INVISIBLE

FRIENDS
How Microbes Shape Our Lives
and the World Around Us

JAK E M. R O B INS ON

PELAGIC PUBLISHING
 Contents

Introduction: A Hidden World 1

1 The Microbiome 9
2 Rekindling Old Friendships in New Landscapes 18
3 Antibiotic-Resistant Landscapes 40
4 Microbes and Social Equity 50
5 The Psychobiotic Revolution 62
6 The Lovebug Effect 80
7 The Holobiont Blindspot 90
8 The Glue that Holds Our Ecosystems Together 102
9 Microbes and Trees 111
10 Rewild, Regenerate, Restore 123
11 Bio-Integrated Design 141
12 Microbiome-Inspired Green Infrastructure (MIGI) 157
13 To Catch a Thief: Forensic Microbiology 172
14 Microbes in Outer Space 186
15 You are What Your Microbes Eat 193
16 Nature Connectedness 210

Conclusion: Great and small 227

Appendix: Microbes 101 231
Glossary 241
Notes 244
Acknowledgements 258
References 259
About the author 271
Index 272
 INTRODUCTION

A Hidden World

A
s soon as the deep-scarlet sunrise burst from the horizon,
the dew-draped meadow glistened like a sea of diamonds.
A light breeze carried the scent of a changing season. It was
springtime in 2006. I was camping on the semi-forested rolling
hills of the Peak District in England. Prematurely awoken by
a fleeting rain shower, sleep inertia came to an abrupt end as a
potent earthy aroma wafted into the tent. However, at the time,
I was completely unaware that my olfactory system – the part of
the body responsible for processing smells – was allowing me to
perceive signals from another world hidden within our own. A
world that we cannot see with the naked eye, brimful of invisible
biodiversity, a bustling microscopic metropolis. Initially, I probably
thought, ‘ahh, the smell of the countryside’ or ‘the musky scent of a
forest’ – but then I asked myself, ‘Why does it smell like this? What
is responsible?’ Much to the annoyance of my parents, I have always
been an inquisitive soul, asking questions at every opportunity.
I trace some of this back to Mr Birch, a slightly eccentric teacher at
my primary school in England.
Mr Birch was keenly interested in geology, and we used to swap
rocks – our nerdy take on a swap shop. ‘You’re so cool,’ my sisters
would say, sarcastically of course. I remember bringing Mr Birch
a small chunk of sedimentary rock I had found in the local nature
reserve, and him exchanging it for a gnarly piece of igneous rock,
or solid lava. ‘Wow, is this from a volcano?’ I asked. ‘Yes,’ Mr Birch
responded. To my surprise, he told me he had found this volcanic
rock in England. I was suitably confused for a seven-year-old. I had
travelled around the British Isles to see all the great Norman and
Anglo-Saxon castles – one of my father’s hobbies – but never once
2  Invisible Friends

had I seen a volcano. As far as I was concerned, a volcano was a

gigantic rocky cone spewing red-hot lava, consuming everything
in its path. Mr Birch explained that the area we today know as
England once contained many active volcanoes.1 The rock he gave
me was a fragment of one of these, formed thousands of years ago.
I was amazed and still slightly confused. Mr Birch responded
with words to the effect that ‘There is more to the world than we
initially perceive. And remember, the most important word in
the world is… why?’ From this point on, at every opportunity,
I would say to my parents and probably everyone around me,
‘That’s interesting, but why?’… ‘Why is this the case?’… ‘Why did
that happen?’ I now see this as both a curse and a blessing. This
constant questioning from an untempered child was undoubtedly
annoying for the recipient. However, it opened the door to a world
of fascination. What else exists in the world that we cannot see?
What happens in the world that we may not initially notice? Does
what we perceive of the world match the reality? Is everything we
thought we knew about the universe even true? These profound
questions would both overwhelm and excite me as a child – and
they continue to do so even now.
Let’s return to the earthy and evocative scent I noticed in 2006.
When I arrived home from the camping trip, I remember searching
the internet to try and find out what was responsible for that
musky smell particular to the countryside, ‘the Earth’s perfume’.
I couldn’t find anything. Rudimentary academic literature search
engines existed in 2006, but I certainly was not aware of them back
then. However, a couple of years later, I discovered that the earthy
odour was called petrichor, first named by two geologists in 1964.2
Petrichor is caused by a potent chemical called geosmin.
The human nose is incredibly sensitive to geosmin. We can
detect this compound at one hundred parts per trillion. In other
words, we can detect geosmin better than sharks can detect blood.3
Geosmin is produced by a group of soil bacteria called Strepto-
myces, and all the known 550 Streptomyces species can produce
this chemical. This suggests that geosmin confers a selective
advantage on the bacteria; otherwise, it is doubtful that all species
would produce it. By ‘selective advantage’, I mean the production
 Introduction: A Hidden World   3

of geosmin must bring an essential benefit to the bacteria, and

therefore the bacteria evolved to keep this trait and pass it on to
future generations.
Some scientists think that Streptomyces produce geosmin
because of a mutual relationship between the bacteria and a group
of six-legged creatures called springtails. These insect-like creatures
evolved at least 400 million years ago and are still around today.
To disperse across the landscape, Streptomyces produce spores –
as a plant produces seeds. But how do these spores spread? Well,
Streptomyces have an ingenious trick up their sleeves. It turns out
that geosmin is attractive to springtails, and the bacteria probably
produce it as a signal specifically to lure springtails: ‘Hey springtail,
come and get me!’ Scientists think that springtails gobble up the
Streptomyces as a nutritious food source, spurred on by the fact
that Streptomyces also produce antibiotic compounds that can
kill off pathogens. This is a mutual relationship. The springtails
disperse the Streptomyces’ spores by consuming and excreting
them; thus, the bacteria also benefit.4 This is much like when a
badger consumes elderberries and defecates the seeds, allowing
them to disperse and germinate – which is why you often find
elder trees with their white florets and deep-purple fruits next to
badger setts.

I’ve often wondered why humans have evolved such an acute sense
for geosmin. Could it be that humans also receive a health benefit
from the Streptomyces, and are therefore attracted to the earthy
perfume they produce?
Cue inflammation. We’ve all seen the effects of inflammation
on our bodies. It causes that ensuing pain and swelling after a
paper cut or a grazed knee. But it also happens inside our bodies as
harmful stimuli such as pollution or pathogens trigger a protective
response by the human immune system. It’s an entirely natural
process and involves shuttling immune cells and chemicals to
the site of injury or infection, often leading to heat and swelling.
Too little inflammation and the harmful stimuli can destroy the
body’s tissues. Too much inflammation can damage the cell’s DNA,
leading to severe health conditions.
4  Invisible Friends

A 2018 scientific publication highlighted that persistent in-

flammation contributes to chronic diseases like diabetes and
cancer.5 This is widely known. However, the paper also pointed
out that Streptomyces produce numerous anti-inflammatory
compounds. Importantly, Streptomyces species occur in the human
gut microbiome – ‘microbiome’ meaning the entire collection of
microbes and their theatre of activity in a given environment, such
as guts, armpits, soil or plants. In their conclusion, the authors
argued that Streptomyces may have evolved to be friendly with
humans, helping to suppress colon cancer. So, if this is proven to be
accurate, a soil-dwelling bacterium that produces geosmin could
also help prevent human diseases. This is only speculation, but
perhaps it goes some way towards explaining why humans have
evolved to detect geosmin so acutely. By wandering around natural
environments and allowing Streptomyces spores to hitch a ride, we
could also be their dispersers, just like the springtails – another
mutual relationship. For me, this fascinating and potentially
important relationship demonstrates why we should always ask
why – even if it’s just to ourselves.

Many fascinating phenomena in our world often go unnoticed.

The incredible diversity of the microscopic realm around us holds
many secrets. It is a shame that we cannot easily see this invisible,
bustling metropolis of biodiversity, because it is always challenging
to appreciate what you cannot see. However, technological break-
throughs and the rapidly plummeting costs of machines that
decipher the building blocks of microbial life (DNA) allow us to
understand the dynamics and interactions of this hidden world.
Rapid technological advances have opened the door to many
new scientific endeavours, from sequencing the human genome to
editing genes for therapeutic purposes. Microbial ecology, now a
booming field of research, has capitalised on these breakthroughs.
We now know the air we breathe is thronging with microscopic
life-forms: moss spores and plant pollen, dense clouds of bacteria,
archaea, tiny fungi and algae, along with protozoans and vast
quantities of viruses, each communicating, interacting, sharing
and competing all around us. There may even be a few microscopic
 Introduction: A Hidden World   5

Moss piglets (tardigrades) often live among moss and lichens.

moss-dwelling animals called tardigrades, also known as water

bears or moss piglets because of their mammal-like appearance –
under the microscope, at least. A single gram of moss on the forest
floor may contain over 100,000 of these tiny animals, and because
they are exceedingly light, they are easily swept up by gusts of
wind, making them airborne.

Researchers can now analyse vast quantities of microbial samples,

providing novel insights into the complex but unseen communities
around us. I have done this myself as a researcher, in the course of
completing a PhD in microbial ecology.
In this book, I aim to reveal the weird and wonderful roles
microbes play in shaping our health and behaviour, and indeed
in the wider world around us. Highlighting the etymology of the
mainly Greek and Latin scientific names is another thread running
6  Invisible Friends

through the book. The roots of words provide associations that

allow us to remember the complex names of species or concepts,
but they also indicate their function and sometimes environment.
For instance, Thermus aquaticus is a species of bacterium that
grows in hot (Thermus, from the Ancient Greek thermós, ‘hot’)
springs (aquaticus, from a Latin word relating to water). It was first
‘discovered’ in Yellowstone National Park in the United States back
in 1969.
Incidentally, T. aquaticus played a pivotal role in advancing
DNA technology and thus the field of microbial ecology. The
bacterium is the source of a heat-resistant enzyme that can
withstand the high temperatures in the ‘PCR’ (short for polymerase
chain reaction) process. PCR is a method of amplifying small
samples of DNA so that scientists can study them in detail. It can
target a specific gene conserved in all bacteria, allowing one to
inspect only the bacterial members of a sample (which is often
teeming with DNA from other microbes, plants and animals). It
can ‘pull a needle out of a haystack’, enabling a rare component of
a large and messy mixture to be identified. Indeed, it’s the same
tool widely used to test for COVID-19 infections. The chemicals
used in a PCR reaction hook onto a segment of the virus’s genetic
material so that it can be amplified. Therefore, in a sense, we have a
hot spring-loving bacterium to thank for our ability to fight against
COVID-19 and other maladies.

Historically, our general perception of microbes has been negative

due to the relatively few invisible foes that cause diseases. In this
book, my intention is not to play down the severity of pathogens.
Instead, I intend to stimulate a more balanced view of microscopic
life-forms and showcase fascinating stories about their underap-
preciated and often beneficial roles in all aspects of our lives.
Let’s cast our minds back to the dawn of germ theory, which
Hungarian physician Ignaz Semmelweis anticipated and French
chemist and microbiologist Louis Pasteur consolidated in the
mid- to late nineteenth century. It was a remarkable development
in human thinking when scientists understood that microorgan-
isms were responsible for many human maladies. Before this,
 Introduction: A Hidden World   7

our understanding of human diseases was limited. One of the

predominant theories in the Western world was the miasma theory.6
This held that diseases such as cholera or plague were caused by a
noxious form of ‘bad air’ emanating from rotting materials. Germ
theory, on the other hand, states that some microbes can cause
diseases by invading the hosts (whether humans, other visible
animals and plants, or even other microbes) and causing physi-
ological harm. People often refer to microbes as ‘germs’ (from the
Latin germen for ‘seed’, ‘bud’ or ‘sprout’). Presumably this is due to
their budding-like lifecycle and seed-like appearance. Knowledge
of pathogenic microbes has undoubtedly saved millions of lives
since germ theory was first posited. However, knowing that
some microbial species – though in truth it is far fewer than one
in ten thousand – cause human diseases has led many people to
fear and loathe all microbes.7 This ‘germophobia’ has likely been
compounded by decades of relentless advertising campaigns, such
as those selling household detergents or that instil fear of nature
and dirt. These campaigns have created a negative perception of
all microbes.
Often, the result of this perception is the avoidance of natural
environments and their dirt, the mass sterilisation of surfaces with
detergents, and reduced human exposure to biodiversity – the
variety of life around us, including the invisible kind. It turns out
that this avoidance of biodiversity could be contributing not only
to a loss of appreciation for the vital, invisible universe around us,
but also to an explosion in human immune-related disorders.8 So,
wiping out all the microbes in our lives with a view to preventing
diseases could be having the reverse effect. It is important to note
that targeted hygiene remains essential around food, sinks and
toilets. However, attempting the total elimination of dirt from our
lives is where the danger lies.
The truth is that relatively few microbes cause human diseases,
and many others benefit us. Bacteria and bacteria-like organisms
called archaea, along with algae, fungi and tiny animal-like critters
called protozoans – and even some viruses – all play vital roles
in our ecosystems. They are the glue that holds it all together –
our invisible friends. Indeed, microbes play essential roles in
8  Invisible Friends

plant health and communication, animal health, nutrient cycling

and climate regulation, among many other ecological processes.
Without microbes, our food systems would collapse. Without
microbes, our societies would crumble, and our bodies would not
function in the long term. As microbiologists Gilbert and Neufeld
said in a paper published in 2014, ‘if we include mitochondria and
chloroplasts (the energy-producing cells in animals and plants) as
bacteria, as we should, then the impact [of their absence] would
be immediate – most [creatures] would be dead in a minute’.9
I want to challenge the prevailing negative perception of
microbes and take you in a different direction, shining a light on
all the fascinating roles that microbes play in our daily lives and
discussing their relationships with all other life on Earth. In what
follows, we will hear from world-leading experts in microbial
ecology, neuroscience, restoration ecology and immunology, and I
even visit a regenerative agriculture farm. I discuss some of the risks
to our relationship with our invisible friends, such as antimicro-
bial resistance, the biodiversity crisis and the rise in germophobia
mentioned earlier, in addition to framing microbes as a facet of
social equity (Chapter 4). Microbes are essential features of our
ecosystems, health, social structures, behaviour, food systems and
cultures. They are infinitely small but do infinitely great things.
Stories of interconnectedness weave their way into each
chapter, and there are occasional philosophical musings around
our affinity with the natural world. I believe we need to redefine
our relationship with nature culturally, socially, psychologically
and emotionally – particularly in Western societies. Still, there’s
scope for all people in all communities to redefine their relation-
ship with nature microbiologically, through knowledge of the
unseen cosmos outside and in. I hope you enjoy reading about our
invisible friends.
For those who would like to know more about microbes before
reading this book, I’ve included an appendix called ‘Microbes 101’.
If you’re new to the world of microbes, this should help with some
of the terminology and references used.
 CHAPTER 1

The Microbiome
‘The role of the infinitely small in nature is
infinitely great.’
—Louis Pasteur

I
’m sitting on a rickety old camping chair in a pine forest, at
the top of a steep hill. The forest receives few visitors. It has a
calming aura, helped by the trickling sound of a boulder-hugged
stream. This is where I come to clear my mind, and sometimes to
work. It could be to write. It could be to zone out and run code on
my laptop. It could be to draw some inspiration for new research or
simply to reflect, find solace and, as nineteenth-century naturalist
John Burroughs said, ‘to have my senses put in order’. The forest is
a beacon of serenity.
The ground beneath my feet is carpeted with the creeping
shamrock-shaped leaves of the edible wood sorrel. The air is rich
with buzzing hoverflies, shield bugs and ladybirds. My eyes drift
left, right, up and down across the trees’ diverse contours, textures
and pleasing fractal patterns. I find myself considering the rich
bounty of ecological niches and elegant adaptations surrounding
me. And how each individual from the consortia of plants and
animals I see with the naked eye is a diverse conglomerate of many
organisms, the vast majority of which I cannot perceive. The trees
are host to trillions of microbes. The trees need the microbes for
development, communication and, ultimately, their survival. The
mosses that creep across the boulders are also home to trillions of
microbes, as are the wood sorrel and the hoverflies, and my solitary
self. But this means I am in fact anything but alone. My body is a
hive of activity, a bustling jungle full of life. I sit here emitting my
10  Invisible Friends

personal signature in the form of a microbial cloud, and I bathe

in the microbial clouds of the plants and animals around me. Our
microbiomes are in constant flux, and constant communication.

Before we go any further, I should define some terms. For instance,

what is a microbe and a microbiome? A microbe, also known
as a microorganism, is a microscopic organism that can either
be single-celled (unicellular) or multicellular. The word comes
from the Greek mikrós (‘small’) and bíos (‘life’). Microbes include
both prokaryotes (pronounced ‘pro-carry-ohts’) and eukaryotes
(pronounced ‘you-carry-ohts’).
The prokaryotes are single-celled creatures that lack both a
membrane-bound nucleus (where DNA is stored) and organelles –
which literally means ‘tiny organs’. Prokaryotes include bacteria
and similar-looking microbes called archaea. Eukaryotes, on the
other hand, do have a membrane-bound nucleus and organelles.
Microscopic eukaryotes include fungi, algae and protozoans – tiny
animal-like creatures.
Lastly, and by no means least, there are the viruses. These are
neither prokaryotic nor eukaryotic. Viruses can only replicate
within the cells of a host creature. As such, scientists often give them
the unflattering description ‘obligate parasite’. Essentially, microbes
include any organism you would need a microscope to see, along
with viruses, which most people consider to be non-living entities.
Microbes are also incredibly diverse and incomprehensively
abundant. For example, current estimates suggest 1012 microbial
species exist on Earth; that’s one trillion different species.1 For
those who enjoy snappy analogies, there are thought to be ten
times as many microbial species on our planet as there are stars in
the Milky Way.

Biodiversity – or the variety of life on Earth – is so much more

than meets the eye. It would be easy to inadvertently perceive
biodiversity, from which we acquire a rich bounty of provisions
and aesthetic values, as simply the trees, flowers, insects, birds,
amphibians, reptiles, mammals and other wondrous visible
life-forms that inhabit the planet. After all, these are the organisms
 The Microbiome  11

that we can see, as well as hear and sometimes feel. There are an
estimated eight million species of meso- and macroscopic (visible)
animals and plants on the planet. However, dig a little deeper, and
we find this figure is dwarfed 125,000 times over by the number
of different microbial species. And speaking of digging deeper, if
I were to move the wood sorrel beneath my feet to one side and
plunge a teaspoon into the soil, I would likely return with between
10,000 and 50,000 different microbial species, or one to seven
billion individuals, on the spoon. To cite a quote often attributed
to Leonardo da Vinci (1452–1519), ‘we know more about the
movement of celestial bodies than about the soil underfoot’. This
could still be true today, although we are at last catching up, thanks
to rapid advances in technology.
Microbes form complex and dynamic communities, much
like the so-called ‘higher organisms’ (a rather grandiose title often
given to larger and visible animals and plants), and they inhabit
all the world’s ecosystems. Some microbes are uniquely adapted to
extreme environments where others would simply fail to survive.
For example, if I took a bacterium from the mossy boulders next
to the woodland stream and placed it in a hot spring, it would be
unlikely to survive, and vice versa – a specialist hot-spring microbe
would not fare well in the chilly temperate forest moss. Still, many
other microbes are ‘generalists’ and can adapt to a wide range of
environmental conditions. In addition to the tremendous number
of microbial species and the variety of their ecological niches, a
diverse range of shapes and sizes exist. Some are tubular, spherical,
crowned or filamentous, and others form long chains. Some are
rod-shaped, and others are ‘icosahedral’ with 20 triangular faces.
Bacteriophages, or viruses that prey on bacteria, are often depicted
as spider-like spaceships complete with landing gear. This is quite
an accurate description, as shown in the sketch below.

The smallest known microbe on the planet is a virus, and it is

­approximately 20 nanometres (nm) in diameter. Discovered in
1965 by R.W. Atchison,2 we call this an adeno-associated virus or
AAV. The largest known microbe is a bacterium called Thiomar-
garita namibiensis. It’s a spherical bacterium around 0.75 mm in
12  Invisible Friends

The alien spider-like bacteriophage, or ‘phage’ for short. This is a sketch of the
T4 phage that infects E. coli bacteria.

diameter and is found in ocean sediments off the coast of Namibia.

This one is easy to notice because it shines like a pearl, which gives
its colloquial name, the ‘sulfur pearl of Namibia’.3
The size difference between the virus and the bacterium might
not seem so vast. However, 20 nm is 0.00002 mm, and there are
750,000 nm in 0.75 mm. Therefore, the bacterium is 37,500 times
bigger than the virus. If the virus sat down on the bacterium,
this would be the equivalent of a human lying down inside the
boundary of the M25 motorway in London, which has a diameter
of 75 km. It’s also the equivalent of placing a poppy seed on top of
 The Microbiome  13

a blue whale – the largest animal on the planet. I had to re-run this
calculation several times before I believed it myself. But we shouldn’t
let the diminutive size of viruses fool us – they really do pack a
punch. In fact, every 48 hours, phage viruses kill half of all bacteria
on the planet.4 They play vital roles in maintaining the biological
equilibrium of ecosystems – including that in our bodies. Indeed,
a healthy person is home to a hundred times more viruses than
there are individual trees on the planet – a hundred global forests
of phages inside you!5 Many of your 380 trillion viruses play a role
in controlling bacterial populations. Hence, it’s likely that we need
them, just as they need us; sweet reciprocity between our bodies
and our residents, unbeknown to our minds. And there’s another –
perhaps surprising – reason we should tip our hats to viruses: their
role in providing the air we breathe. Take a deep breath. Each time
we draw air into our lungs, around 21% is oxygen. Photosynthetic
organisms have been releasing this oxygen into the atmosphere for
over 2 billion years. Some of them are plants (in the last 500 million
years), but many are microbes – particularly in the ocean. While
the ratios have changed over time, photosynthetic cyanobacteria in
the ocean generate at least half of the oxygen in the atmosphere.6
But where do viruses enter the equation? Scientists think that the
photosynthetic machinery in the cyanobacteria is of viral origin.7
Because viruses can transfer genes between different organisms
like prolific market traders, they may well have played a crucial
role in cyanobacteria evolution. This includes their ability to pho-
tosynthesise and thus produce oxygen. Moreover, scientists believe
some phage viruses insert photosynthesis genes to keep the host
cyanobacteria on ‘life support’ during infection.
Draw in another deep lungful of oxygen and reflect: a diverse
team of oceanic bacteria and viruses made this possible.

Microbiome
What is a microbiome? You might describe a microbiome as ‘the
entire collection of microorganisms in a particular environment’.
This is a simplified definition. It sounds relatively straightforward.
However, molecular biologists might define it more precisely as ‘the
14  Invisible Friends

collection of microbial genetic material in a given environment’.

Others will include environmental conditions and different aspects
of the ecological theatre in which the microbes operate.8 For clarity,
in this book, I will be using a definition that encompasses this
broader idea – so, all the microorganisms in a given environment,
and their entire ecological theatre of activity. The word microbiome
comes from the Ancient Greek mikrós (‘small’), bíos (‘life’) and
ōma, meaning a ‘complete or collective body of ’.
We can trace theories about the interactions between different
microbes back to the late nineteenth century, and perhaps the
first microbial ecologist was Ukrainian Sergei Winogradsky. In
1888, he recognised and studied the interconnections between
aerobic (­oxygen-requiring) and anaerobic (requiring an absence
of oxygen) bacteria.
Despite steady advances in microbiology during the twentieth
century, it was only in 2007 that microbiome studies gained rapid
momentum with the launch of the Human Microbiome Project.
This US government-funded initiative aimed to conduct the most
comprehensive assessment of the microbial communities living in
and on the human – a huge ecological survey on a microscopic
scale. A subsequent initiative, the Earth Microbiome Project
(2010), did the same for global ecosystems. These projects have
inspired many of the insights in this book.

I continue to sit in the forest with a vivid picture in my mind. I

visualise the ground beneath my camping chair humming with
activity. With every breath I take, I picture a constant flux of
life-forms being exchanged between myself and my surround-
ings. All these life-forms – the bacteria, archaea, fungi, viruses,
algae and protozoa – often live together in complex dynamic
communities, like the microbiomes of the pine forest I am sitting
in. I look at the trees next to me. The aboveground part of the trees
is referred to as the phyllosphere (pronounced ‘fill-lo-sphere’), and
it has a distinct microbiome. I look down to the soil beneath my
chair and see the area surrounding the roots; this is known as the
rhizosphere (pronounced ‘rye-zo-sphere’), which also has a distinct
microbiome. The microbiome of the air I breathe, meanwhile, is
 The Microbiome  15

known as the aerobiome. Much like the habitats around us, our
bodies also harbour distinct microbiomes. Indeed, we could view
ourselves as walking ecosystems.

Humans as walking ecosystems

Like the trees in the pine forest, we too have our own microbiomes.
Each of us has several distinct microbial communities living in
and on our bodies. Microbiome researchers say that the microbial
genes in our bodies outnumber human genes by 150 to 1, and if we
could line the microbes from a single person’s gut up end to end,
they would be able to circle the Earth two and a half times. As Walt
Whitman said, ‘I contain multitudes’ – which by no coincidence is
also the name of a fantastic book on the human microbiome by the
science journalist Ed Yong.9
A complex and dynamic conglomeration of molecules, cells,
tissues and organs clinging on to a gangly, mineralised frame and
working harmoniously like a quintessential symphony orchestra. I
am, of course, referring to the human body. Add a potent sprinkling
of consciousness to the mix, and you have a genuinely momentous
system capable of unimaginable feats. Yet, as complex as human
beings are, we are descended from the single-celled archaea. Jump
into a time machine and travel back far enough – some 3.5 billion
years – and you will find your ancestors are like those diminutive
but extraordinarily resilient germs we often discover in so-called
extreme environments today, such as hot springs and salt lakes.
The next revelation is perhaps equally peculiar. Within each
of our cells are hard-working organelles called mitochondria.
These bean-shaped intracellular structures are responsible for
producing a chemical known as ATP (adenosine triphosphate)
through a tongue-twister of a process called oxidative phospho-
rylation. These tiny organelles produce over 90% of our cellular
energy. There’s no wonder they’re often called the ‘powerhouses’
of our cells. Yet we think mitochondria also evolved from bacterial
ancestors. It may seem surprising that the tiny organs that provide
energy to our cells and are essential to respiration are microbial
in origin. Yet scientists increasingly accept that this is indeed the
16  Invisible Friends

case. Many scientists consider an internal symbiosis (where two

different organisms live in close physical association) to be the
leading theory for how mitochondria evolved; the mechanism for
this phenomenon is called endosymbiosis.10 One theory states that
a bacterium was phagocytosed (aka ‘gobbled up’) by a eukaryotic
organism. This eventually led to a remarkable symbiotic relation-
ship whereby one organism lives inside the other.

By now, you may have noticed a theme of interconnectivity

weaving its way through the narrative. All things connect, whether
socially, biologically or evolutionarily, and microbes are the glue.
As humans, we are intertwined with microbes, and throughout
evolutionary history, they have shaped our bodies and minds. They
were here billions of years before us, curating our DNA, our cells
and the ‘metaorganism’ we embody today. Despite our egos, which
may tell us otherwise, it seems they are the dominant life-forms
on the planet. Our fleeting existence will not ensure our resident
microbes live for an eternity, but there is no doubt they will find
another home once we are gone.
Now that we understand the importance of microorganisms,
we have an opportunity to redefine our relationship with the natural
world. Indeed, there is a whole cosmos of invisible biodiversity out
there, and with the help of next-generation DNA sequencing, we
can look much closer to home to find a diverse array of species –
within and upon the human body. In recent years, researchers have
collected samples from various locations in living human bodies
to analyse the content and identify microbial DNA signals. The
results: around 150 microbial species on our hands, 700 in our
mouths, and 1,000 in our guts.11
We each emit somewhere in the region of a million biological
particles (including microbes and ‘human’ cells) per hour from our
breath, skin and hair. The presence of just one person in a room
can add 37 million bacteria to the air every hour from emission
and displacement. We can view ourselves as dynamic ecosystems
– a human host plus trillions of microbial symbionts (organisms
that live in close association with others) openly interacting with
the environment via complex biological exchanges. Indeed, we
 The Microbiome  17

are deeply embedded within the natural world – both physically

and psychologically – and we are highly dependent on biodiver-
sity at multiple scales. In just a cubic centimetre of our walking
ecosystem (our bodies), millions of collaborating and competing
microbes contribute to nutrient cycles and energy flows without
us even noticing.

As I sit on my camping chair, admiring the life around me, I feel

like I’ve metamorphosed from an object into a group of subjects.
Like a psychedelic trip, albeit fleeting, this process of introspection
has momentarily altered the contours of my consciousness.
A hoverfly lands on my arm. Moments before, it was perched
on a creaking Scots pine tree. Before that, on the boulders that hug
the stream. I’ve become acutely aware that the hoverfly delivers and
collects a new group of microbes with each stepping stone it lands
on in this forest. Microbial life-forms even adhere to the hoverfly’s
body as it sails through the air. And now it has landed on my arm.
Touch-down. This ultra-light organic connection allows a
flurry of microbes already on my arm to join the hoverfly’s personal
ecosystem, and for the hoverfly’s microbes to join mine. Yet the
microbes joining my body didn’t come from just the hoverfly,
but also from the pine tree, the mossy boulders and the air: a
phenomenal multi-species correspondence, a biological internet.
The term constant flux springs to mind over and over. We are all in
this together. We are all connected through our invisible friends.