Infestations, Microbes & Parasites


Micrococcus (Actinobacteria)Staphylococci, Corynebacteria, Actinobacteria, Clostridiales, and Bacilli. They’re the most common, but they’re not the only ones. Bacteria. Microbes. Yes, even parasites.  Living in your belly button. And on your skin. Your hair. But the belly button flora and fauna fascinate me the most.*

We’ve known ever since the microscope was invented that we had a population of hitchhikers living on our skin, scalp – and even inside us. The great Antony van Leeuwenhoek is known as the “father of microbiology” for his explorations through his fledgling, primitive microscope in the late 17th and early 18th centuries. But we are still learning about the biodiversity we all have.**

There was a recent story in the Atlantic that researchers had found, of 2,368 species of bacteria living in our navels recorded so far, 1,458 new species.

New as in previously unknown until some scientist stuck a Q-tip into his or her belly button and examined the results. Which is what they are still doing, exploring this brave new frontier in microbiology. It must have been one of those eureka moments.

Gawd, dontcha love science? To bold go where no Q-tip has gone before…

The Atlantic story opens:

Instead of taking your fingerprint, maybe police should swab our belly buttons with Q-tips. No, that’s ridiculous, actually. But the idea illustrates a point made by a group of North Carolina-based researchers in their new Belly Button Biodiversity (BBB) project. Last month, the group published results of their first of many experiments, in which they swabbed 60 belly buttons and identified a total of 2,368 species of bacteria. People’s individual profiles were snowflake-ily, bacterially unique.

Most of the microbes that live on our skin are harmless, and many are actually beneficial: they protect us from more virulent invaders. What’s remarkable is the sheer number and variety of them.***

The scientists at Your Wildlife wrote that among all those species, there are some common forms found in most navels:

Turns out, belly buttons are a jungle of microbial biodiversity: we detected over 2300 species! And get this, only eight of those 2300 species– we call them oligarchs – were quite frequent and abundant, present in more than 70% of the individuals we sampled.

Oligarchs. Make me think of the Politburo. Or Putin’s new Russian clique. What role do these bacterial oligarchs play in their micro-environment?

We’re an entire ecosystem, Scientific American tells us:

Over the past 10 years or so, however, researchers have demonstrated that the human body is not such a neatly self-sufficient island after all. It is more like a complex ecosystem—a social network—containing trillions of bacteria and other microorganisms that inhabit our skin, genital areas, mouth and especially intestines. In fact, most of the cells in the human body are not human at all. Bacterial cells in the human body outnumber human cells 10 to one. Moreover, this mixed community of microbial cells and the genes they contain, collectively known as the microbiome, does not threaten us but offers vital help with basic physiological processes—from digestion to growth to self-defense.

By the way, you can contribute to this ongoing research; check the notes at about how to help. The belly button experiment is over, as researchers assess their samples, but they are moving on to armpits, a whole new territory.

Bacteria also live in us, mostly in our intestines, where they have a symbiotic role. Wikipedia tells us we have more passengers in our guts than we have cells in our bodies:

The human body carries about 100 trillion microorganisms in its intestines, a number ten times greater than the total number of human cells in the body. The metabolic activities performed by these bacteria resemble those of an organ, leading some to liken gut bacteria to a “forgotten” organ. It is estimated that these gut flora have around a hundred times as many genes in aggregate as there are in the human genome.

However, while we’ve known about intestinal flora for centuries, we don’t really have full knowledge about what or who they are and what they’re doing down there:

Not all the species in the gut have been identified because most cannot be cultured, and identification is difficult. Populations of species vary widely among different individuals but stay fairly constant within an individual over time, even though some alterations may occur with changes in lifestyle, diet and age.

So a vegetarian diet may actually help improve the flora and fauna in your gut. One study found:

Consuming a vegan or vegetarian diet results in different profiles of gut microflora, with lower levels of potentially pathogenic bacteria such as E. coli, says a new study.

Ars Technica reported that, “Feeding our gut bacteria meat may enhance heart disease risks” and noted:

…researchers at the Cleveland Clinic decided to check out how different intestinal microbiota metabolize the components of meat. They found that bacteria present in the intestines of omnivores, but not present in the intestines of vegans or vegetarians, generate a molecule that promotes atherosclerosis when they are fed red meat.

Strangers they are to us, these little creatures that dwell within, but plentiful. The Human Microbiome Project was created in 2009 to study just what lives within and on us. It has found:

…more than 10,000 microbial species occupy the human ecosystem and they have identified 81 – 99% of the genera. In addition to establishing the human microbiome reference database, the HMP project also discovered several “surprises”, which include:
Microbes contribute more genes responsible for human survival than humans’ own genes. It is estimated that bacterial protein-coding genes are 360 times more abundant than human genes.
Microbial metabolic activities; for example, digestion of fats; are not always provided by the same bacterial species. The presence of the activities seems to matter more.
Components of the human microbiome change over time, affected by a patient disease state and medication. However, the microbiome eventually returns to a state of equilibrium, even the composition of bacterial types has changed.

When you eat yogurt, you introduce other bacteria into your existing population:

Dairy yogurt is produced using a culture of Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus bacteria. In addition, other lactobacilli and bifidobacteria are also sometimes added during or after culturing yogurt. Some countries require yogurt to contain a certain amount of colony-forming units of microorganisms.

You’d think that swallowing a few million bacteria into an environment that numbers in the trillions, the newcomers would have the genes beaten out of them in the process, and simply wiped out by the incumbents. Bacterial gang wars, as it were. But, it turns out, the little buggers survive, at least enough to be counted at the exit:

Whether Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus can be recovered after passage through the human gut was tested by feeding 20 healthy volunteers commercial yogurt. Yogurt bacteria were found in human feces, suggesting that they can survive transit in the gastrointestinal tract.

Not sure I’d like the job of counting, mind you.****

Whether it’s really effective or simply a placebo effect, Susan and I have found on many trips to Mexico that eating yogurt once to three times a day has kept us from any travellers’ diarrhea that so many visitors get (exacerbated, of course, by an excess of alcohol). In 30 years, it’s worked for us.

The Scientist told us how probiotic yogurt worked, back in 2011:

The bacteria found in some fermented dairy products, such as yogurt, may alter gene expression in human gut microbes, and resultant tweaks to metabolic processes could be behind gastrointestinal benefits often observed in people consuming such probiotic products, according to a study published today (26 October) in Science Translational Medicine. The work was funded by several grants from the National Institutes of Health and from Danone Research, the scientific research arm of Groupe Danone, a Paris-based multinational food products corporation that specializes in dairy products.

However, don’t expect your life to change simply by eating yogurt. As the article continues,

Jeffrey Gordon, a microbiologist at Washington University in St. Louis, and his team gave a commercially-available probiotic yogurt containing five strains of bacteria to healthy adult volunteers and administered the same five strains to mice that harbored a subset of genetically-characterized human gut microbes. The yogurt bacteria did not significantly alter population structure in any of the entrenched gut microbes, in humans or mice—a result that is not surprising, according to Mills. “To assume that you could eat a yogurt and numerically challenge what’s in your gut is kind of like dumping a gallon of Kool-Aid in your swimming pool and expecting it to change color,” he said.

MIT storyStill, because bacteria are both fecund and have loose morals, they exchange a lot of DNA with one another. It’s called “horizontal gene transfer.” Humans call it “doing the hokey pokey.”

…RNA sequencing of the human gut microbes in the mice revealed that the probiotic bacteria changed the expression of gut microbe genes encoding key metabolic enzymes, such as those involved in the catabolism of sugars called xylooligosaccharides, which are found in many fruits and vegetables. Mass spectrometry of metabolites in urine, which result from the ramped up metabolic processes in the probiotic-fed mice, confirmed the alterations, and when the researchers ran similar analyses on gut microbes from the human yogurt eaters, they found upregulation of the same genes.

“The results show that in this particular set of conditions [probiotic] organisms are capable of altering the metabolic properties of a human microbial community,” said Gordon.

And as the MIT story suggests, this is is good for the bacteria because they share benefits and learned behaviour:

Much as people can exchange information instantaneously in the digital age, bacteria associated with humans and their livestock appear to freely and rapidly exchange genetic material related to human disease and antibiotic resistance through a mechanism called horizontal gene transfer (HGT).

It may also be good for their hosts, when bacteria are fighting invaders which could harm the hosts. These relationships help, as this site tells us:

Commensal bacteria supply the host with essential nutrients and defend the host against opportunistic pathogens. They are involved in the development of the intestinal architecture and immunomodulatory processes. On the other hand, the host provides the bacteria with nutrients and a stable environment.

Our gut flora are also necessary for our existence. Without them, we might not be able to get enough energy from our food to survive.

Symbionts are another really strange but fascinating relationship. Our cells have mitochondria in them – symbionts that were once independent cells but became part of our own cells, and now exist within them. Parasites, some might say. But without them we could not survive. They make the energy that powers our cells – but still retain their own DNA. How this all happened is too long to go into here, but here is an interesting, albeit technical, description of the two theories and another description here.

Symbiosis is also external: humans have symbiotic relationships with many domestic animals and cultivated plants. But let’s save that for another post.

demodexWe also have a lot of parasites living on us. That may make you think of head lice and crabs, or bedbugs, but they only infect a small number of us. Parasites like Demodex infect us all (stop reading now if you have acarophobia):

Demodex is a genus of tiny parasitic mites that live in or near hair follicles of mammals. Around 65 species of Demodex are known. Two species living on humans have been identified: Demodex folliculorum and Demodex brevis, both frequently referred to as eyelash mites.

Demodex, which infests only humans, is harmless to the vast majority of us. But they are ubiquitous:

Demodex mites live inside the sebaceous glands and hair follicles, sucking nutrients from the hair roots and damaging the cell walls. After mating they burrow into the skin, laying eggs, introducing bacteria and infection to the skin. Throughout the five phases of their life cycle, these mites destroy the skin by excreting wastes and secretions, laying eggs and dying within its layers. After death, their corpses become liquid and decompose inside the skin.

DemodexDiscover magazine tells us:

The mites spend most of their time buried head-down in our hair follicles – the stocking-shaped organs that enclose and produce our hairs. They’re most commonly found in our eyelids, nose, cheeks, forehead and chin. That’s not to say they’re restricted to the face: Demodex has been found in the hairs of the ear canal, nipple, groin, chest, forearm, penis, and butt too. Generally, dry skin is a turn-off for them. They prize bodily real estate that’s flooded with oils (sebum). This explains why they love your face. It might also explain why their numbers are apparently higher in the summer, when hot temperatures ramp up sebum production.

The whole parasite biology is really intriguing and presents all sorts of challenges to evolutionary theory and food web theory. But they’re really ugly critters.

The Atlantic story ends with this note:

…the BBB project could make important progress in understanding how the bacteria that colonize us actually affect our health. Analogous to the parasite Toxoplasmosis gondii — which we only recently found out is present in 20-50 percent of our brains, subtly shaping our personalities and maybe even making us try to hurt ourselves — some of these little bacteria that go unnoticed are probably affecting us in ways unknown, good and bad. Ways that we’re currently just chalking up to chance or genetics or God or gluten.

A parasite that is changing our personalities? Yes, says The Atlantic in a separate, rather frightening story:

Toxoplasmosis gondii, the parasite that uses cats as a host and is easily transmitted to humans (about 1 in 5 people in the United States have it, primarily via cat feces), is associated with a series of personality and behavioral changes. We become more “expedient, suspicious, jealous, and dogmatic.” Those infected are three times more likely to die in car accidents, and more likely to develop schizophrenia. It even appears to alter our sexual attractiveness. Last month there was a massive study in Denmark that noted an association between Toxoplasmosis and suicidality in women. But the effects of toxo notoriously vary with the gender of the host.

The Center for Disease Control has listed Toxoplasmosis as one of the “five parasitic diseases that have been targeted by CDC for public health action.” The CDC notes:

The major Neglected Parasitic Infections identified at this time for further action include the agents that cause Chagas disease, cysticercosis, toxocariasis, toxoplasmosis, and trichomoniasis.
These infections are considered neglected because relatively little attention has been devoted to their surveillance, prevention, and/or treatment.
Anyone, regardless of race or economic status, can become infected although minorities, immigrants, and people living in poor or disadvantaged communities appear to be most at risk.

Think of this the next time you clean your kitty litter box. The Journal of Experimental Biology has several articles about how parasites affect us, including our behaviour. One of these notes:

For millions of years, parasites have altered the behaviour of their hosts. Parasites can affect host behaviour by: (1) interfering with the host’s normal immune–neural communication, (2) secreting substances that directly alter neuronal activity via non-genomic mechanisms and (3) inducing genomic- and/or proteomic-based changes in the brain of the host. Changes in host behaviour are often restricted to particular behaviours, with many other behaviours remaining unaffected.


…there is one group of parasites that is particularly pernicious – they are the parasites that hijack their host’s nervous system, turning their victims into zombies. ‘The fact that parasites can so efficiently alter host behaviour is fascinating’, says JEB Editor Michael Dickinson, from the University of Washington, USA, adding, ‘There is something horrifying and wondrous about a tiny “implant” being able to control such a large animal machine’. What is more, it appears that these minute manipulators can have a significant, and often under-appreciated, impact on ecology, physiology and evolution, orchestrating the behaviour of vertebrates and invertebrates alike. ‘Neuroparasitology is a science where science meets science fiction’, Dickinson observes.

Hmmm. Might parasitic infestations be controlling the minds of cult followers, and be responsible for the behaviour of their members – or that of ideologues and dogmatic believers?***** That’s more than I can deal with here.

The other, more commonly recognized parasite is fungus. Opportunistic, adventurous little blighters: fungi grow anywhere they can latch onto (even the space station has them). A fungus is a strange beast, neither plant nor animal. Some fungi play important roles in our lives – yeast, for example, for fermenting and baking. Others break down waste material and turn it into nutritious (for plants, anyway) soil. We eat many of them-mushrooms and puffballs. Others, like most household molds, are a pest that can be potentially dangerous (black mold – one of the main reasons the former Mountainview Hotel was considered unfit for rehabilitation). Mycologists love this stuff.

They are also invaders. Your feet host more than 200 types of fungus, researchers have found:

Although fungi also inhabit other areas of the body – such as behind our ears – the researchers found that most of them are living between our toes.

The study, carried out and published in the journal Nature, is the most extensive analysis of the body’s fungal diversity to date.

Although only about half of all types of fungi are harmful, they commonly live on the skin and can be a major cause of infection. This finding is key to discovering new ways to treat skin conditions caused by fungal infection…

The part of the body with the most fungi was the heel with 80 different types of fungi, followed by toenail clippings (60 types) and the toes (40 types). The head contained the fewest types of fungi (only 10).

Some fungi are pathogens, too and cause  disease and infection. Some, like candida, can be fatal. Fungalinfectiontrust tells us:

Candidaemia infections occur can be predicted at around 300,000 worldwide per year – with a mortality of 30-55%.

Invasive aspergillosis can occur in different patients groups- so around 10% of new leukaemic cases will go on to develop invasive aspergillosis – so 30,000 per year. Of stem cell transplants – 54,000 are carried out in USA, UK, Europe and Japan annually, of which 5,400 will need treatment for aspergillus infection.

In chronic obstructive pulmonary disease -1.2% of these will need antifungals for aspergillosis- 216,000 per year. Over 50% of invasive aspergillosis patients will die from their infection – even with treatment.

In AIDS patients 1 million contract cryptococcal meningitis resulting in 600,000 deaths – 70% of which are in sub-Saharan Africa.

Less fatal infections but which affect large numbers of people worldwide include cutaneous fungal infections, nail infections and athletes foot – affects some 1.5 billion people – or 25% of the worlds population.

Tinea capitis -or hair infection- which is common in young children is predicted to affect some 200 million worldwide.

Lions, and tigers, and bears – have nothing on bacteria, fungi and parasites. After reading about all this, I’ll pay closer attention to cleaning my belly button and other crevices than I ever did in the past. I’m not sure how much swimming in the local pool helps, but I’m pretty sure all that chlorine keeps the external hitchhikers down, at least until I get dressed again.

Regardless of the sometimes scary nature of these microscopic creatures, this is really fascinating, exciting stuff. Were I of the age to enter university today, I would give microbiology serious consideration.


* And you probably thought with that title I was going to rant about local bloggers…

1960s microscope kit** I first read about van Leeuwenhoek when I was perhaps 10 or maybe 11. I was immediately hooked. I read everything in the local library about him and about the microscopic world.

I got a microscope from my parents for my 12th birthday (as I recall, but it may have been 11th) and spent many, many hours happily exploring the unseen world. I recall it came in a wooden case, had four lenses (the strongest was 600 power), a battery-powered light underneath, as well as a tiltable mirror, and came with a box of prepared slides and a few tools for my own preparation, to make my own slides. Which I did passionately for many years. It looked similar to the image here, but had four, not three lenses. Not sure whatever happened to it, but I was still using it well into high school. Might want to get another one, now that I did the reading for the above…

*** Virulent, as an adjective,  was first used in English circa 1400 CE, used in reference to wounds, ulcers, etc., meaning “full of corrupt or poisonous matter.” It comes from Latin virulentus, meaning “poisonous,” from virus, Latin for “poison.” The sense of virulent for “violent, spiteful” is attested from c.1600 but has been used recently to describe  bloggers and newspaper editorials. Toxic, also used for that purpose,  is a bit later: the 1660s. it comes from French toxique, from Late Latin toxicus “poisoned,” from Latin toxicum “poison.”

**** I would be interested in finding if any study has ever measured the effects on intestinal flora of yogurt with and without additives. A lot of yogurt contains meat by-products (gelatin), and I wonder what effect it has, compared to that without it. Gelatin is not vegetarian!

***** Could the entire Tea Party be the result of an infestation of mind worms?. Opens a lot of questions about the mindset of true believers. is the New World Order really a coven of cats?

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Ian Chadwick
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One comment

  1. Some of this came from questions and ideas that arose while reading Frank Ryan’s excellent book, Virolution. And I still have more, including:

    • If the bacteria in our guts are exchanging data with one another, genetically, what – if anything – are they exchanging with our gut cells? And if not, why not?
    • What’s the role of viruses in all this? Viruses exchange DNA with their hosts. Could they be the transport mechanism between bacteria?
    • How do we best harness this exchange mechanism for therapeutic uses? I know it’s being done, but how do we ensure the DNA we transfer is the right stuff?
    • Could we use that technology to, say, dilute or neuter the toxicity of some molds or other pathogens? Or change the behaviour of parasites?
    • Where do prions fit in all of this?
    • What power microscope (and what type) would I need to be able to study our microbes with reasonable efficiency, without taking out another mortgage to buy one?

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