This excellent article by Carl Zimmer gives a brief history of the development of antibiotics. It makes the usual points that the microbes within us improve our health and killing them (with antibiotics) can have bad effects. One study found that children given antibiotics had a higher risk of developing inflammatory bowel disease (IBD) later in life. Giving antibiotics to a child younger than one year was especially dangerous — the risk of IBD increased by a factor of 6.
The article makes the minor mistake of taking seriously what researchers say about number of species:
Each of us is home to several thousand [bacterial] species. . . . My own belly button, I’ve been reliably informed, contains at least 53 species.
Counting the number of species inside us is like measuring the length of the coast of England. The more closely you look (in the case of coastlines, the shorter the ruler you use), the larger the number you will arrive at. I’d be surprised if the researchers who count bacterial species adjust for this.
What I found most interesting about the article is it says nothing about fermented foods. Apparently the connection is not so obvious.
Ahoy, Seth. If you type
The sin of bad science
into google and then click on the FT link you can read this article without wrestling with their paywall.
First time I’ve come across that point about the number of species.
Similar to the notion of Mandelbrot fractals.
Nice story. Now could you please beat up one or more of these idiots who coerce their doctors into prescribing antibiotics for the common cold?
Brilliant article on immunotherapy in nytimes today:
https://www.nytimes.com/2012/12/23/magazine/is-the-cure-for-cancer-inside-you.html?src=me&ref=general&pagewanted=all
Interesting article. Just a quick correction: IBD is short for Inflammatory Bowel Disease, which is a collective term for the two serious inflammatory bowel conditions – Crohn’s disease and Ulcerative Colitis. This is not the same as irritable bowel.
Seth: Thanks for the correction.
“Counting the number of species inside us is like measuring the length of the coast of England.”
There are different definitions for the term “species” throughout biology and the use of this word in reference to bacteria appears to be controversial. Apparently enough scientists think bacterial species don’t exist that you can publish a peer-reviewed paper in 2012 called “Bacterial species may exist, metagenomics reveal.”
Carl Zimmer certainly knows this and has written about it, though I personally find the use of the term to be confusing to those of us who like to dig deeper.
I think it is possible that some scientists are using the term without due care, but good microbiology papers will be clear on what they mean by the word if they use it at all. It is sometimes defined with agonizing rigor.
Mostly I’ve seen “species” used to refer to “operational taxonomic units” (OTUs), defined as a specified level of sequence similarity in a particular segment of genetic material (e.g. certain variable regions of 16S ribosomal RNA). The boundaries between OTUs depend on what level of sequence similarity you specify (in other words, the size of the ruler you are using to measure the coast of England). OTU classifications vary from one paper to another and can depend, for example, on which software is used to crunch the sequence data (see e.g. https://hmpdacc.org/HMQCP for the Human Microbiome Project).
Seth: Good points. Even when the definition of “species” is made clear, there is still the problem of coverage. As you sample more and more exhaustively, the number of species will get larger and larger.
Its an interesting brief… but in My personal opinion, its suggested to choose a natural antibiotic that can be found surround us. they’re still the best we get.