Happy new year everyone one, and welcome to another year of science (and other stuff). I did give my blog a little update and despite finishing up my PhD thesis the next month blog more actively again.

It has been a very productive 2016 with newly developed software (PrimerMiner, JAMP) and several metabarcoding projects being completed and currently being in review. Of cause we have preprints available for our big freshwater metabarcoding primer manuscript and size sorting study. The next weeks we will also upload a preprint for our Finland project where we compared the performance of DNA metabarcoding to morphological identification on real monitoring invertebrate samples.

There is one additional project in the pipeline where we are trying to improve metabarcoding accuracy, and once that’s done I’m bundling my papers together and hand in my PhD thesis end of March. So what’s next?

Metabarcoding on haplotype level accuracy

Figure 1: We are currently testing 2 primer sets (A) on several mock and complete communities (B) with our haplotyping approach (C).

Metabarcoding for monitoring macroinvertebrates has come a long way the last few years, thanks active research in the community. DNA metabarcoding reliability detects taxa often on species level, but we might be able to get this method to sequence accuracy using clever laboratory and bioinformatic methods. For microbes haplotype level metabarcoding already works (Eren et al. 2013, Tikhonov et al. 2015) and we have to see if we can pull it of for our inverts.

Population genetics on whole communities

Depending on how well or metabarcoding on haplotype level will work, we are planning a project under the lead of our postdoc Edith Vamos on the restoration and recolonisation of whole stream catchments. If and how species can reach restored sites is essential for the success of river restorations. We hope that we can apply population genetics methods to whole stream communities with our developed haplotyping methods.

Focus on laboratory automatisation

This year we are going to (hopefully) make big leaps with our pipetting robot. The first methods are running now but we will spend many more hours programming additional methods and further optimising old ones. Longterm we want to run our metabarcoding methods mostly automated on our pipetting robot.

More bioinformatics and picking up tutorials

Finally after all the “getting your PhD” stress is over, I hope to spend more time on programming user-friendly and more optimised bioinformatic tools for metabarcoding. Also, I really want to pick up my YouTube science tutorial channel again and produce a “Metabarcoding 101” series. Both things will probably don’t earn me any publications, but having more accessible metabarcoding tutorials / resources out there is really important to spread the knowledge and encourage discussion in the metabarcoding community.

Back in Cali?

I might go on a research stay at a food monitoring startup in California after handing in my PhD thesis. Would be really fun, California is amazing.

 

So already lots of things planned for 2017! Make sure to follow me on twitter to stay up to date ; )

References

  • Eren, Maignien, Sul, Murphy, Grim, Morrison, Sogin (2013). Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data. Methods in Ecology and Evolution
  • Tikhonov, Leach, Wingreen (2015). Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution. The ISME Journal
What to expect in 2017!?
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2 thoughts on “What to expect in 2017!?

  • 2017-03-20 at 13:54
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    Hello Vasco,
    My name is Jo I have to thank you for your Science blog:-)
    I am in my Phd tird year and really struggling with the subject DNA monitoring of sea macrofaulers. We have samples from 12 month submerged scraped panels and still many doubts about the better approach to start.
    I know that you have experience with freshwater macroinvertbrates, so will you please give me your opinion please?
    Thank you very much
    Regards and all the best for your PhD.

    Reply
  • 2017-06-04 at 18:16
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    Please come and visit the Connon Lab at UC Davis if you make a trip to California!
    Best of luck with your PhD,
    Sarah

    Reply

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