Hi,
I'm working on soil microbiology and I want to check the microbial diversity in the soil. so, I have 2 options,PE illumina or 454-Pyrosequencing. I want to ask that which technique is better to use and why is this so?
In a word: Illumina. A few of the reasons I think Illumina is a better option:
First, although it costs more to run the machine, the number of sequences obtained is much greater. It's been a few years since I've done 454 sequencing, but in my experience (MiSeq vs GS Junior) Illumina is about 2-3 times the price but gives you over 10 times the data.
Quality filtering Illumina data is also simpler, and you don't need to worry about artefacts like homopolymer runs. Also, if you're doing amplicon sequencing, such as 16S rRNA gene sequencing, getting overlap between your forward and reverse sequences allows for more stringent quality control.
Finally, Roche is discontinuing 454 sequencing in 2016 so if you're looking for a long-term platform to work with this isn't a viable option. If you think you only need a brief period of sequencing this may not bother you so much, but there's usually a certain amount of investment required in getting your wet-lab protocols optimised so if your group is planning to do a lot of this work, Illumina or Ion Torrent will be more long lasting option.
I agree with what David has said regarding sequencing technology choice, however, your best choice for metagenomics experimental design is not 16S rRNA subunit. Shotgun microbiome sequencing is far superior and you data will have greater impact because of the confidence in you bacterial identification.
Also look at this before you start regarding contamination from DNA kits and MolBio water
http://www.biomedcentral.com/1741-7007/12/87
Illumina sequencing approach to explore the microbial diversity has more advantages over 454-pyrosequencing method. specially when aims to identify the both bacteria and fungi population. Normally the cost of illumina is quiet high than pyro-method, however the quality of processed data have emerge with great difference. i prefer illumina sequencing in my soil microbial experiments. the cost of each sample is normally 650 RMB in china for both bacterial and fungal sequence. The popular sequencing companies process the data by these two methods are Majorbio Co, Shanghai, Denovo lab Guangzhou.
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