Table 3.

Advantages and limitations of major high-throughput technologies.

Technologies	Advantages	Limitations
•Amplicons (16S/18S /ITS)	•High-throughput, low-cost rapid detection •Flexibility to target one or more variable regions •Longer sequence reads and more accurate analysis •Identification with very low abundance	•Bias caused by PCR amplification, sequencing errors and chimeric sequences •Low repeatability and low quantification •Vulnerability to host genome interference
Pyrosequencing	•Rapid and accurate analysis of short DNA sequences with a high throughput capacity	•Limited read lengths
Metagenome	•More information •Functional Analysis •Identification of microbiota to species or strain level	•More expensive •Time-consuming •Host-generated contamination
Meta-transcriptome	•Detection of active microorganisms in the environment, active transcripts, and active functions •Comparison of differentially expressed genes and differential functional pathways in different environments	•The highest costs •The most complex sample preparation and analysis process •mRNA, and rRNA contamination of the host