16S Rrna Sequencing In Industry Applications

Question

[Estebanpv]

Hi,

I am new to bioinformatics and have just developed a pipeline for a microbial diversity report based on 16s rRNA sequencing in Roche 454.

I would like to know if this kind microbial diversity reports are being applied in any industry, for example in food/water quality control or clinical venues surveillance.

Thank you... I would really appreciate your advise!

[antonioggsousa]

Hi,

I just would like to comment that Roche 454 left the sequencing market (in 2013): https://en.wikipedia.org/wiki/454_Life_Sciences.

This is important depending on how biased/tailored your pipeline report is for pyrosequencing. I would say that if it can be easily adapted to Illumina, that currently dominates the market, the general interest on that would greatly increase.

Answer 1

[luisa.hugerth]

Hello,

There are indeed plenty of applications in industrial and life technologies based on pyrotags of 16S rRNA. A quick look through http://www.ncbi.nlm.nih.gov/pubmed/ will give you many results, many of which open access. It's probably easier for you to direct the search yourself, as I don't know what your specific interests are and the field is so vast.

There is also a wide array of literature discussing which region to target for sequencing (I say V3, V4), which primers to use (reviewd in http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3592464/) and how to post-process the data. Pyronoise ( http://www.biomedcentral.com/1471-2105/12/38 ) is generally considered the best application for that, at least as far as error correction is concerned.

After that Usearch might be a good alternative, although I don't know how it performs with 454. Most research centers are moving on to Illumina MiSeq however, due to lower costs and higher throughput.