Table 1

Comparison of molecular methodologies

TechniqueStandard cultureFingerprinting methodsHigh throughput sequencing methods
ExampleCulture on blood MacConkeys agar for Gram negative speciesTemperature or Denaturing Gel electrophoresis (T/DGGE)454 pyrosequencing; ‘illumina’ etc
Brief description of how organisms are identifiedGrown in a laboratory on specific media or with specific conditions; physical/chemical characteristics used to speciate16S rRNA isolated and amplified. Separation by sequence differences within amplicons using temperature or chemical gradientBased on 16S rRNA extraction and sequencing, utilisinge extensive databases of 16S gene to identify species
AdvantagesLots of experience in technique; cheap; limited equipment needed; target key organismsGreater depth of analysis than culture; cheap (for molecular technique); can be run against a ‘standard ladder’Very detailed information; complex communities can be examined; quick
Disadvantages∼90% species remain undetected; need to already know species of interestTime consuming; separate steps needed to sequence amplicons and identify species; PCR biasCostly; PCR bias; specialised equipment needed, available in few localities; enormous amounts of data generated require ‘handling’ and analysis