Microbiomes, Metabolism and Omics

Conceição Egas

PhD, Principal Investigator

Microbiomics, the genomic study of a population of microbes, is a recent field propelled by the rapid evolution of high-throughput sequencing. Microbiomics facilitates the study of the diversity and the role of microorganisms in diverse habitats. The study of microbial communities associated with hosts has received attention by the recognition of the important role of microbes in host development, homeostasis and the pathophysiology of chronic diseases including type 2 diabetes or non-alcoholic fatty liver disease.

The Advanced Microbiomics group takes advantage of the accumulated know-how in the field of bacterial genome sequencing, microbial community profiling (structure and dynamics) and metagenomics of the PI and her team and the available high-throughput DNA sequencing and HPC infrastructures at CIBB to address the following research lines:

  • Microbiomes and hosts: Investigate the role of microbes in host-associated communities through network analysis to derive patterns of co-occurrence, microbial relationships or high-level functional roles. Identify key organisms and derived biomarkers;
  • Microbes and disease: Characterize adaptation of microbes to environmental niches to understand adaptation to human hosts and disease, in particular the relationship between the gut microbiome and cardiometabolic diseases. Investigate conserved and newly acquired biochemical and metabolic functions through comparative genomics of Bacteria and Archaea from extreme environments to gut to identify key metabolic functions in disease;
  • Biotechnology applications: Identify novel protein families with biotechnological potential from extremophile communities using protein interaction network approaches, focusing on glycosyl hydrolases, lipases and proteases;

Collaboration with other research groups at the Metabolism, Aging and Disease research line allows to correlate genotype with phenotype, including investigating the regulation of host metabolism by bacterial metabolites.

Group Members

Group Members

Conceição Egas (PhD), Cristina Barroso, Daniel Martins, Diogo Pinho, Gabriela Simões, Luciana Pinto, Nadine dos Santos, Raquel Varandas.

Selected Publications

da Costa MS, Albuquerque L, Rainey FA, Froufe HJC, Roxo I, Raposo P and Egas C (2019). Elioraea. In: Whitman, WB (Ed), Bergey's Manual of Systematics of Archaea and Bacteria, pp 1–6. Published by John Wiley & Sons, Inc., in association with Bergey's Manual Trust. DOI 10.1002/9781118960608.gbm01458.

Albuquerque L, Castelhano N, Raposo P, Froufe HJC, Severino R, Roxo I, Gregório I, Barroso C, Egas C, and da Costa MS. (2020). Comparative genome sequence analysis of the strains of the species of the genus Tepidimonas and the description of a novel species Tepidimonas charontis sp. nov. International Journal of Systematic and Evolutionary Microbiology. DOI 10.1099/ijsem.0.003942.

Severino, R., Froufe, H. J. C., Barroso, C., Albuquerque, L., Lobo-da-Cunha, A., da Costa, M. S., & Egas, C. (2019). High-quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep-branching lineages of the phylum actinobacteria. MicrobiologyOpen, 8(9) doi:10.1002/mbo3.840.

Raposo, P., Viver, T., Albuquerque, L., Froufe, H., Barroso, C., Egas, C., ... da Costa, M. S. (2019). Transfer of Meiothermus chliarophilus (Tenreiro et al.1995) (Nobre et al. 1996), Meiothermus roseus (Ming et al. 2016), Meiothermus terrae (Yu et al. 2014) and Meiothermus timidus (Pires et al. 2005), to Calidithermus gen. nov., as Calidithermus chliarophilus comb. nov., Calidithermus roseus comb. nov., Calidithermus terrae comb. nov. and Calidithermus timidus comb. nov., respectively, and emended description of the genus Meiothermus. International Journal of Systematic and Evolutionary Microbiology, 69(4), 1060-1069. doi:10.1099/ijsem.0.003270.

Reis, A. C., Kolvenbach, B. A., Chami, M., Gales, L., Egas, C., Corvini, P. F. -., & Nunes, O. C. (2019). Comparative genomics reveals a novel genetic organization of the sad cluster in the sulfonamide-degrader 'Candidatus Leucobacter sulfamidivorax' strain GP. BMC Genomics, 20(1), 885. doi:10.1186/s12864-019-6206-z.

Ramos, A. M., Usié, A., Barbosa, P., Barros, P. M., Capote, T., Chaves, I., ... Gonçalves, S. (2018). The draft genome sequence of cork oak. Scientific Data, 5 doi:10.1038/sdata.2018.69.

Pinto, C., Sousa, S., Froufe, H., Egas, C., Clément, C., Fontaine, F., & Gomes, A. C. (2018). Draft genome sequence of Bacillus amyloliquefaciens subsp. plantarum strain fito-F321, an endophyte microorganism from Vitis vinifera with biocontrol potential. Standards in Genomic Sciences, 13(1) doi:10.1186/s40793-018-0327-x.

Albuquerque A, Polónia ARM, Barroso C, Froufe HJC, Lage O, Lobo-da-Cunha A, Egas C, da Costa MS. (2018). Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov. International Journal of Systematic and Evolutionary Microbiology. 68(4):982-989. doi: 10.1099/ijsem.0.002556.

Cerqueira T, Barroso C, Froufe H, Egas C, Bettencourt R. (2018). Metagenomic signatures of microbial communities in the deep-sea hydrothermal sediments of Azores vent fields. Microbial Ecology. 76(2):387-403. DOI:10.1007/s00248-018-1144-x.

Cerqueira, T, Pinho, D, Froufe, H, Santos, RS, Bettencourt, R, Egas, C. 2017. Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores. Microb Ecol (2017). doi:10.1007/s00248-017-0943-9.

Selected Grants

Metafluidics: Advanced toolbox for rapid and cost-effective functional metagenomic screening - microbiology meets microfluidics. European Commission (2016-2020). PI: Conceição Egas.

GenomePT. Project for the development and implementation of research infrastructures within RNIE. 01/SAICT/2016. 2017-2019. PI: Conceição Egas.

Immunotargeting efflux systems for therapeutic modulation of multidrug resistant bacteria. FCT - Fundação para a Ciência e Tecnologia (2018-2021). PI: Ricardo Pires.

Interações nemátode da madeira do pinheiro-árvore hospedeira: à descoberta de alternativas sustentáveis para a gestão da doença da murchidão do Pinheiro. FCT - Fundação para a Ciência e Tecnologia (2018-2021). PI: Luis Fonseca.

Symbioreactor - Sustainable Production of Bioactive Metabolites from Microbial Symbionts of Marine Sponges and Corals. Fundo Azul (2020-2022) PI: Conceição Egas.

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