A simple solution for a big challenge

There are approx­i­mately  5 non­il­lion bac­teria on earth (where a mil­lion has six zeros after the one, a non­il­lion has 30 zeroes). The microor­gan­isms that live in the envi­ron­ment and in animal “micro­biomes” (the col­lec­tion of all the bac­teria that call an animal home) rep­re­sent the most diverse group of species around. They can be used to dis­cover new antibi­otics (some of them are very good at killing their neigh­bors) and iden­ti­fying those in the human micro­biome could lead to a much better under­standing of many dis­eases like var­ious can­cers and meta­bolic syndromes.

But for unknown rea­sons, the vast majority of these little guys cannot be grown in the lab.

A few weeks ago I men­tioned two pro­fes­sors who have fig­ured out how to coax pre­vi­ously “uncul­tivable” bac­teria into sur­viving on a petri dish. Kim Lewis and a post-​​doc in his lab have set up a non-​​profit called Sample America to put some of those tech­niques into action as they scour the nation for new antibiotics.

Today I want to tell you about one tech­nique in par­tic­ular, which Slava Epstein’s team recently pub­lished in the journal Applied and Envi­ron­mental Micro­bi­ology. “It is much sim­pler than it may appear,” he said. “It is remark­ably simple: it involves cul­ti­va­tion in nature as opposed to the lab, cul­ti­va­tion of cells in their nat­ural envi­ron­ment using the soup of nat­ural growth fac­tors as the medium…And that’s all.” That’s the kind of thing that makes

Of course, he con­tinued, we don’t know exactly what the soup con­tains; we don’ know which growth fac­tors are crit­ical for the cul­ti­va­tion of cer­tain bac­teria over others. “But who cares?” he said. All they’re trying to do for now is grow the suckers.

So, how do they do it? Also simple. They put a “petri dish” with per­me­able mem­branes (like the one above) into the native envi­ron­ment of the bac­teria they’re trying to grow and let them hang out with their friends and family, just sep­a­rated a little…Kind of like the boy in the bubble.

Sev­eral (or sev­eral hun­dred, your choice) mini petri dishes so designed can be fash­ioned into a little mul­ti­well plate like the one to the right. By adding a solu­tion of var­ious bac­teria of known con­cen­tra­tion to the plate, you can ensure that only one cell makes it into each of the wells. This means you have many more oppor­tu­ni­ties for suc­cess. Some bac­teria cul­ti­vated will have already been iden­ti­fied and are easily grown in the lab, but others could be new species or even rep­re­sen­ta­tive of an entirely unknown species group.

First the team did this in the envi­ron­ment, placing little mul­ti­well petri dish plates under a rock in the ocean or on land. But the most recent paper describes the first use of this approach to study bac­teria in the human body. Specif­i­cally, they grew bac­teria inside someone’s mouth.

Now, I never wore my retainer as a kid and there­fore I ended up with braces. Twice. But if I knew that my retainer was con­tributing to sci­ence, I may have thought dif­fer­ently about it. The folks at Forsyth rigged up a retainer for one human sub­ject that had one of these plates embedded on the plastic part that meets the roof of the mouth.

These two methods (single-​​cell and multi-​​cell approaches) along with a stan­dard bac­te­rial cul­ti­va­tion approach yielded a total of 10 species that had only pre­vi­ously been seen as a mol­e­c­ular sig­na­ture and 20 species that had not pre­vi­ously been cul­ti­vated in the lab.

The team is sequencing the genomes of 27 of these new­bies, five of which have already been released.

Cover photo: Nathan Reading, “ChromID Sal­mo­nella Agar — neg­a­tive sample” Sep­tember 12, 2011 via Flickr. Cre­ative Com­mons Attribution.