C. el­e­gans' Mi­cro­biome

by Roberto

Not long af­ter par­tic­i­pat­ing in the dis­cov­ery of mRNA and the triplet code, Syd­ney Bren­ner set out to study "how genes might spe­cify the com­plex struc­tures found in higher organ­isms." Those are the words in the open­ing sen­tence of his 1974 foun­dational pa­per, which estab­lished the nema­tode Caenorhab­di­tis el­e­gans as a model sys­tem for develop­mental and behav­ioral gene­tics. His­tory proved that not only did he choose the right organ­ism, but he also chose the right ques­tions to ask. Today's thriv­ing com­munity of "worm scien­tists" is testa­ment of his legacy. From the out­set he spel­led out the strain of C. el­e­gans to use, the compos­ition of the agar medium and even the bac­terial food for the worm, a strain of Es­cherichia coli B. For half a cen­tury, C. el­e­gans invest­igators have used the same strains and growth con­ditions. In so do­ing, they have achieved out­standing reprod­ucib­ility and ma­jor ad­vances. All this won­derful sci­ence did come at a price; the ecol­ogy of the nema­tode was largely dis­missed. But not by all.

Fig. 1. Wild-type C. el­e­gans her­maph­ro­dite stained with the flu­o­res­cent dye Texas Red to high­light the nu­clei of all cells. Source

For sev­eral years, stud­ies on the nat­ural his­tory of C. el­e­gans advan­ced but some­how, they were out of the lime­light. That changed in 2015. As part of a se­ries on the nat­ural his­tory of model organ­isms pub­lished in eLife, Lise Frézal and Marie-Anne Félix wrote an ar­ti­cle on "C. el­e­gans out­side the Petri dish," describ­ing the worm's nat­ural life­cycles and habi­tats. While they did not di­rectly spell it out, the ar­ti­cle prac­tically shouts out the ques­tion: what about C. el­e­gans' micro­bial part­ners? Then, in 2016, al­most as if the ar­ti­cle had served as a cat­a­lyst, three groups (Shapira, Schu­len­burg and Ru­vkun) pub­lished pa­pers attempt­ing to de­fine the micro­biome of C. el­e­gans. Now, each group could have con­tinued work­ing separ­ately. The beauty in this case is that they joined forces and pub­lished a joint pa­per in 2017 synth­esizing the signifi­cance of their three ap­proaches and outlin­ing the fu­ture chal­lenges. And here is the clincher. In 2020 they pub­lished the descrip­tion of "CeM­bio — The Caenorhab­di­tis el­e­gans Mi­cro­biome Re­source" and made the re­source widely avail­able. This is a synth­etic com­munity of twelve bac­terial strains that rep­resent the core micro­biome of C. el­e­gans, along with an enor­mous amount of ground­work character­ization of the strains and their inter­actions with their host. In­deed, a won­derful gift to the scien­tific com­munity at large. I have been advo­cating for years that many groups should work on one model synth­etic bac­terial com­munity. I think this is the one. I am hop­ing it will at­tract the atten­tion of many groups world­wide. If that hap­pens, I'll be cheer­ing from the side­lines!