2.1 Microbes everywhere

The most important parts of our world are invisible. We can’t see air, but we can’t live without it. Similarly, our bodies are literally bathed in living, eating, reproducing lifeforms that we can’t see but that have profound effects on all that we do.

Life is tenacious, finding its niche, fighting for it, and stubbornly holding on in every environment it encounters. Living organisms inhabit the sky, deep underground, in the most barren habitats cold or hot anywhere on earth. The vast majority of these are microbes, so small we can’t see them, but small doesn’t mean irrelevant. In fact, the more that science understands about the invisible microbial world, the more it becomes clear that these uncountably numerous creatures exert a much bigger effect than we think.

Every traditional culture recognizes a role for the invisible, often translated with words like “spirit” or “life force”, sometimes with more expressive terms like “angels”, “demons”, “gods” or even, simply, “God”. It’s tempting to dismiss these invisible forces as so much superstition, as though truth is made only of things we can see, but of course that’s not quite true either. With the right instruments, we can see many invisible things; some of the greatest discoveries happen when a new gadget like a microscope or telescope makes people aware of a world that was previously hidden.

The invisible world of microbes is like that, with new, low-cost technologies showing us an incredible, rich, living universes of over 1 trillion species5 waiting to be explored.

The word “microbe” refers to any tiny organism that carries its own genetic information for purposes of propagating itself. Far too small to see with the naked eye, dozens could fit inside a typical human cell. Although it’s common to think of microbes synonymously with bacteria, in fact there are at least seven different types of microorganism:

  • bacteria
  • archaea: extremophile life forms that live and thrive in environments too challenging for bacteria
  • protozoa
  • algae
  • fungi
  • viruses
  • a few multi-cellular animal parasites such as helminths.

Each of these has its own characteristic body type, means of reproduction, ways of moving around, and a deep, long history that is far older than humans.

Let’s look next at some of these environments and see the odd places where microbes have been found.

2.1.1 Microbes above and below

Scientists studying a water-filled fracture two miles underground at the Mponeng gold mine near Johannesburg, South Africa, discovered Candidatus Desulforudis audaxviator by accident, after noticing odd levels of hydrogen compounds, by-products of the activity of an isolated bacterial colony.6 Interestingly, this organism is a member of the same Firmicutes phylum that dominates human guts, though this particular bacterium evolved quite separately from us: it hasn’t been exposed to surface water for millions of years. A systematic study of its genome revealed that, unlike other bacteria that usually live in co-dependent colonies, this one can survive all by itself, feeding on tiny bits of radioactive energy from uranium decay in an environment far removed from all other energy sources. It’s not a great life: these creatures reproduce rarely, only once every few hundred or thousand years. But at least they don’t have to worry about being consumed by predators down there.

Subglacial Lake Whillans is a lake buried under more than 800 meters of ice in the West Antarctic. A careful underground bore hole inserted by a team from Louisiana State University in 2014 found almost 4,000 different kinds of bacteria and archaea surviving under that ice.7 The total bacterial count was not that different from what you’d find in surface lakes on other parts of the planet, a fact that is especially surprising for an environment that hasn’t had a ray of light in millions of years. The bacteria instead thrive on iron, sulphur, and nitrogen as energy sources. 8

Go 2,600 feet further to find microbes. Photo: [NASA/JPL-Caltech](https://www.jpl.nasa.gov/news/news.php?release=2013-077)

Figure 2.1: Go 2,600 feet further to find microbes. Photo: NASA/JPL-Caltech

Those may not be the deepest examples. A Cold War-era Soviet team drilling the world’s deepest hole, were forced to abandon the project in 1994 at 12,261 meters (or 7.5 miles) underground, when they hit temperatures above 180 °C (or 356 °F), too hot for their equipment. Apparently the conditions weren’t too hot for life, though: the nine-inch diameter Kola Superdeep Borehole 9 found 24 species of fossilized plankton among the two-billion-year-old rocks down there. Of course, fossils are not the same thing as living microbes, but even dead remnants at that depth is evidence of the tenacity of life.

Closer to the surface, a 2015 Chinese study10 showed that 32% of the variety in an ecosystem is associated with variation in the life below ground, mostly bacteria that sustain the ability of roots to take nutrients out of the soil. Just knowing the temperature or precipitation levels of an environment won’t tell you about the plants likely to be found there – the microbes matter too.

Even the sky contains living microbes. Scientists at the Institut de Chimie de Clermont-Ferrand in France have for decades sampled clouds to determine their precise contents, and sure enough: they find plenty of life there, usually between 1,000 and 10,000 bacterial cells per milliliter — not all that different from the amount you’d find in alpine snow. Like every living organism, these cells must soak up water and other nutrients, converting them into energy and various by-products, which collectively have a massive effect on the overall atmosphere, more than enough to affect climate. 11

source: ASMScience

The upper atmosphere is a harsh place for life: regular freezing and thawing, constant bombardment of UV radiation from the sun during the day, cold, subzero freezing temperatures at night, high speed, unpredictable winds that quickly disperse any colonies. Plus, at any moment these organisms can find themselves flushed to the ground in a rainstorm, where they’ll need to adapt again.

These extreme conditions are just another day in the life for one species commonly found in clouds, Pseudomonas syringae, which harbors a protein in its cellular wall that reacts to cold temperatures, alternately preventing and allowing a water molecule to turn into ice and back. It doesn’t take many of these reactions to generate precipitation. With so many cells constantly floating in the atmosphere, even small changes in concentration — perhaps due to human activity on the ground — can, at least theoretically, make the difference between rainfall and drought. How much of an effect is hard to say: you can imagine how difficult it is to study bacteria floating in the sky.

Our inability to access these environments is often the biggest reason we remain ignorant of the life that is found there, but there have been many attempts to learn more. Formal studies about the viability of microbes in space have been conducted since the early 1960s 12, when Apollo-era scientists wanted to understand the dangers of space travel, both to any humans in space as well as to those of us on the ground who might be exposed to any intersteller visitors.

Although new and bizarre extremophiles are discovered regularly, so far it appears that even the hardiest of known organisms have a tough time when directly exposed to solar ultraviolet radiation. But the particularly resilient spore-making Bacillus subtilis, for example, it is estimated could survive for at least six years if it were shielded somehow from direct sunlight, say embedded inside a meteorite.13

Several lichen species, including rock colonizing Rhizocarpon geographicum and Xanthoria elegans, and the vagrant Aspicilia fruticulosa, remained alive after ten days of direct UV exposure on board a European Space Agency spacecraft. 14 Some especially hardy cyanobacteria that came with the lichens didn’t survive, so perhaps space offers a better chance for multicellular life, which has the luxury of outer protective pigmented layers.

Could be lichen outer space. Photo: [J Brew](https://www.flickr.com/photos/brewbooks/4784053254)

Figure 2.2: Could be lichen outer space. Photo: J Brew

Traces of sea plankton, for example, have been found in space, on the surface of the International Space Station, where they are believed to have floated from the upper atmosphere. 15 Why?! How did they get there! Who knows!

What is known is that between a quarter and two-thirds of microbes in the air are entirely new and undiscovered organisms. A study of the “air microbiome” above New York City found bacteria and viruses that apparently originated in water, soil, vegetation, as well as in animals and humans, but even then few patterns emerge. Although there appear to be distinct microbial environments, on the land versus water, for example, overall many of these organisms are quite hardy and seem to find themselves migrating all over the place.

Still other microbes thrive in radioactive environments, like the dangerous interior of a nuclear reactor. Deinococcus radiodurans is an extremophile member of Phylum Deinococcus-Thermus that boasts an impressive built-in DNA repair mechanism that lets it survive cold, vacuum, acid, light, dehydration – you name it. It remains unbothered by radiation levels more than 1,000 times higher than would kill a human.

Microbes seem capable of living off just about anything. Ideonella sakaiensis, discovered in 2016 by a Japanese team16, can break down and metabolize plastic, just like the fungus Aspergillus tubingensis, found in 2018 in a garbage dump in Pakistan, which eats polyurethene in months rather than decades.17 The waxworm Plodia interpunctella, observed eating plastic in a lab probably owes its digestive abilities to other, as-yet-to-be-studied microbes.

In fact, many non-microbial organisms owe their most defining characteristics to microbes. Termites wood-eating abilities are thanks to a whole community of synergistic bacteria, archaea, and protists. Aphids can’t live off sap without Buchnera, a microbe that supplies them with essential amino acids. Some microbes even play a role in the mineralization of copper and gold.18

2.1.2 Microbes around you

You don’t have to go to extreme conditions to find unusual microbes. Microbes thrive whereever humans live, and they are in our everyday environment too. The PathoMap Project, studying DNA collected from the New York City area found that, like the air above, half of the microbes we walk past everyday are unknown to science. 19 Most of the organisms are apparently benign, with no obvious affect on humans one way or another. Even when known pathogens are found, including Yersinia pestis (Bubonic plague) and Bacillus anthracis (anthrax), the lack of reported infections indicates that probably these organisms are busying themselves for some other, unknown, and maybe even useful purpose20

Half of the organisms collected by the Pathomap study are unknown. Source: @afshinnekoo_geospatial_2015

Figure 2.3: Half of the organisms collected by the Pathomap study are unknown. Source: Afshinnekoo et al. (2015)

Generally the microbes seem content to exist patiently with no apparent affect on the environment. A station flooded by Hurricane Sandy showed a similarity to a marine environment a year after the disaster.

Humans are the source of many unusual microbes in our environment. Regularly shedding 1.5 million skin cells per hour, your body’s leftover inhabitants can colonize a hotel room in less than six hours.21

Your household pets carry microbes, of course, but simply having a pet seems associated with different microbes in humans. One study showed that babies living in a household with pets have more Clostridiaceae, Veillonella (especially for dogs), Peptostreptococcaceae and Coprococcus. Cats in particular seemed associated with lower Bifidobacterium while dogs seemed to spell doom for Eggerthella.22

2.1.3 Microbes within you*

Finally, to round out our overview of how biologists study the microbiome, let’s get specific about aspects of our own human bodies, and break it down into components, each of which as we’ll see play hosts to unique microbial communities.

But first let’s clear up the common misconception that life is a pyramid that goes from “primitive” (bacteria) to “advanced” (humans). While the human body is certainly more complex, with many more moving parts, it’s important to remember that humans and our ancestors evolved in a world that was already full of microbes. No bacterium is going to let a new multi-cellular life form emerge without a fight – or an adaptation – and the evidence of that struggle is seen in every one of us.

Case in point: we think of our body as consisting of an external “skin” covering an internal set of organs that generally have no access to the outside world. But when multi-cellular life was evolving, why would the bacteria allow such privacy to some of the most important parts of the new bodies? In the constant struggle between existing microbes and newly-emerging multi-cellular life forms, a truce emerged that gave microbes access to the entire body, not just the exterior.

We don’t normally think about it this way but all multi-cellular life forms, including humans, are shaped like a tube, with the skin on the outside and the gastrointestinal system on the inside. From the mouth to the anus, every creature from fish to mammals is built this way. Furthermore, the inside tube for each of us is airless – devoid of the oxygen that we think of as essential to life. To our kind of life anyway.

But the interior of a human looks remarkably similar to the world that bacteria would have seen when the very first pre-mammals appeared: low to non-existent amounts of oxygen, no light, steeped in a mucousy salty goo. Think about it that way and you gain more respect for the capabilities of these microbes.

And there are a lot of them. You have 40 trillion bacterial cells in your body – slightly more than the number of human cells. Combined with the viruses, fungi, and other microscopic DNA-carrying organisms inside you, that’s close to 5 million unique genes, compared to only 25,000 human ones. 23

When Stanford scientists turned a gene sequencer on DNA fragments found floating in human blood, only about 1% came from previously-identified sources. The rest – the vast majority – came from organisms that have never been studied before. 24

Now on to the body itself. The first place to start is with the organ that literally covers us from head to toe.


We usually think of bacteria, fungi, or viruses, as something to eradicate, pests that can only be there to cause problems. The natural state of the body is pristinely washed: clean, with no dirt or other blemishes. This pristine state has never been true. Humans, like all other multi-celled creatures, have lived forever in a bath of foreign ride-hitchers of all types. This micro-fauna is as natural to us as the air we breath, and like air, our bodies need a good environment to be at our best.

The body maintains its temperature well, occasionally cooling itself off by channeling excess water through the sweat glands and onto the surface of the skin. Besides water, this sweat contains small amounts of other matter, including elements that toss molecules into the air, many of which, upon landing on the olfactory glands of another person will be sensed as a smell — also known as body odor.

Nature does not like waste, especially not anything associated with a living body like us, and as soon as those micro elements in sweat are exposed to the air, in the natural state there will be other lifeforms available to devour them, taking out some of the leftover energy in the process of converting them to simpler chemical compounds like carbon dioxide.

One such hanger-on is the bacterium Nitrosomonas eutropha25. It thrives in your skin and makes a living from oxidizing, that is, converting to oxygen, the ammonia that is naturally present in the waste secreted by your sweat glands.

Later we’ll discuss what I learned from my own skin microbiome testing.

Healthy skin exhibits a slightly acidic pH (4.2 to 5.6) a level that inhibits pathogenic bacterial colonization but skin pH rises as we age.26

Streptococcus salivarius, found in the mouth, may combat acne by secreting “bacgeriocinlike inhibitory substance (BLIS).27

Free radical oxidation seems to play a roll in how sometimes the out-of-control microbes result in acne. Applying a topical lotion containing the anti-oxidizing Vitamin E seems to lessen the symptoms, perhaps by suppressing Bacillus coagulans.28

New research by Emma Barnard (2017)29 on Propionibacerium acnes show that acne comes from versions of P. acnes that express different (metabolic-related) genes.

Your body is covered in microscopic Demodex, a parasitic mite harbored by all humans, but over-represented in people with rosacea (15x). There is evidence that Demodex is associated with P. acnes 30

Your armpits contain glands whose only purpose is to feed bacteria. Applying antiperspirant or deoderant causes significant changes to the ecology of those microbes, and may actually cause more odors by increasing numbers of smelly Actinobacteria31

Skin microbes colonize each pore individually.32 The genetic sequence of a microbe strain in one pore can be different than those in another pore. This may be one reason that some skin conditions are so hard to treat. If every pore contains a slightly different colony, there may not be a one-size-fits all way to modify them.


The first stop for any microbe that wants access to your gut, the oral cavity is among the most diverse environments in the body. There’s something here for any kind of microbe: low, but fluctutating oxygen levels, generally moist conditions but with plenty of tiny places to hide for those that are water-shy, soft surfaces that rub against the hard enamel of the teeth, all overseen by a tongue that can sweep bits of material from one place to the next.

See what I learned about my mouth microbiome in the chapter on my oral microbiome.

As with other parts of the body, the microbes here not passive travelers. Many of them perform important functions.

Even your enjoyment of wine appears to be related to the types of microbes in your mouth, according to a 2017 study by Spanish researchers33.


Like the skin, your nose microbiome is permanently exposed to the outside world so it faces different challenges than the mouth or gut, which have some say over when or how they’ll come into contact with new microbes. With every breath, your nose microbiome risks exposure to intruders which, once they are inside, may cause major changes to the rest of the microbiome. Unsurprisingly, noses that are regularly exposed to new and different threats will develop more diverse microbiomes.

Dairy farmers, for example, have a wider variety of nasal microbes than do their urban non-farming counterparts. Interestingly, one study shows farmers have lower Staphylococcus too, and none of the microbial-resistant kind found in urban dwellers, an indication that the greater competition from all those diverse microbes is actually preventing the emergence of resistance.34

Although the noses of farmers and non-farmers are dominated by the same three phyla, Firmicutes, Actinobacteria, and Proteobacteria, the farmers have much more Bacteroidetes, Tenericutes and Verrucomicrobia.

There is a clear association between the microbiome and smell. Both Alzheimers and Parkinsons researchers have long noted that changes in smell precede symptoms35. Some early AD symptoms, like a loss of smell, may be clues that the brain has been attacked by something that came from outside.

The nasal microbiome appears to change during a viral infection, and the overall microbial composition seems to depend on the types of viruses, and whether the person was vaccinated or not.36 In a study of 200 New Yorkers, healthy people seemed to have an abundance of Corynebacterium and Streptococcus, whereas the people with viruses had much lower Corynebacterium slightly lower Streptococcus, and more Dolosigranulum.

Researchers from the University of Graz in Austria published a small study (n=67) Koskinen et al. (2018)37 that found clear differences between those with normal sense of smell (n=29) and those without (n=10). In particular, “butyric acid-producing microorganisms were found to be associated with impaired olfactory function”.

Some of the microbes most associated with poor ability to smellinclude: Actinomyces, Corynebacterium, Bacteroides, Anaerococcus, Faecalibacterium, Pseudomonas, and others.38

When I tested my own nose microbiome, I found that the vast majority of microbes are Corynebacterium and Moraxella, with a steady small amounts of Dolosigranulum and Propionibacterium. I occasionally have a spike of Staphylococcus, a usually benign and perhaps even beneficial microbe that can turn pathogenic under some circumstances.

Nowhere are the microbes more numerous or obvious than in our guts. The tiny bacteria that come sliding down your insides eventually exit the body entirely, in a pile you’ve been making anew every day since your birth.


After chewing, the first big tranformation of your food happens in the stomach, where powerful acids wreak havoc on any microbes that may have come with the food. At a pH of between 1.5 and 3, stomach acid is literally industrial strength: acids of that strength are useful for applications from oil production to household cleaning.

The acidity denatures the proteins in food, making them susceptible to digestive enzymes like pepsin, but what happens to the microbes that came along for the ride?

Not all microbes are destroyed by stomach acid. One in particular, the notorious Helicobacter Pylori actually thrives in such environments, by producing urease, an enzyme that neutralizes the area around the microbe.

The Appendix

Somewhere near the border between the small intestine and the large intestine (colon), there is a small, pinkie-like appendage bulging inconspicuously into the abdominal cavity. For most of the period of modern western medicine, nobody knew its function other than as a source of severe pain when it occasionally exploded in infections that until the development of antibiotics were usually fatal.

Appendicitis used to be very rare (3-4 cases/year till 1890, up to 113 by 1918), which was fortunate, because there was no treatment. It was a sad fact that, for example the only death among the hundred or so frontiersmen and explorers on the Lewis and Clark expedition in the early 1800s was caused by appendicitis — a terrible, painful death in the wilderness but one that would have been just as inevitable at the finest hospitals in the world at the time. A Soviet doctor working at a remote base once did a successful appendectomy on himself39, but that’s not something for most people to try. Even today, appendicitis is so dangerous that a prophylatic appendectomy is a requirement to live in Villas Las Estrellas, a remote research village housing about 100 scientists and crew in Antarctica. 40

What’s known is that the appendix apparently houses three things: tissue from the immune system, a bunch of what are called IgA antibodies that fight infections, and tons of bacteria. What’s also known is that people who have their appendix removed surgically — usually as a result of one of those terrible infections — recover to live apparently normal lives, with no side effects even decades upon decades later. So what is the appendix doing?

One clue comes from a 2011 study of 254 patients recovering from a C. Difficil infection41, a horridly tenacious bacterium that has gained near-complete resistance to antibiotics and is notoriously difficult to treat. In the study, those with an appendix saw their infections come back 11% of the time, but those with no appendix suffered re-infection rates of 44% — a large and significant difference that has caused most scientists to speculate that the appendix is harboring something that enables the body to recover after a microbial disaster.

Another clue comes from a phylogenetic study of the evolutionary history of 533 mammals42. Some mammals have an appendix and others don’t – it seems to have evolved independently over 30 times – but interestingly whenever an evolutionary lineage evolves an appendix, it never “devolves”. After accounting for all the factors you can think of, from diet to climate, to sociability, the one notable factor among mammals with an appendix is that they tend to have higher concentrations of immune tissue in their bowels. Again, this all adds up to the idea that the appendix has something to do with the body’s response to microbes.

My own interest in this subject is not idle curiosity. About fifty years ago, doctors at a small town hospital gave an appendectomy to my five-year-old self in order to treat an unusual belly ache. While doing what was apparently an exploratory surgery to find the cause, they came upon my otherwise healthy-looking appendix and decided on the spot to simply remove it. “Why not?” I’m sure they thought at the time. “If nothing else, it’ll prevent him from appendicitis”, which is as tautologically sound a reason as any.

Did that change me, somehow? Am I fundamentally different because for most of my life I’ve been missing an important microbe safety zone that the rest of you enjoy? Science doesn’t know the answers, and even when there are studies based on well-conducted experiments, I can’t know the answer unless I do the experiment on me.

Hint: that’s exactly what I did as you’ll see in the chapter on my self-experiments.

Small Intestine


The cells lining the colon, called colonocytes, get much of their energy from butyrate, an acid that has long been known to play a role in digestive health. Named after the Latin word for butter, which contains up to 5% butyrate, its presence in the colon has been linked to lower rates of colitis and colon cancer. Too little butyrate and the colonocytes whither and die.

You can buy butyrate supplements that supposedly help digestion but you can also get it naturally in dairy fats, especially butter, which can be almost 5% butyrate. In fact, both words are derived from the Latin term butyrique

But why eat it directly? Many gut microbes produce it for you, right where it’s needed, by fermenting the fiber that makes it to your colon.

Interestingly a low-carb diet doesn’t affect levels of Bacteroidetes or Clostridium, but it can have a substantial impact on Bifidobacteria, Roseburia, and Eubacterium Rectale, all sources of butyrate production.

Butyrate is a one many Short Chain Fatty Acids (SCFA)?

For example, 80% of your serotonin is made in the gut.43

2.1.4 Microbes and food*

We like our food pure and clean, and so do microbes. Well, some microbes. Freshly-washed produce is a just a colonization opportunity for many species, for whom the lack of competition is a shot at a fresh start.

Before washing, plants are covered in microbes, from the flowers and branches to the roots. Seeds planted in sterilized soil will germinate, but can’t grow regardless of the nutrients, water, or sunlight you give them. The relationship between soil microbes and plants is a complicated and understudied one, but what is known is that every plant hosts its own unique species of microbe in a symbiotic relationship as tight as any on earth. The microbes tangled in the roots of a corn or wheat plant, for example, are highly specific to that particular strain. Swap out the microbes, or – worse – sterilize the soil, and the plant can’t take advantage of the nutrients sitting right at hand, because they are in a form that is useless until digested by microbes.

Incidentally, many of the important soil microbes are fungi, not bacteria – an entirely different kingdom of life, more closely related to animals than to plants. The root-fungi interaction, known as a mycorrhiza, enables plants to absorb moisture and nutrients that would otherwise be unavailable to them. The fungi break down the tough fibers in dead plants, returning important nutrients to the soil, enabling a cycle without which the rest of life almost certainly would not be possible.

After harvest and processing, our meals still contain a surprising variety of microbes. Of course, sometimes this is deliberate: some of us eat fermented foods like sauerkraut or yogurt to ingest the microbes that were grown to make their special flavor or texture. But even everyday foods, like raw vegetables, will naturally be covered with healthy levels of microbes.

You will ingest somewhere between 1.4 million and 1.3 trillion microbes per day, depending on what type of diet you follow. Eat according to USDA guidelines and you’ll be at the high end of the range, emphasizing fruits and vegetables, lean meat, dairy, and whole grains; the lower end is more typical of a vegan diet, or even a typical American convenience food-style diet of “junk food”. Interestingly, you’ll get roughly the same diversity of microbes no matter which diet you follow, although there can be a difference depending on whether the food is raw or cooked.44

We eat plants for their nutrients, but what exactly counts as a “nutrient” is often in the eye of the beholder. Plants don’t like to be eaten any more than the rest of us, and they have developed powerful defense mechanisms to keep out predators, including microbes. In fact, it’s those anti-microbial properties that make many plants medicinally useful. One estimate showed that of 18,000 plants available to Native Americans, only 1,625 were used as food; but 2,564 were used as drugs, many of which are specifically there to manipulate microbes. 45 Extrapolate that to the estimated 500,000 different plants on earth, only about 1-10% of which are useful as foods to humans, and it becomes clear that microbes play a big role in which plants thrive and which don’t.

Even plants that depend on pollinators, or those that spread their seeds by being ingested by birds, don’t necessarily like to be eaten whole and completely. Leafy grasses attract ruminants like cows or sheep with large tasty fibrous leaves that the plant offers in order to bring in the high-nitrogen feces that will help the plants grow better.46.

One powerful deterrent to insects is the chemical caffeine, produced in abundance by plants in the genus Coffea, including the species Coffea arabica, commonly known as coffee. A powerful toxin against insect invaders, caffeine in the seeds of this plant will kill nearly all invaders. In fact, few insects are known to have any tolerance to caffeine, ensuring that the plant can continue to reproduce unmolested by predators.

But no matter how clever, these self-defense mechanisms aren’t foolproof. One beetle, the coffee berry borer is a notorious bane of Brazilian coffee growers for the way it munches on the coffee beans without any ill effects. When scientists studied this pest, they discovered something missing in the berry borer’s feces: caffeine.47 How could these bugs eat so much caffeine without becoming poisoned? The reason turned out to be Pseudomonas fulva, a tiny inhabitant of the beetle’s gut, and the only microbe with a gene called ndmA that can metabolize caffeine. Borer beetles without this microbe accumulate large amounts of unmetabolized caffeine and are unable to reproduce.

Even a strict diet of healthy, organically-grown plants, won’t necessarily prevent accidental antibiotic ingestion. Between 70% - 90% of the antibiotics given to farm animals are ultimately discharged in their manure, which if administered as fertilizer, can coat the soil used for growing food plants. Although antibiotics naturally degrade over time, the process can take months and under many conditions, giving ample time to be taken up in to plants that we eat, so even hard-core vegans may be getting more antibiotics than they like. 48

Meanwhile, junk food doesn’t necessarily wreck your microbiome as much as you’d think. Careful experiments show surprisingly few differences between mice fed a high fructose, high fat diet – unless there was something else messed up to begin with49

And what about microbes in the kitchen? When food is contaminated by bacteria, in the vast majority of cases, the source is fecal. In other words, it’s relatively rare for raw food to be contaminated by something from within – the danger is almost always from pathogens that are brought in during food preparation.50


The International Scientific Association for Probiotics and Prebiotics (ISAPP) defines probiotics as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host”. Experts reserve the term “probiotic” for supplements, as opposed to foods that happen to contain live, healthy microorganisms, but that distinction is lost on most people, who just want to be sure they consume enough “good” bacteria.51

Perhaps this is a good time to keep up my regular rant about why I don’t like the term “good” or “bad” when it comes to microbes. Everything depends on context: it’s possible to have too much of a good thing, just as it’s possible to have too little of some bad things. Nature knows how to manage a delicate balance and it’s foolhardy to pretend we know all the consequences of a major change in either direction. Martin Blaser, in his excellent book Missing Microbes, reminds us of the native proverb:

Elk are there to feed the wolves; wolves are there to keep the elk strong.”

You may not want to get rid of everything, nor would you want to fill yourself up with too much of anything.

Like anything you put into your body, you can’t just assume it’s all upside.

Presumably you’re reading this because you are convinced that microbes have a powerful affect on the body, perhaps as powerful as prescription drugs, yet you wouldn’t consider taking random prescription drugs just to see what happens. The billions of microbes you send into your gut is in a concentration and quantity far greater than anything you’d get from nature. Please remember that.

Here’s an analogy: let’s say scientists discover a breed of parrot that is found in abundance in healthy ecosystems in Costa Rica, so they decide to introduce it to Yellowstone Park. They dump thousands of live parrots all over the park and when they count the overall species diversity the following day, they note with pride that the experiment worked: Yellowstone is now home to a new species, one that is associated with healthy ecosystems! Unfortunately, upon testing again a week later, they learn that the parrots are gone. What happened? You and I can laugh at the idiots who thought they could transplant a tropical species into Wyoming, but maybe that’s exactly what you’re doing if you try to introduce a new species that is not adapted to your microbiome. It may show up in a couple of early gut tests, but if it disappears soon thereafter, was it helpful at all? In the parrot example, it may actually be harmful if it served as food to dangerous predators.

Fortunately, the body is pretty robust and, for better or for worse, it’s hard to deliberately change the microbiome.

Fermented food

In some foods, living microbes aren’t along just for the ride – they are the ride. Most raw foods will quickly spoil if left uneaten for too long. We say “spoiled”, but really we mean the food is consumed by bacterial species who leave by-products that are not edible or pleasant for humans.

Under the right circumstances, though, food can nourish microbes.52

Before refrigerators, long-term preservation of food was a constant concern. You either eat the food now or let the microbes eat it.

Yes, much of that yogurt makes it past the stomach and into the gut.

Fiber and your gut microbes

Short-chain fatty aides (SCFA) created when gut bacteria break down fiber.

Pulverising and juicing reduces fiber content.  e.g. whole wheat grains have 12g, but fine-ground has only 3g.  a 200ml bottle of orange juice has 1.5g fiber, but four oranges has 12.53


Afshinnekoo, Ebrahim, Cem Meydan, Shanin Chowdhury, Dyala Jaroudi, Collin Boyer, Nick Bernstein, Julia M. Maritz, et al. 2015. “Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics.” Cell Systems 1 (1): 72–87. https://doi.org/10.1016/j.cels.2015.01.001.
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