Table 1

Main features of culture-independent detection methods of gut microbiota

QuestionTargetApproachData generatedCan microbes be identified directly?Main benefitMain limitation
Which microbes are present in the GI tract?IsolatesCultivationPhenotypic characterisationYesAccurate species identificationNot representative
16S rRNA geneCloning and sanger sequencingPhylogenetic identificationYesComplete 16S rRNA gene sequence dataCloning bias
16S rRNA geneHigh-throughput sequencingPhylogenetic identificationYesHigh-throughput data generationShort reads
16S rRNA geneFingerpintingCommunity profileNoFast comparison between communitiesNo direct link with phylogeny
16S rRNAFISHCell numbersYesAccurate enumerationDependent on 16S rRNA databases
16S rRNA geneqPCR16S rRNA gene abundancesYesWide dynamic rangeDependent on 16S rRNA databases
16S rRNA genePhylogenetic microarrayPhylogenetic identificationYesHigh-throughput phylogenetic profilingDependent on 16S rRNA databases
What microbial genes are present in the GI tract?Community DNASequence-based metagenomicsGene sequencesNot alwaysHigh-throughput data generationFunction mainly based on predictions
Community DNAFunction-based metagenomicsFunctional properties encoded on DNA fragmentNot alwaysFunctional properties linked to DNA sequencesSuitable cloning host/system and screening assays needed
What are GI tract microbes doing?mRNAMetatranscriptomicsCommunity gene expressionNot alwaysDirect information about microbial activityCommunity RNA extraction challenging
ProteinsMetaproteomicsCommunity protein productionNot alwaysDirect information about microbial activityNo uniform protocol for all cell fractions
MetabonomicsMetabonomics/metabolomicsCommunity metabolity profilesNoMicrobiota activity representationNo link with microbes or its function
Lactulose hydrogen breath testMeasuring GI tract gas productionHydrogen and methane breath contentNoUnclear, simple test but not validated for diagnosing SIBOMay simply measure small intestinal transit time to caecum
Glucose hydrogen breath testMeasuring GI tract gas productionHydrogen breath contentNoSame as abovePoor sensitivity; misses distal SIBO
  • FISH, fluorescent in situ hybridisation; GI, gastrointestinal; qPCR, quantitative PCR; SIBO, small intestinal bacterial overgrowth.