Yes, We Can Isolate Most Human Gut Microbes

A long-standing canard that really bothers me is the notion that most (“99%”) human gut microbes are unculturable–that is, we can’t grow them in the lab. As I noted a long time ago, that’s not the case:

This false statement stems from the observation that if you take any sample (soil, water, clinical samples) and look under a microscope we see many more bacterial cells that contain DNA than we can grow. The problem is that, if you look at the paper that claimed this, they attempted to grow bacteria on a single, rich medium.

One weekend, when I was a post-doc, I did a very simple comparison. I took standard rich lab medium (‘nutrient agar’ which is basically one of those high protein nutrient bars minus the artificial flavorings. That’s why I don’t eat them. Seriously, if you dilute one bar in a liter of water, you basically have nutrient agar). Anyway, the other medium was a home-brew very-low nutrient agar that had one-thousandth of the ingredients in the standard nutrient agar. I also used extremely high-grade agar (electrophoresis grade) to solidify the medium (standard agars actually contain a fair amount of nutrients). I did this because we know that many bacteria can’t grow in environments with a lot of carbon or protein sources–they basically end up choking on their own excreta. I also added cycloheximide to kill off fungi, as well as catalase to protect the bacteria from their own metabolisms.

After 72 hours, my special plates had 20-40 times as many bacteria as the standard plates. So I’ve never bought into the 99% percent.

It appears some researchers took a serious stab at this, and blew the ‘99% unculturable’ figure out of the water (boldface mine):

We used metagenomic sequencing to sequence the DNA of all the bacteria present in a fecal sample, and we then compared this to the sequence of the bacteria growing on a Petri dish that came from a fecal sample. This way, we can compare what we are growing in the lab and what we are missing. We discovered that we can actually grow the majority of the bacteria that are present in your gut….

As these bacteria do not survive in oxygen we grew them in anaerobic chambers and we used a publicly available growth media containing lots of different carbon sources and fatty acids that encourage the growth of a wide range of bacterial species.

And there you have it. TEH SCIENTISMZ!

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