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  Diogo Pinho  
  Phone:  
  e-mail: diogofp@ua.pt  
  Category: PhD Student  
  Department: Biology  
  Research group: Marine and Estuarine Ecology
 
 
  Direct URL for this page: http://www.cesam.ua.pt/diogo.pinho  
     
  Thesis title: Cork oak microbiome: Deciphering the rhizosphere microbial community of Quercus suber
  Supervisor: Newton Gomes, Danieal Cleary, Conceição Egas (Biocant)
  Category: BO
  Grant type: BD
  Funding entity: FCT
  Grant reference: SFRH/BD/100665/2014
  Start date: 2015-09-01
  End date: 2019-08-31
Current research interests

My research interests are focused Genomics, Metagenomics and Transcriptomics to study microbiomes using large amounts of data generated by NGS platforms.


Specific research interests


- Microbiome


- Microbial Ecology


- Metagenomics and Biodiversity


- Genomics and Transcriptomics


- Next Generation Sequencing


- DNA and RNA Sequencing


- Rhizosphere


- Cork oak

Participation in Projects

- GenoSuber – Sequencing of the genome of Quercus suber. (CCDRA:ALENT-07-0224-FEDER-001754)


- DoIt – Development and Operationalization of Translation Medicine, from a 20 promotor consortium of portuguese companies and SCT. Specific task: Genetic susceptibility of multisystemic complications of Type 2 Diabetes: novel biomarkers for diagnosis and monitoring of therapy QREN 2012-2015


- HoliWine: Holistic approaches to oenology. (EXCL/AGR-TEC/0336/2012)


- The indigenous microbiome of Portuguese wine fermentations. (PTDC/AGR-ALI/098292/2008)

Work and Research Experience

2015-present: PhD Student


Biocant and University of Aveiro (CESAM)


PhD student grant to develop the thesis "Cork oak microbiome: Deciphering the rhizosphere microbial community of Quercus suber" (SFRH/BD/100665/2014) under scientific supervision of Conceição Egas (Biocant), Newton Gomes and Daniel Cleary (University of Aveiro). The rhizosphere microbiome plays an important role on plant health and productivity. The high impact of cork at economic and social level in Portugal and the currently cork oak forests declining contribute to start to study the rhizosphere microbiome of Quercus suber. The main goal is to study the natural rhizosphere microbial consortium of healthy and diseased cork oaks and test the hypothesis that a specific microbial community is associated with Q. suber health.


 


2013-2015: Research Fellow


Genoinseq - Next Generation Sequencing Unit at Biocant, Portugal


Genoinseq offers a broad range of next generation sequencing services using Ion Proton (Ion AmpliSeq Exome Service Provider Certification), 454 GS-FLX+ Titanium platform and MiSeq Sequencer (Illumina). Genoinseq provides services to companies and research groups in the field of Life Sciences, collaborates in R&D projects with other companies or institutes and has its own R&D program aimed towards innovation in scientific and technical aspects of sequencing and data analysis.


 


2012-2013: Research Fellow


Genomic's Unit at Biocant, Portugal


The indigenous microbiome of Portuguese wine fermentations


Characterization of complex microbial populations associated with wine fermentation through 454 GS FLX Titanium plataform (Roche). Data processing and analysis obtained by Next Generation Sequencing in collaboration with the Bioinformatics Unit at Biocant.


 


2011-2012: Master Thesis/Research Trainee


Genoinseq - Next Generation Sequencing Unit at Biocant, Portugal


Assessment of Quercus suber Soil Microbiome using DGGE Fingerprints and Barcoded Pyrosequencing


 Metagenomics and biodiversity studies of cork oak soil microbiome through 454 GS FLX Titanium plataform (Roche). Data processing and analysis obtained by Next Generation Sequencing in collaboration with the Bioinformatics Unit at Biocant. Comparison of microbial populations using DGGE at MicroLab of University of Aveiro.


 


2009-2010: Research Fellow


Univerity of Aveiro, Portugal


Metabolomic Study of Mistranslating Yeast by NMR and FTIR Spectroscopy


Metabolomics study of Saccharomyces cerevisiae with mistranslations by NMR and FTIR-ATR in order to understand the role of these errors in aging and cellular degeneration.

Prizes

Best international sequencing run in Ion Proton sequencer in 2014 January (Run RecognitION League, Life Technologies)


1st Prize in the competition of Entrepreneurship "InnovationNow 11". Best Aveiro/ University of Aveiro (2011)

Education

- Biotechnology, MSc (University of Aveiro, 2010-12)


- Biotechnology, BSc (University of Aveiro, 2007-10)

Publications
  1. Pinto C., Pinho D., Cardoso R., Custodio V., Fernandes J., Sousa S., Pinheiro M., Egas C., Gomes A.C. (2015) Wine fermentation microbiome: a landscape from different Portuguese wine appellations. Frontiers In Microbiology. 6, (see details) ISI paper
  2. Pinto C., Pinho D., Sousa S., Pinheiro M., Egas C., Gomes A.C. (2014) Unravelling the Diversity of Grapevine Microbiome. Plos One. 9, 1, (see details) ISI paper
  3. Figueiredo J., Simoes M.J., Gomes P., Barroso C., Pinho D., Conceicao L., Fonseca L., Abrantes I., Pinheiro M., Egas C. (2013) Assessment of the Geographic Origins of Pinewood Nematode Isolates via Single Nucleotide Polymorphism in Effector Genes. Plos One. 8, 12, (see details) ISI paper
  1. Cerqueira T., Pinho D., Egas C., Froufe H., Altermark B., Candeias C., Santos R.S., Bettencourt R. (2015) Microbial diversity in deep-sea sediments from the Menez Gwen hydrothermal vent system of the Mid-Atlantic Ridge. Marine Genomics. (see details)
  1. Pinho D (2012) O Microbioma do Solo: Influência do Estado Fitossanitário do Sobreiro. MSc Thesis. (see details)
    Link: http://ria.ua.pt/handle/10773/10876
  2. Pinho D (2010) Estudo do metaboloma de Saccharomyces cerevisiae com erros de tradução por FTIR-ATR. (see details)
  1. Pinho D Gomes P, Barroso C, Pinheiro M, Henriques I, Correia A, Telles M, Silva C, Egas C Assessment of Quercus suber soil microbiome using DGGE fingerprints and barcoded pyrosequencing. (see details)
  2. Pinho D, Pinto C, Cardoso R, Sousa S, Pinheiro M, Egas C, Gomes AC Microbial Dynamics During wine fermentation. (see details)
  3. Pinho D, Pinto C, Sousa S, Pinheiro M, Gomes AC Microbioma das uvas e fermentações espontâneas de diferentes regiões vitivinícolas portuguesas. (see details)
  4. Pinho D Gomes P, Barroso C, Pinheiro M, Henriques I, Correia A, Telles M, Silva C, Egas C O microbioma do solo e o declínio do sobreiro (Soil microbiome and Cork oak decline). (see details)
  5. Pinho D, Carmona S, Barroso C, Froufe H, Wang X, Simões MJ, Egas C Rapid Exome Sequencing using the Ion Proton System and Ion Ampliseq Technology. (see details)
  6. Pinho D Metagenomics: a cutting-edge approach to microbial communities. (see details)
  7. Pinho D Data interpretation for microbial community characterization. (see details)