03. Understanding the microbiome: How can we determine/analyse it? Technical issues

Vicente Pérez Brocal.
Fundación para el Fomento de la Investigación sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain.

 

[tabs] [tab title=”Presentació ” icon=”desktop” icon_color=”#87B1B5″]<
[/tab] [tab title=”Abstract” icon=”book” icon_color=”#87B1B5″]

Understanding the microbiome: How can we determine/analyse it? Technical issues.

 

Vicente Pérez Brocal.
Fundación para el Fomento de la Investigación sanitaria y Biomédica de la Comunitat Valenciana (FISABIO), Valencia, Spain.

 

The microbiome harboured in the human respiratory tract represents a complex ecosystem, consisting of more than 600 species, and subject to environmental fluctuations and changes. Determining the diversity of such elusive community has been a permanent challenge for researchers until the advent of metagenomics contributed to circumvent it. However, these culture-independent approaches are not exempt of limitations, not only in the experimental steps, but also during the bioinformatic analyses arisen from the huge amount of data generated. Those have to be suitably processed in order to extract proper conclusions, therefore avoiding erroneous interpretations of the results. Here, the relevance of choosing an appropriate database is set out. Moreover, after outlining the initial processing steps, the problems of chimeras and their removal are addressed. Finally, other shortcomings of the metagenomic approach are also tackled and suggestions to avoid them in order to reliably assign taxonomy are suggested. The main conclusion is that there are still technical issues associated to the biological limitations inherent to the data themselves and the databases that bioinformatic tools alone cannot easily discriminate, despite our efforts. Therefore, we must be cautious when it comes to draw conclusions, since results represent usually a trade-off between their accuracy and the necessity to present them unambiguously.

[/tab] [tab title=”Currículum Vitae” icon=”briefcase” icon_color=”#87B1B5″]

Vicente Pérez Brocal. 

I got my degree in Biology, at the University of Valencia in 2001, where I did my PhD research project in the program ‘Biodiversity and Evolutionary Biology’ from 2002 to 2006. I worked on bacterial genome reduction and minimal genomes. I sequenced the smallest bacterial genome at that time, that of Buchnera aphidicola, the primary endosymbiont from the cedar aphid.

Next, I worked as a postdoctoral researcher at the London School of Hygiene and Tropical Medicine from the University of London, from 2006 to 2009. My topic there was the genetic evolution of mitochondrial and related organelles during the transition from an aerobic to a strictly anaerobic lifestyle working on Blastocystis.

Next, I held a ‘Sara Borrell’ contract at the ‘Genomics and Health Area’ at the, FISABIO (Valencia), from 2010 to 2014 to work on Metagenomics of microbial and viral communities associated to inflammatory bowel disease and other pathologies affecting the gastrointestinal tract. Since then, I have also collaborated with groups of Barcelona (respiratory microbiome and virome), Madrid (celiac disease virome), Italy (fermenting bacteria), Girona (gut microbiota-brain relationship) etc., with  a contract at the FISABIO.

[/tab] [/tabs]

Translate »