NGS Expert Blog

There are many volcanoes and earthquakes in Japan, but it is not always a bad thing, they are also responsible for the many hot springs. Most Japanese people love soaking in a hot spring and they believe that this eliminates fatigue and improves health. Hot springs also had a great contribution to biotechnology via the heat resistant DNA polymerase from Thermus aquaticus (Taq) and its derivatives. Not only PCR, but also Sanger sequencing was accelerated by these heat resistant enzymes as we all know well.

Scientists have started to study the genome/transcriptome world in hot springs with NGS technologies. Murakami et al., peformed 16S-rRNA (Sanger sequencing) and meta-transcriptome analysis from small RNA (GS FLX sequencing) of groundwater (up to 1,000 m depth) from Yunohara hot spring, Japan. Their phylogenetic analysis using 16S rRNA showed the classification of 17 species including archaea and eubacteria.  There are only 2 or 3 dominant species in typical cases of other hot springs, but this one is rich in diversity. Furthermore, they found the very unique group “Archaeal Richmond Mine Acidophilic Nanoorganisms (ARMAN)” which is a small organism/cell with only 200 nm size! Their small RNA analysis identified 64,194 (20,057 nonredundant) cDNA sequences, and they found several novel non coding RNAs which have a very stable secondary structure.

Therefore, hot springs may still be gold mines for useful genes and important biological knowledge of unknown underground ecosystems.

Rather than resting on the successes of the MiSeq launch, Illumina is continuously improving the performance of their small Benchtop Next Generation Sequencing System. Geoff Smith is talking about improvements in the read lenght of the MiSeq in the video attached.

This instrument is not only another next gen sequencing device but really has remarkable advantages over other instruments when sequencing for example bacterial genomes. This is why I am really delighted that we now can offer services using the MiSeq instrument. (More info on our MiSeq services can be found here)

16S rRNA sequencing of samples from 54 office-common surfaces in 3 different cities (New York, San Franscisco, Tuscon) revealed that offices of men are dirtier than these of women and the offices in San Francisco are the cleanest among the three cities. This is part of the results from Hewitt et al. published in PLoS ONE just recently. Overall they found “more than 500 bacterial genera from 20 different divisions” (Hewitt et al.) whereas most could be found on chairs and phones (see graph). But interestingly the bacterial population from Tuscon was significant different to the one from San Francisco and NewYork although the distance between Tuscon and San Francisco is smaller. From my point of view this is a great study showing that distribution is not as obvious as we think and that we haven’t revealed every secret on earth yet.

In the NGS (Next Generation Sequencing) group of the networking platform LinkedIn I came across a lively discussion about the best strategy for de novo sequencing of a bacterial genome. The discussion was about technology (Roche versus Illumina), coverage (from 10-fold on Roche GS FLX to 500-fold on Illumina HiSeq 2000) and library types. The comments and advices given coincide with our experience that this question can not be answered without any further information on the genome to be sequenced. GC content, amount and size of repeat structures as well as the genome size of the bacterium have to be considered. We have meanwhile de novo sequenced more than 100 microbial genomes and according to our experience GS FLX technology with a combination of shotgun and long paired end libraries will deliver a high quality genome sequence that is suitable for gap closing projects.

The multiple library approach is described in detail in our Application Note and in a Press Release. Depending on the complexity and size of the genome, we select the appropriate library.