Buildingblocksformicrobiomeresearch

Kielresearchers,togetherwithaninternationalteam,presentanematodemodelsystemasthebasisforcomprehensivemicrobiomeresearch

Allmulticellularlivingbeingsarecolonizedbyanunimaginablylargenumberofmicroorganismsandhaveevolvedtogetherwiththesemicrobialsymbiontsfromthebeginning.Thenaturalmicrobiome,i.e.theentiretyofthebacteria,virusesandfungithatliveinandonabody,isofcentralimportancefortheentireorganism:itsupports,forexample,theabsorptionofnutrients,fendsoffpathogensandcanalsobeinvolvedinthedevelopmentofseriousdiseases.Researchersuseso-calledmodelsystemstounravelthehighlycomplexinteractionsofhostorganismsandmicroorganisms,includingforexample,animalandplantspeciesthatcanbeeasilystudiedinthelaboratory,andaspecific,simplifiedselectionofcolonizingmicroorganisms.

AresearchteamfromKielUniversity,togetherwithinternationalexpertsfromforexampletheUniversityofCaliforniainBerkeleyandtheBaylorCollegeofMedicineinHouston,hasnowdevelopedanovel,improvedmodelsystemformicrobiomeresearch,theso-called'Caenorhabditiselegansmicrobiomeresource'(CeMbio).Itisbasedonasetof12bacteriathatarerepresentativeofthenaturalcompositionofanematodemicrobiome.Thisresourcewillallowmorerealisticmicrobiomestudiesinavarietyofresearchfields,therebytakingadvantageofthenematodeC.elegansasanexperimentalsystemformicrobiomeresearch.TheKielUniversityresearchteamfromtheEvolutionaryEcologyandGeneticsgroupheadedbyProfessorHinrichSchulenburgandtheMedicalSystemsBiologygroupheadedbyProfessorChristophKaletarecentlypresentedtheCeMbioresourceanditsmaincharacteristicsinthescientificjournalG3:GenesGenomesGenetics.
 

Anear-naturalnematodemicrobiome

ThestartingpointfortheCeMbioprojectwaspreviousworkbytheresearchersfromKiel,inwhichtheydeterminedforthefirsttimethenaturallyassociatedbacterialcommunityofthenematodeC.elegans,whichisusuallystudiedundersterileconditions.Thisenabledthemtoinvestigatetheeffectsofthenaturalmicrobiomeontheworm'slifefunctionsandfitness.Thecomponentsofthenematodemicrobiomethatwereidentifiedintheirentiretyatthattimewerethennarroweddowntotwelverepresentativebacterialspecies.Thescientistsusedthemforcolonizationexperimentsofthenematode."Wetransferredthesebacteriaindividuallyinpurecultureandinmixedculturesintogerm-freewormsandthenobservedtheirgrowth,"pointsoutfirstauthorDrPhilippDirksen,formermemberoftheSchulenburggroup."Inthisway,wewereabletocharacterizetheabilityofindividualbacteriatocolonizethewormgutandtherelationshipofthedifferentbacteriatoeachotherinthenaturalhostenvironment,"Dirksencontinues.

Inasecondpartofthework,thescientistsusedwholegenomesequencesofallorganismspresentinthemicrobiometoreconstructthemetabolicnetworksandmetaboliccompetencesofthebacteria.Usingbioinformaticsmethods,theywerethusabletopredictwhichmetabolicproductscouldbeexchangedbetweenhostandmicrobiome.Overall,theythuscreatedthebasisforarealisticmicrobiomemodelforthedetailedstudyofhost-bacteriainteractionsinC.elegans.
 

Anopensourcemicrobiomemodel

WiththeCeMbiomodel,theKielresearchersarenowofferingaresourcethatispubliclyaccessibletocolleaguesintheC.elegansresearchcommunityworldwide.Inadditiontothebacterialstrainsthatcanbeeasilycultivatedunderlaboratoryconditions,thisincludestheircompletelydecodedgeneticinformationaswellasthecompletemodelingofthemetabolicnetworks.Theresourceandgenerateddatabasenowprovidestheinternationalresearchcommunitywithanoveltoolkitthatcanbeusedtostudynumerousaspectsofnematodebiologyfromgrowthtodevelopmentinthecontextofinteractionswithitsnaturalmicrobiome."OurCeMbiomodelopensthedoorforamorerealisticcharacterizationofabroadspectrumofinterestingresearchquestionsrangingfromdiseasedevelopmentandthebiologyofagingtoneurobiologicalaspects,"emphasizestheevolutionarybiologistSchulenburg,headoftheKielEvolutionCenter(KEC)atKielUniversity."Thepossibilityofinvestigatingtheassociatedprocessesinthehostsinteractionwithitsnaturalmicrobiomeofferscompletelynewperspectivesforunderstandingtheunderlyingmolecularmechanisms,"continuesSchulenburg.

Inaddition,theKielresearchershopethatthenewtoolwillalsohelptoestablishC.elegansmorestronglythanbeforeasamodelsystemformicrobiomeresearch.Allinall,CeMbioprovidesscientistsaroundtheworldwithanovelresourcetostudythismodelnematodeinitsnaturalcontext.Theworkthusmakesanimportantcontributiontoimprovingtheoverallunderstandingofthemechanismsbywhichthemicrobiomeinfluencesthehealthanddiseaseofitshostorganism,asisbeingpursuedbyseveralresearchinitiativesinKiel,forexampletheCollaborativeResearchCenter(CRC)1182"OriginandFunctionofMetaorganisms"ortheClusterofExcellence"PrecisionMedicineinChronicInflammation"(PMI).

Moreinformation:

A scientist at the microscope
© Christian Urban, Kiel University

First author Dr Philipp Dirksen investigated the ability of individual bacteria to colonize the intestine of the worm and the relationship between different bacteria in the natural host environment.

Microscopic image of a threadworm
© Antje Thomas, Prof. Hinrich Schulenburg

The nematode Caenorhabditis elegans is a well-suited model organism for microbiome research.

Animation of a threadworm
© Dr Philipp Dirksen

The bacterial colonization (stained orange) is mainly found in the threadworm’s intestine.

Originalpublication:

PhilippDirksen,AdrienAssie,JohannesZimmermann,FanZhang,Adina-MalinTietje,SarahArnaudMarsh,Marie-AnneFelix,MichaelShapira,ChristophKaleta,HinrichSchulenburgandBuckSamuel(2020):CeMbio-TheCaenorhabditiselegansmicrobiomeresource.G3:GenesGenomesGenetics 
DOI:10.1534/g3.120.401309

Contact:

Prof.HinrichSchulenburg
EvolutionaryEcologyandGeneticsresearchgroup,
ZoologicalInstitute,KielUniversity:
0431-880-4141
hschulenburg@zoologie.uni-kiel.de

Presscontact:

ChristianUrban
SciencecommunicationKielLifeScience",
KielUniversity:
+49(0)431-880-1974
curban@uv.uni-kiel.de