuries, or even millennia. The adjustments that we make today should be considered in a long-term view: How will they affect futures to come? Additionally, we have to think about living in mutualistic symbiosis with Nature: How can we do things with Nature rather than to or even for. Thinking about legacy is important: let us think about hundreds of years at a time.
Some urban landscape developments are currently designed for the relatively short term, particularly when it comes to natural features. Several reports suggest that 25% to 50% of urban trees die in the first few years of life. A common perspective is that these can simply be replanted. However, this short-term perspective fails to consider that ecosystems require many years to build up complexity and resilience.
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A focus on the diversity, quality, and longevity of urban ecosystems is vital for future generations of humans and the rest of the biotic community. A conceptual framework called microbiome-inspired green infrastructure (MIGI) is being developed. This sets out steps that can be taken now to enhance the health of urban ecosystems and highlights important considerations for the near future, with an emphasis on the foundational roles of microbiomes. MIGI sets a grounding framework for assessing the quality of a green space or a natural environment. This is crucial as many green spaces are not being allowed to fulfil their role, which is to nourish our air and soil, so we can all breathe good air. Whilst there are many ways that Nature supports our healing, Nature should provide us with good air as a rudimentary baseline, which, at the moment, is due to a degraded microbiome. Therefore, we need to move past whether or not people are physically accessing natural spaces, which, although highly important, is not the whole picture, access should also be supported with good quality natural spaces.
