How microbes make you sick

After Pasteur, most of us were taught that microbes are bad. Germs and bacteria are often mistakenly thought of as pathogens that we must kill, every single time. The only good germ is a dead germ.

And for good reason. The development of antibiotics –germ killers –was one of the greatest medical achievements of all time, conservatively saving the lives of hundreds of millions of people. And even before antibiotics, how many lives were saved as a result of the improved hygiene that came thanks to the Germ Theory of disease?

Every day of your life, modern amenities like running water and flush toilets keep you healthy simply by controlling the growth of microbes.

Some of these are truly nasty. The bacterium that causes Cholera, Vibrio cholerae, after infecting the small intestine, promptly hijacks the body’s natural defense systems into sending a large stream of water through the colon to flush out all other bacteria. Normally, this would be an appropriate response to an invasion, but by hiding above the colon, Vibrio cholerae continues to breed above the main flow of water. The resulting diarrhea is so fierce that the patient is literally unable to drink enough to make up for the outflow, and dies of dehydration within days. As an added bonus, that water that the body pushes out so fiercely is itself full of V. cholerae, who use the opportunity to infect people who come in contact with the water.

Some bacteria simply use the darkness and wet warmth of the colon as a breeding ground, happily feasting on the materials they find there. They cause trouble not by what they eat, but by what they excrete: nasty toxins that mess up some other part of the body. Clostridium botulinum produces a neurotoxic protein that can weaken or freeze nerve cells. Botulinum is the most acutely lethal toxin known – only 2 billionths of a gram can kill. Almost as deadly to people as the plutonium in a nuclear bomb, just a few pounds under the right conditions would kill everyone on earth.

Does Proteobacteria play a role?

[TS: Only 52 of the 4200 compounds found in normal mice blood were identified in germ-free mice. The implication is that most of the chemicals in our blood are synthesized by microbes.

The toxins produced by the Clostridium genus are among the most dangerous. Botulism (C. Botulinin) Tetanus (C. Tetani), gangrene (C. perfringens), and of course C. Dificile.

Toxic food and fast food mice

Feed junk food to germ-free mice and nothing happens. (

Western diet induces dysbiosis with increased E coli in CEABAC10 mice, alters host barrier function favouring AIEC colonisation.

Martinez-Medina M1


Food Allergies

If you attended elementary school before the 1980s, you can remember a time before nut allergies, when school lunches served peanut butter to everyone without the slightest worry that it might cause problems.

Where did this modern plague come from?

The first case to appear in medical journal didn’t happen until 1969 (Golbert), and examples were extremely rare before that. In fact, the very first mention of a food allergy happened about 100 years ago (Schloss).

Martin Blaser thinks something odd has happened because of the overuse of antibiotics.

Amish microbes are very diverse [google: “Zupancic microbiota Old Order Amish” PLOS 2012]

partly because they drink lots of raw milk

[requested paper Genetic Architecture of the immune system ]

“We have probably seen the worst of the asthma epidemic which was at its height in the 80s and 90s"

[google: “Song cohabiting family members share microbiota with one another and with their dogs”]

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