- Thesis title: Cork oak microbiome: Deciphering the rhizosphere microbial community of Quercus suber
- Supervisor: Newton Gomes, Danieal Cleary, Conceição Egas (Biocant)
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- Department: Biology
- Research Group: Coastal and Deep-Ocean Ecology & Conservation (CDEC) 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
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 more
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 more
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 more
Pinho D (2010) Estudo do metaboloma de Saccharomyces cerevisiae com erros de tradução por FTIR-ATR. . See more
Pinho D, Pinto C, Cardoso R, Sousa S, Pinheiro M, Egas C, Gomes AC Microbial Dynamics During wine fermentation. 36th World Congress of Vine & Wine, June 2-7, 2013, Bucharest, Romania. See more
Pinho D, Pinto C, Sousa S, Pinheiro M, Gomes AC Microbioma das uvas e fermentações espontâneas de diferentes regiões vitivinícolas portuguesas. 9.º Simpósio de Vitivinicultura do Alentejo, May 15-17, 2013, . See more
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). I Encontro Ibérico sobre o Declínio do Montado (1st Iberian Meeting on the Cork oak forest decline), May 17-18, 2013, Beja, Portugal. See more
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. Ion Mini Tour by Life Technologies, May 12-14, 2014, CHUS (Santiago de Compostela, Spain), IBMC (Porto, Portugal) and Biocant (Cantanhede, Portugal). See more
Pinho D Metagenomics: a cutting-edge approach to microbial communities. Advanced Course in Biochemical and Molecular Techniques in Ecology, December 2, 2014, Cantanhede, Portugal. See more
Pinho D Data interpretation for microbial community characterization. Advanced Course in Biochemical and Molecular Techniques in Ecology, December 3, 2014, Cantanhede, Portugal. See more
- Biotechnology, MSc (University of Aveiro, 2010-12)
- Biotechnology, BSc (University of Aveiro, 2007-10)
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)
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.
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)
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
- Microbial Ecology
- Metagenomics and Biodiversity
- Genomics and Transcriptomics
- Next Generation Sequencing
- DNA and RNA Sequencing
- Cork oak
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