One of the common sayings in microbiology that drives me up a wall is the notion that 99% of all bacteria can’t be grown in the lab. 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 standar 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.
One of the interesting developments from the Human Microbiome Project is that we’re discovering that, in fact, we can culture many human-associated bacteria. Since we have culture-independent, DNA sequencing-based methods of determining which bacteria live in and on you, we can also see if, when we try to grow things, if those bacteria show up.
Indeed, they do. Several groups, working with gut and oral microbes, are able to culture most of what the DNA surveys are yielding–which is also a good confirmation of the molecular methods. Yes, they have to be clever: Tom Schmitt of Michigan State University grows bacteria from your gut (yes, shit) at levels of oxygen typically found in the intestinal tract and finds all sorts of ‘uncultured’ bugs. Floyd Dewhirst, who works on oral microbes, and who has done extensive surveys of bacteria from the mouth says that 92% of bacteria for which we have sequence data exist in culture collections (again, you have to be clever). And Jeff Gordon reported that 70% of genera found in the gut, and ~60% of species could be grown without too much work (you did have to wait a week, however).
These are very cool results, and I hope they put the 99% of bacteria are unculturable myth to rest.
Seriously, have some pride, fellow microbiologists, and be clever when you isolate….