Page path:

Ana­lysis of un­known mi­crobes is get­ting easier

Mar 6, 2020

Marine microbes like to play hide and seek. Some bacteria often appear in samples but do not grow in the lab. At the same time, they are too few to be discovered via genetic analysis. Scientists of the Max Planck Institute for Marine Microbiology now succeeded in finding a method to locate them nevertheless.

 

The samples used for the current study were obtained in the North Sea near Helgoland. (© Wikimedia Commons/ CC BY-SA 4.0/ A. Savin)
The samples used for the current study were obtained in the North Sea near Helgoland. (© Wikimedia Commons/ CC BY-SA 4.0/ A. Savin)

Us­ing a com­bin­a­tion of sev­eral meth­ods, the sci­ent­ists from Bre­men have man­aged to de­scribe the func­tional ca­pa­cit­ies of less com­mon or­gan­isms in a mar­ine mi­cro­bial com­munity us­ing the meta­gen­ome. The meta­gen­ome is the sum of all genes ex­ist­ing in a mi­cro­bial com­munity. In this large amount of ge­netic in­form­a­tion, the DNA of the rare mi­croor­gan­isms was suc­cess­fully re­cog­nized and sub­sequently ana­lyzed. This is im­port­ant be­cause many mi­cro­bial com­munit­ies are dom­in­ated by one or two spe­cies. Yet, many other or­gan­isms are also part of the com­munity and play an im­port­ant role, even though they are less nu­mer­ous. Un­til now, it was dif­fi­cult to identify their func­tion.

A spe­cific case con­cerned bac­teria that were found after al­gae blooms off the is­land of Hel­go­land in the North Sea.  “We re­peatedly came across an un­known spe­cies in our samples and wanted to learn more about their func­tional ca­pa­cit­ies and their role in the en­vir­on­ment,“ says An­issa Grieb, re­searcher at the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy and first au­thor of the study. But as these bac­teria could neither be grown in the lab nor be found via the meta­gen­ome us­ing stand­ard meth­ods, the team with Grieb star­ted to look for other solu­tions.

We combine several methods for the specific enrichment of bacteria: (1) Using FISH, we fluorescently label a specific bacterial species of our Helgoland water sample. (2) Based on that signal, cells are sorted. (3) The DNA of that enrichment is sequenced and further analyzed. (© Max Planck Institute for Marine Microbiology/ A. Grieb)
We combine several methods for the specific enrichment of bacteria: (1) Using FISH, we fluorescently label a specific bacterial species of our Helgoland water sample. (2) Based on that signal, cells are sorted. (3) The DNA of that enrichment is sequenced and further analyzed. (© Max Planck Institute for Marine Microbiology/ A. Grieb)

The good into the pot

The idea: „As we have a flow cyto­meter with a cell sort­ing sys­tem in our re­search group, we had the idea to se­lect the cells be­fore se­quen­cing the DNA“, says Grieb. That way, the di­versity is re­duced and the rare spe­cies can no longer hide. Thus, the sci­ent­ists used the FISH-method to la­bel DNA sec­tions of the mi­crobes with fluor­es­cent dyes to de­tect and sort the bac­teria they were in­ter­ested in. “However, we faced two chal­lenges: Firstly, a very bright FISH sig­nal was needed for the de­tec­tion and sort­ing of tar­geted cells us­ing flow cyto­metry,” says Grieb. “Secondly, suf­fi­cient un­im­paired DNA ma­ter­ial was re­quired for high qual­ity gen­ome se­quen­cing.”

The team around Grieb, to­gether with re­search­ers from the Joint Gen­ome In­sti­tute, tested how this could work. At the end, they suc­ceeded by us­ing a re­cently de­veloped ver­sion of the FISH-method, the hy­brid­iz­a­tion chain re­ac­tion (HCR)-FISH. First, they op­tim­ized this pro­ced­ure with pure cul­tures in the labor­at­ory and af­ter­wards used it on the en­vir­on­mental samples, which had been taken off the coast of Hel­go­land. 

Mi­crobes be­come vis­ible

“As a res­ult, we are able to isol­ate the gen­ome of rare mi­croor­gan­isms and ana­lyze it af­ter­wards with stand­ard-meth­ods of gene ana­lysis,” says Bernhard Fuchs, leader of the flow cyto­metry re­search group at the Max Planck In­sti­tute for Mar­ine Mi­cro­bi­o­logy. “Spe­cific groups or spe­cies can now be ge­n­om­ic­ally in­ter­rog­ated, open­ing a win­dow into the bio­sphere of rare mi­croor­gan­isms, even of highly com­plex samples.” This new method en­abled the re­search­ers to cla­rify the iden­tity of a less com­mon genus, whose DNA re­peatedly ap­peared in wa­ter samples from the North Sea off Hel­go­land. In other words: The game of hide and seek is over.

Anissa Grieb at the flow cytometer (© Max Planck Institute for Marine Microbiology/ K. Matthes)
Anissa Grieb at the flow cytometer (© Max Planck Institute for Marine Microbiology/ K. Matthes)

Ori­ginal pub­lic­a­tion

An­issa Grieb, Robert M. Bowers, Monike Og­gerin, Dani­elle Goudeau, Janey Lee, Rex R. Malmstrom, Tanja Woyke and Bernhard M. Fuchs: A pipeline for targeted metagenomics of environmental bacteria. Mi­cro­bi­ome 8, Feb­ru­ary 2020.

DOI: 0.1186/s40168-020-0790-7

Behind the paper: Finding the needle in a haystack via targeted genomics 

Par­ti­cip­at­ing in­sti­tu­tions

  • Max Planck Institute for Marine Microbiology, Bremen, Germany
  • DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, USA

Please dir­ect your quer­ies to:

Group Leader

Flow Cytometry Research Group

PD Dr. Bernhard Fuchs

MPI for Marine Microbiology
Celsiusstr. 1
D-28359 Bremen
Germany

Room: 

2222

Phone: 

+49 421 2028-9350

PD Dr. Bernhard Fuchs
 
Back to Top