Does Next Generation Sequencing give a better estimate of microbial diversity than terminal restriction fragment length polymorphism (T-RFLP) analysis?

The development of next generation sequencing has challenged the use of more classic molecular fingerprinting methods used to study microbial diversity. We analysed the bacterial rumen diversity of sheep after the progressive colonization of rumen protozoa, using both next generation sequencing (NGS) and terminal restriction fragment length polymorphism (T-RFLP). The rumen microflora harboured 864 operational taxonomic units (OTU). Correlation between NGS and T-RFLP was high with an R value of 0.836 and 0.781 for richness abundance and Shannon-Wiener index, respectively. Dendrograms of both datasets were also correlated (Mantel test = 0.742). 21 OTUs were significantly impacted by the progressive colonization of rumen protozoa, with an increase in the relative abundance of Bacteroidetes, related with an increase of the free ammonia levels in the rumen. Our findings suggest classic fingerprinting methods are still valuable tools to study microbial diversity in complex environments.