By Josh Harkinson, Mother Jones

The chlorination of municipal tap water is considered one of the 20th century’s best public health ideas. The American Water Works Association credits the practice with increasing life expectancy by 50 percent over the past century by virtually eliminating water-borne diseases such as typhoid fever and cholera.

But chlorine in drinking water can cause health risks of its own. And while some of the of those risks, such as reactions with organic compounds that can yield toxic byproducts, are relatively well understood and managed, at least one has been largely overlooked: The effect of chlorinated drinking water on the beneficial bacteria in our guts.

We simply don’t know enough about the microbial ecosystem in the human gut to identify every type of bacteria that’s important, much less how well those bacteria survive when we guzzle mildly chlorinated tap water.

The notion that our bodies’ 100 trillion bacteria act as a crucial internal ecosystem, a sort of sixth human organ, has only recently gained currency among mainstream scientists. Researchers now believe a lack of beneficial bacteria in the gut can trigger certain autoimmune diseases, among them diabetes, asthma, and even neurological conditions such as autism. Those conditions have spread in step with Western society’s war on germs, which has scorched our good bacteria along with the bad, throwing our bodies’ microbiomes off balance in the same way that a slashed and burned rainforest becomes susceptible to invasive weeds.

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