Unraveling the ties between irritable bowel syndrome and intestinal microbiota

Table 2 Advantages and limitations of the principal techniques used in the characterization of the intestinal microbiota[16,39]

	Advantages	Limitations
Culture	Cheap, easy to use	Limited estimate intestinal microbiota
PCR-T/DGGE	High sensitivity in detecting difference in bacterial populations, semi-quantitative	Does not identify bacteria unless bands on the gel are cut out and sequenced
FISH	Microbial in situ identification, high sensitivity, quantitative	Few species can be simultaneously detected, only known species are detected
T-RFLP	Low cost	Low biodiversity resolution, no species-level identification, not quantitative
Quantitative PCR	Can detect small number of bacteria and quantify them	Laborious
Phylogenetic microarray	High biodiversity resolution, quantitative	Only known species are detected
NGS phylogenetic analysis (e.g., pyrosequencing)	Enormous quantities of data at individual Species level	Very costly, need bioinformatics analysis

16S rRNA: 16S ribosomal RNA; PCR-T/DGGE: PCR temperature/denaturing gradient gel electrophoresis; FISH: Fluorescent in situ hybridization; T-RFLP: Terminal restriction fragment length polymorphism; qPCR: Quantitative PCR; NGS: Next-generation sequencing.