The meta­bol­ism of bac­teria un­der the mi­cro­scope: new method re­veals host-mi­crobe in­ter­ac­tions

The fas­cin­at­ing world of bac­teria that live as sym­bionts or para­sites in an­imal hosts of­ten re­mains a mys­tery to re­search­ers. The Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy in Bre­men and Kiel Uni­versity (CAU) are con­trib­ut­ing to solv­ing this puzzle with their re­search into the in­ter­ac­tions between mi­crobes and their host. Un­der the lead­er­ship of Prof. Dr Manuel Liebeke, head of the Meta­bolic In­ter­ac­tions Re­search Group at the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy and the Meta­bolo­m­ics De­part­ment at the CAU's Fac­ulty of Ag­ri­cul­tural and Nu­tri­tional Sci­ences, a re­search team has made a break­through that provides in­sights into this mys­ter­i­ous mi­cro-world.

Of­ten, bac­teria can­not be cul­tured in the labor­at­ory, and re­search­ers must rely on in­form­a­tion from the bac­terial gen­ome ob­tained from en­vir­on­mental samples to gain the­or­et­ical in­sights into the meta­bol­ism of mi­croor­gan­isms. However, there has been a lack of in­sight into what they ac­tu­ally do in their nat­ural en­vir­on­ment. To solve this puzzle, sci­ent­ists began re­search­ing the so-called meta­bolome of bac­teria – everything that has to do with their meta­bol­ism, in­clud­ing meta­bol­ites such as sug­ars or fats.

In a pi­on­eer­ing study, Liebeke's team de­veloped a method with which they can identify in­di­vidual bac­teria and sim­ul­tan­eously de­term­ine which meta­bol­ites are present in the cells - all without cul­tiv­at­ing the bac­teria in the labor­at­ory. This method al­lows them to study how bac­teria live and sur­vive as sym­bi­otic sub­ten­ants, for ex­ample in mus­sels. The team ana­lysed hun­dreds of meta­bol­ites on an area smal­ler than one square mil­li­metre. The Kiel and Bre­men re­search­ers pub­lished their res­ults in the journal Nature Protocolsin Septem­ber.

"We cre­ate a snap­shot, so to speak, of the bac­teria at work, ex­actly as they are act­ive in their nat­ural en­vir­on­ment, par­tic­u­larly within an an­imal cell," Liebeke ex­plained. "And we can do that at an im­press­ive res­ol­u­tion of a few mi­cro­metres, about ten times thin­ner than a hu­man hair."

A spe­cial fea­ture of this method is the use of flash-frozen tis­sue, which is cut wafer-thin. The re­search­ers then use a spe­cial mass spec­tro­metry tech­nique called MALDI-MS ima­ging to cre­ate a snap­shot of the chem­ical com­pounds in the cells.

However, draw­ing the cor­rect con­clu­sions from the im­ages of the meta­bol­ites is only pos­sible if they know which bac­teria pro­duce or use them. To solve this prob­lem, the re­search­ers also use fluor­es­cence in situ hy­brid­isa­tion (FISH) to identify and loc­al­ise in­di­vidual bac­terial cells in the sample.

"Ap­ply­ing this method to host-mi­crobe com­munit­ies will give us many ex­cit­ing new in­sights into chem­ical com­mu­nic­a­tion between or­gan­isms," said Patric Bourceau from the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy, lead au­thor of the pro­tocol de­veloped to ap­ply the method.