???global.info.a_carregar???
I am an Assistant Researcher at the Faculty of Pharmacy, University of Lisbon, with over 15 years of experience in Microbiology, Bacterial Signal Transduction, Synthetic Biology, and One Health-focused pathogen surveillance. My scientific trajectory spans fundamental and applied microbiology, synthetic genetic circuits, bacteriophage biology, and environmental genomics, integrating laboratory, computational, and field-based methodologies. This multidisciplinary background positions me strongly to lead innovative projects aligned with national research priorities in antimicrobial resistance (AMR), infectious diseases, and biotechnological innovation. My research has combined molecular biology, genomics, bioinformatics, synthetic biology, and environmental surveillance to address pressing challenges in bacterial physiology, pathogen detection, and antimicrobial strategies. Early in my career, I contributed seminal work on the viable-but-nonculturable (VBNC) state in foodborne pathogens, producing highly cited studies and a comprehensive PhD on Listeria monocytogenes and Escherichia coli resuscitation mechanisms. During international postdoctoral training (LMU Munich, TU Dresden, University of Copenhagen), I became recognised for my contributions to the study of extracytoplasmic function (ECF) siga factors - key regulators of bacterial stress responses - and their application as tunable genetic switches. This work resulted in high-impact publication (e.g., Nature Microbiology, Nucleic Acids Research, Molecular Microbiology, iScience) and laid the foundation for my current line of research in synthetic biology applied to health. Since returning to Portugal, I consolidated and interdisciplinary research portfolio at iMed.ULisboa and CE3C/FCUL, leading and contributing to projects on environmental and genomic surveillance of Mycobacterium bovis, a Mycobacterium tuberculosis complex bacteria, phage-based therapeutics, and AMR spread at the livestock-wildlife interface. I am co-author of multiple studies demonstrating, for the first time in Portugal, the detection of viable environmental M. bovis in multi-host systems and the integration of flow cytometry, PCR, and ecological modelling to map transmission hotspots. These contributions directly address One Health priorities and have supported national authorities and surveillance programs. I have a consistent publication record across top journals in microbiology, infectious diseases, genomics, and synthetic biology, including recent first-author or co-leading works in FEMS Microbiology Ecology, Science of the Total Environment, Journal of Hazardous Materials, IJMS, and Microbiology Spectrum. My productivity reflects both independence and leadership, with >20 peer-reviewed articles, numerous conference contributions, and active participation as reviewer and editorial board member for international journals. I currently lead the project Engineering Probiotics for Production and Delivery of Protein Drugs (PEX 2023.12038) as Principal Investigator, demonstrating my capacity to coordinate funding, supervise students, and drive innovative research agendas. My experience supervising MSc and PhD trainees, organizing scientific events, and serving as main arguer in academic juries further reinforces my leadership profile. I have also secured competitive individual funding throughout my career, including an FCT CEED.IND contract, an EMBO Short-Term Fellowship, a Marie-Curie Intra-European Fellowship, and an FCT PhD Scholarship. Overall, my career combines international excellence, interdisciplinarity, and proven ability to generate impactful results in microbiology, synthetic biology, and antimicrobial strategies. I am well positioned to lead competitive PTDC projects that integrate fundamental research with translational potential, aligned with national and European priorities in AMR, One Health, and biotechnological innovation.
Identification

Personal identification

Full name
Daniela Sofia Marques Pinto
Date of birth
1984/04/06
Gender
Female

Citation names

  • Pinto, Daniela

Author identifiers

Ciência ID
D51B-438E-D184
ORCID iD
0000-0002-2405-8755
Google Scholar ID
ApwDzmEAAAAJ&hl
Researcher Id
D-1496-2013
Scopus Author Id
56720128200

Email addresses

  • dspinto@ff.ulisboa.pt (Professional)

Telephones

Telephone
  • (+351) 21794640 Ext.: 514515 (Professional)

Addresses

  • Faculdade de Farmácia da Universidade de Lisboa, Avenida Professor Gama Pinto, 1649-003, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Microbiology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Advanced (C1) Proficiency (C2) Proficiency (C2)
German Elementary (A2) Elementary (A2) Beginner (A1) Elementary (A2) Elementary (A2)
Education
Degree Classification
2013/11/11
Concluded
Biology (Doutoramento)
Major in Speciality: Microbiology
Universidade de Lisboa Faculdade de Ciências, Portugal
"Understanding Resuscitation Process of Viable But Nonculturable Cells of Two Food Borne Pathogens: Escherichia Coli and Listeria Monocytogenes" (THESIS/DISSERTATION)
Distinção e louvor
2007/10/25
Concluded
Molecular Biology and Genetics (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Caracterização de enterococos isolados de areias" (THESIS/DISSERTATION)
18
2006/07/18
Concluded
Microbiology and Genetics (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
14
Affiliation

Science

Category
Host institution
Employer
2024/10 - Current Auxiliary Researcher (Research) Universidade de Lisboa Faculdade de Farmácia, Portugal
2022/02 - 2024/09 Researcher (Research) Centro de Ecologia Evolução e Alterações Ambientais, Portugal
2020/01 - 2022/02 Researcher (Research) Universidade de Lisboa Instituto de Investigação do Medicamento, Portugal
2019/07 - 2019/12 Researcher (Research) Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2016/01 - 2019/06 Researcher (Research) Technische Universität Dresden, Germany
2018/07 - 2018/09 Visiting Researcher (Research) Københavns Universitet, Denmark
2014/02 - 2015/12 Researcher (Research) Ludwig Maximilians Universität München Department Biologie I, Germany
2009/03 - 2013/11 Research Trainee (Research) Universidade de Lisboa Faculdade de Ciências, Portugal
2010/05 - 2010/08 Visiting Researcher (Research) Newcastle University, United Kingdom
2007/05 - 2009/12 Researcher (Research) Instituto de Biologia Experimental e Tecnológica, Portugal
2007/11 - 2007/11 Visiting Researcher (Research) Universiteit Gent, Belgium
2006/09 - 2007/10 Research Trainee (Research) Instituto de Biologia Experimental e Tecnológica, Portugal
Projects

Grant

Designation Funders
2018/07 - 2018/09 Divergent evolution and horizontal gene transfer in the extracytoplasmic function sigma factor protein family
EMBO Short-Term Fellowship 7462
Post-doc Fellow
Center for Macroecology, Evolution and Climate, Denmark
Concluded
2014 - 2016 Synthetic ECFdevices - Extracytoplasmic Function (ECF) Sigma Factors: From Regulatory Specificity to Synthetic
FP7/2007-2013-628509
Post-doc Fellow
Conseil de l'Union Europeenne
2009 - 2013 Understanding resuscitation process of two foodborne pathogens: Escherichia coli and Listeria monocytogenes
SFRH/BD/46111/2008
PhD Student Fellow
Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2025/02/20 - Current Engineering Probiotics for Production and Delivery of Protein Drugs
2023.12038.PEX
Principal investigator
2023/10/16 - Current OCELOT: AbOrdagens EmpiriCo-MEcanísticas na ModeLaçãO da Resistência a AnTimicrobianos sob o Paradigma de Uma Só Saúde
2022.01539.PTDC
Researcher
Centro de Ecologia Evolução e Alterações Ambientais, Portugal
Fundação para a Ciência e a Tecnologia
2023/01 - 2023/07/31 Systematic Surveillance of SARS-CoV-2 and its variants in wastewaters, Portugal
060701/2021/864489/SUB/ENV.C2
Researcher
Centro de Ecologia Evolução e Alterações Ambientais, Portugal
Concluded
2022/02 - 2022/12 ControlO de tubercuLOSe na interface bovinoS-faUna Silvestre com recurso a soluções inovadoras inspiradas na natureza
PTDC/CVT-CVT/29783/2017
Researcher
2020/01 - 2022/01 Fusion of complementary antibacterial functions as a new strategy to generate alternative agents to fight antibiotic-resistant pathogens
PTDC/EMD-EMD/28109/2017
Researcher
Universidade de Lisboa Faculdade de Farmácia, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2015 - 2019 ECFexpress – an orthogonal, organism-independent expression platform based on extracytoplasmic function (ECF) sigma factors
ERASynBio2-ECFexpress
Researcher
Technische Universität Dresden, Germany

Ludwig-Maximilians-Universitat Munchen, Germany
Bundeministerium für Bildung und Forschung
Ongoing
2007 - 2008 LARGE SCALE SCREENING OF POTENTIAL KEY FACTORS INVOLVED IN THE COMMENSALISM/VIRULENCE TRANSITION OF ENTEROCOCCUS FAECALIS
info:eu-repo/grantAgreement/FCT/SFRH/SFRH2%FBI2%F330842%F2007/PT
Research Fellow
Instituto de Biologia Experimental e Tecnológica, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Pinto, Daniela; Mascher, Thorsten. "The ECF Classification: A Phylogenetic Reflection of the Regulatory Diversity in the Extracytoplasmic Function s Factor Protein Family". In Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, 64-96. John Wiley & Sons, Inc., 2016.
    10.1002/9781119004813.ch7
Conference abstract
  1. Pereira, André C.; Pinto, Daniela; Cunha, Mónica V.. "Breaking the Wall: Mycobacterium bovis transmission at the animal-environment interface". Paper presented in Microbiotec23, Covilhã, 2023.
  2. Pereira, André C.; Pinto, Daniela; Lourenço, José; Ana Rosa Botelho; Cunha, Mónica V.. "A new understanding of the transmission landscape of Mycobacterium bovis boosted by single cell analyses, genomics, and ecological modeling". Paper presented in GenomePT Symposium 2023, Lisboa, 2023.
  3. Pereira, André C.; Reis, Ana C.; Pinto, Daniela; Lourenço, José; Botelho, Ana; Cunha, Mónica V.. Corresponding author: Cunha, Mónica V.. "An ecosystems view of animal tuberculosis powered by environmental genomics and phylodynamics". Paper presented in 2nd Egas Moniz One Health Simposium, Almada, 2023.
Conference poster
  1. Pinto, Daniela; São-José C. Corresponding author: Pinto, Daniela. "Mapping Genomic Safe Harbors in Lactobacillus acidophilus for Synthetic Circuit Integration". Paper presented in Congress of Microbiology and Biotechnology 2025, 2025.
  2. Pinto, Daniela; São-José C. Corresponding author: São-José C. "Enhancing Phage-Based Therapies: Exploring Teichoicases Against Staphhylococcus aureus". Paper presented in iMed.Ulisboa Meeting 2025, 2025.
  3. Pinto, Daniela; Inês Mendes; Cunha, Mónica V.. "Phage hunting across Mycobacterium bovis genomes". Paper presented in Microbiotec23, 2023.
  4. Reis, Ana C.; Pinto, Daniela; Monteiro, Silvia; Ricardo Santos; João Vieira Martins; Cunha, Mónica V.. "SARS-CoV-2 S gene sequencing in wastewater samples enables early lineages detection and uncovers rare mutations". Paper presented in Microbiotec23, 2023.
  5. Pinto, Daniela; Espregueira Themudo, Gonçalo; Pereira, André C.; Ana Rosa Botelho; Cunha, Mónica V.. "Rescue of Mycobacterium bovis DNA obtained from cultured strains during official surveillance of animal tuberculosis". Paper presented in Microbiotec23, 2023.
  6. Pereira, André C.; Pinto, Daniela; Mónica V. Cunha. "Real-time environmental monitoring of Mycobacterium bovis in a multi-host transmission scenario". Paper presented in Congress of the Iberian Society of Cytometry, 2023.
  7. Gonçalo, Raquel; Pinto, Daniela; Gouveia, Ana; São-José, Carlos. Corresponding author: São-José, Carlos. "The strong bactericidal action of a chimeric enzybiotic VAL-based against Staphylococcus aureus, even in conditions that support bacterial growth". Paper presented in iMed.Ulisboa Meeting 2022, 2022.
  8. Pinto, Daniela; Gonçalo, Raquel; Ana Isabel Gouveia; São-José, Carlos. "A VAL-based enzybiotic displaying strong bactericidal action against Staphylococcus aureus in growth supporting media". Paper presented in VoM2022 - 6th Viruses of Microbes International Meeting, 2022.
  9. Pinto, Daniela; Gonçalo, Raquel; Mariana Louro; Marta Sousa Silva; Guillem Hernandez; Tiago N. Cordeiro; Carlos Cordeiro; et al. "On the occurrence and multimerization of two polypeptide phage endolysins encoded in single genes". Paper presented in VoM2022 - 6th Viruses of Microbes International Meeting, 2022.
  10. Pinto, Daniela; Raquel Gonçalo; Sao-Jose, Carlos. "Phage Endolysin Genes with Two In Frame Overlapping ORFs – Why and Where Can We Find Them?". Paper presented in World Microbe Forum, 2021.
  11. Ana Isabel Gouveia; Pinto, Daniela; Sao-Jose, Carlos. "Synergistic Bacteriolytic Action of Phage Endolysins and Antimicrobial Peptides". Paper presented in World Microbe Forum, 2021.
  12. Ana Isabel Gouveia; Pinto, Daniela; Carlos São-José. "Enhancing endolysins bacteriolytic activity through their combined action with antimicrobial peptides". Paper presented in iMed.ULisboa Meeting 2021, 2021.
  13. Raquel Gonçalo; Pinto, Daniela; Carlos São-José. "Two-polypeptide endolysins encoded by a single gene: phage distribution and implications for lytic activity". Paper presented in iMed.ULisboa Meeting 2021, 2021.
  14. Pinto, Daniela; Gonçalo, Raquel; Carlos São-José. "Heteromeric phage endolysins not just an eccentricity of few". Paper presented in Microbiotec 21, 2021.
  15. Ana Isabel Gouveia; Pinto, Daniela; São-José, Carlos. "Determinants of bacterial tolerance to endolysin-based enzybiotics". Paper presented in Microbiotec 21, 2021.
  16. Pinto, Daniela; Dayane Araújo; Franziska Duerr; Rute da Fonseca; Georg Fritz; Friederike Froriep; Xiaoluo Huang; et al. "Extracytoplasmic function sigma factors: diversity, evolution, mechanisms and synthetic biology applications". Paper presented in Microbiotec, 2019.
  17. Liu, Qiang; Pinto, Daniela; Mascher, Thorsten. "Characterization of a novel group of C-terminal extension containing extracytoplasmic function (ECF) ECF42 sigma factor". Paper presented in How microorganisms view their wold, 2018.
  18. Pinto, Daniela; Wiegand, Sandra; Jogler, Christian; Mascher, Thorsten. "New regulatory mechanisms of ECFs in Planctomycetes". Paper presented in How microorganisms view their wold, 2018.
  19. Dürr, F; Pinto, Daniela; Mascher, Thorsten. "A census of extracytoplasmic function sigma factors in underrepresented and newly discovered bacterial phyla". Paper presented in How microorganisms view their world, 2018.
  20. Pinto, Daniela; Dürr, F; Froriep, F; Liu, Qiang; Huang, Xiaoluo; Wu, Hao; Mauri, Marco; Fritz, Georg; Mascher, Thorsten. "Extracytoplasmic function sigma factors as orthogonal switches in Bacillus subtilis". Paper presented in SB7.0: the seventh international meeting on synthetic biology, 2017.
  21. Pinto, Daniela; Dürr, F; Araújo, D; Liu, Qiang; Mascher, Thorsten. "Modulation of the behavior of an Extracytoplasmic Function sigma factor (ECF)-based genetic switch". Paper presented in Mechanisms of Gene Regulation, 2016.
  22. Mauri, Marco; Pinto, Daniela; Vecchione, Stefano; Wu, Hao; Mascher, Thorsten; Fritz, Georg. "Implementation, analysis and mathematical modelling of ECF sigma factor-based synthetic gene cascades in E. coli and B. subtilis". Paper presented in Mechanisms of Gene Regulation, 2016.
  23. Liu, Qiang; Pinto, Daniela; Mascher, Thorsten. "Functional characterization of novel Extracytoplasmic Function (ECF) sigma factors from Streptomyces venezuelae". Paper presented in VAAM General meeting 2016, 2016.
  24. Pinto, Daniela; Liu, Qiang; Mascher, Thorsten. "Optimization of an extracytoplasmic function sigma factor based switch". Paper presented in CAS Conference Synthetic Biology II, 2015.
  25. Huang, Xiaoluo; Tran, NT; Bush, M; Pinto, Daniela; Mascher, Thorsten; Buttner, MJ. "Defining the regulon of genes controlled by SigE, a key regulator of cell envelope stress in Streptomyces coelicolor". Paper presented in VAAM General Meeting 2015, 2015.
  26. Dürr, F; Froriep, F; Pinto, Daniela; Mascher, Thorsten. "En route to an optimized synthetic promoter environment for Bacillus subtilis". Paper presented in VAAM General Meeting 2015, 2015.
  27. Pinto, Daniela; Huang, X; Fritz, Georg; Mascher, Thorsten. "Actinobacterial Intelligence: a comprehensive survey of signal transduction in this phylum". Paper presented in VAAM General Meeting 2014, 2014.
  28. Pinto, Daniela; Huang, Xiaoluo; Fritz, Georg; Mascher, Thorsten. "Actinobacterial Intelligence: a comprehensive survey of signal transduction in this phylum". Paper presented in Mechanisms of Gene Regulation, 2014.
  29. Costa, OC; Pinto, Daniela; Chambel, Lélia. "Injured cells: an unrecognized path for viable but nonculturable state?". Paper presented in How dead is dead III: Life cycles, 2013.
  30. Pinto, Daniela; Santos, Mário A.; Chambel, Lélia. "Resuscitation of VBNC Escherichia coli: a way to escape death". Paper presented in How dead is dead III: Life cycles, 2013.
  31. Pinto, Daniela; Sao-Jose, Carlos; Santos, Mário A.; Chambel, Lélia. "Listeria monocytogenes transglycosylase as a resuscitation promoting factor". Paper presented in Great Wall Symposium 2011, 2011.
  32. Pinto, Daniela; Sao-Jose, Carlos; Santos, Mário A.; Chambel, Lélia. "Viable but nonculturable state in foodborne pathogens: a quest for resuscitation". 2011.
  33. Pinto, Daniela; Santos, Mário A.; Chambel, Lélia. "Escherichia coli VBNC Cells: Variability In Resuscitation Factors". Paper presented in 22nd International ICFMH Symposium, 2010.
  34. Pinto, Daniela; Santos, Mário A.; Chambel, Lélia. "Inability to resuscitate viable-but-nonculturable cells of Escherichia coli and Listeria monocytogenes". Paper presented in III International Conference on Environmental, Industrial and Applied Microbiology, 2009.
  35. Pinto, Daniela. "Characterization of Enterococci isolated from sand". Paper presented in 108th General Meeting from American Society for Microbiology, 2008.
Journal article
  1. Pinto, Daniela; Mendes, Inês; Cunha, Mónica V. Corresponding author: Cunha, Mónica V. "Genomic survey reveals no detectable bacteriophage activity in Mycobacterium bovis across a large population". FEMS Microbiology Ecology 101 8 (2025): https://doi.org/10.1093/femsec/fiaf072.
    Open access • Published • 10.1093/femsec/fiaf072
  2. Ferreira, Eduardo M.; Cunha, Mónica V.; Duarte, Elsa L.; Mira, António; Pinto, Daniela; Mendes, Inês; Pereira, André C.; et al. "Mapping high-risk areas for Mycobacterium tuberculosis complex bacteria transmission: Linking host space use and environmental contamination". Science of The Total Environment 953 (2024): 176053. http://dx.doi.org/10.1016/j.scitotenv.2024.176053.
    Open access • Accepted • 10.1016/j.scitotenv.2024.176053
  3. Pereira, André C.; Pinto, Daniela; Cunha, Mónica V.. "First time whole genome sequencing of Mycobacterium bovis from the environment supports transmission at the animal-environment interface". Journal of Hazardous Materials 472 (2024): 134473. http://dx.doi.org/10.1016/j.jhazmat.2024.134473.
    Open access • Accepted • 10.1016/j.jhazmat.2024.134473
  4. Pinto, Daniela; Themudo, Gonçalo; Pereira, André C.; Botelho, Ana; Cunha, Mónica V.. "Rescue of Mycobacterium bovis DNA Obtained from Cultured Samples during Official Surveillance of Animal TB: Key Steps for Robust Whole Genome Sequence Data Generation". International Journal of Molecular Sciences 25 7 (2024): 3869. http://dx.doi.org/10.3390/ijms25073869.
    Open access • Accepted • 10.3390/ijms25073869
  5. Reis, Ana C.; Pinto, Daniela; Monteiro, Sílvia; Santos, Ricardo; Martins, João Vieira; Sousa, Alexandra; Páscoa, Rute; Lourinho, Rita; Cunha, Mónica V.. Corresponding author: Cunha, Mónica V.. "Systematic SARS-CoV-2 S-gene sequencing in wastewater samples enables early lineage detection and uncovers rare mutations in Portugal". Science of The Total Environment (2024): 170961. http://dx.doi.org/10.1016/j.scitotenv.2024.170961.
    10.1016/j.scitotenv.2024.170961
  6. Ana Isabel Gouveia; Pinto, Daniela; Vítor, Jorge M. B.; São-José, Carlos. Corresponding author: São-José, Carlos. "Cellular and Enzymatic Determinants Impacting the Exolytic Action of an Anti-Staphylococcal Enzybiotic". International Journal of Molecular Sciences 25 1 (2023): 523. http://dx.doi.org/10.3390/ijms25010523.
    Open access • Published • 10.3390/ijms25010523
  7. Pereira, André C.; Pinto, Daniela; Cunha, Mónica V.. Corresponding author: Cunha, Mónica V.. "Unlocking environmental contamination of animal tuberculosis hotspots with viable mycobacteria at the intersection of flow cytometry, PCR, and ecological modelling". Science of The Total Environment 891 (2023): 164366. http://dx.doi.org/10.1016/j.scitotenv.2023.164366.
    10.1016/j.scitotenv.2023.164366
  8. Pinto, Daniela; Gonçalo, Raquel; Louro, Mariana; Silva, Marta Sousa; Hernandez, Guillem; Cordeiro, Tiago N.; Cordeiro, Carlos; São-José, Carlos. "On the Occurrence and Multimerization of Two-Polypeptide Phage Endolysins Encoded in Single Genes". Microbiology Spectrum 10 4 (2022): http://dx.doi.org/10.1128/spectrum.01037-22.
    Open access • Accepted • 10.1128/spectrum.01037-22
  9. Gouveia, Ana; Pinto, Daniela; Veiga, Helena; Antunes, Wilson; Pinho, Mariana G.; São-José, Carlos. "Synthetic antimicrobial peptides as enhancers of the bacteriolytic action of staphylococcal phage endolysins". Scientific Reports 12 1 (2022): http://dx.doi.org/10.1038/s41598-022-05361-1.
    Published • 10.1038/s41598-022-05361-1
  10. Pinto, Daniela; da Fonseca, Rute R. "Evolution of the extracytoplasmic function s factor protein family". NAR Genomics and Bioinformatics 2 1 (2020): http://dx.doi.org/10.1093/nargab/lqz026.
    Published • 10.1093/nargab/lqz026
  11. Pinto, Daniela; Liu, Qiang; Mascher, Thorsten. "ECF sigma factors with regulatory extensions: The one-component systems of the sigma universe". Molecular Microbiology (2019): https://onlinelibrary.wiley.com/doi/10.1111/mmi.14323.
    Published • 10.1111/mmi.14323
  12. Pinto, Daniela; Dürr, Franziska; Froriep, Frederike; Araújo, Dayane; Liu, Qiang; Mascher, Thorsten. "Extracytoplasmic function sigma factors can be implemented as robust heterologous genetic switches in Bacillus subtilis". iScience (2019): http://dx.doi.org/10.1016/j.isci.2019.03.001.
    Published • 10.1016/j.isci.2019.03.001
  13. Tran, Ngat T; Huang, Xiaoluo; Hong, Hee-Jeon; Bush, Matthew J; Chandra, Govind; Pinto, Daniela; Bibb, Maureen J; et al. "Defining the regulon of genes controlled by sE, a key regulator of the cell envelope stress response in Streptomyces coelicolor". Molecular Microbiology (2019): https://doi.org/10.1111/mmi.14250.
    Published • 10.1111/mmi.14250
  14. Sandra Wiegand; Mareike Jogler; Christian Boedeker; Pinto, Daniela; John Vollmers; Elena Rivas-Marin; Timo Kohn; et al. "Cultivation and functional characterization of 79 Planctomycetes uncovers their unique biology". Nature Microbiology (2019):
    Published • 10.1038/s41564-019-0588-1
  15. Liu, Qiang; Pinto, Daniela; Mascher, Thorsten. "Characterization of the Widely Distributed Novel ECF42 Group of Extracytoplasmic Function sigma Factors in Streptomyces venezuelae". Journal of Bacteriology 200 21 (2018): http://dx.doi.org/10.1128/jb.00437-18.
    Published • 10.1128/jb.00437-18
  16. Pinto, Daniela; Vecchione, Stefano; Wu, Hao; Mauri, Marco; Mascher, Thorsten; Fritz, Georg. "Engineering orthogonal synthetic timer circuits based on extracytoplasmic function sigma factors". Nucleic Acids Research 46 14 (2018): 7450-7464. http://dx.doi.org/10.1093/nar/gky614.
    Published • 10.1093/nar/gky614
  17. Kleine, Britta; Chattopadhyay, Ava; Polen, Tino; Pinto, Daniela; Mascher, Thorsten; Bott, Michael; Brocker, Melanie; Freudl, Roland. "The three-component system EsrISR regulates a cell envelope stress response in Corynebacterium glutamicum". Molecular Microbiology 106 5 (2017): 719-741. http://dx.doi.org/10.1111/mmi.13839.
    Published • 10.1111/mmi.13839
  18. Pinto, Daniela; Mascher, Thorsten. "(Actino)Bacterial “intelligence”: using comparative genomics to unravel the information processing capacities of microbes". Current Genetics 62 3 (2016): 487-498. http://dx.doi.org/10.1007/s00294-016-0569-3.
    Published • 10.1007/s00294-016-0569-3
  19. Huang, Xiaoluo; Pinto, Daniela; Fritz, Georg; Mascher, Thorsten. "Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum". Journal of Bacteriology 197 15 (2015): 2517-2535. http://dx.doi.org/10.1128/jb.00176-15.
    10.1128/jb.00176-15
  20. Pinto, Daniela; Santos, Mário A.; Chambel, Lélia. "Thirty years of viable but nonculturable state research: Unsolved molecular mechanisms". Critical Reviews in Microbiology 41 1 (2013): 61-76. http://dx.doi.org/10.3109/1040841x.2013.794127.
    Published • 10.3109/1040841x.2013.794127
  21. Pinto, D.; Sao-Jose, C.; Santos, M. A.; Chambel, L.. "Characterization of two resuscitation promoting factors of Listeria monocytogenes". Microbiology 159 Pt_7 (2013): 1390-1401. http://dx.doi.org/10.1099/mic.0.067850-0.
    Published • 10.1099/mic.0.067850-0
  22. Pinto, Daniela; Ruivo, Marta; Vandamme, Peter; Lopes, Maria de F. S.. "Hospital-Adapted Clonal Complex Enterococcus Faecium Found among Sand Enterococcal Isolates". Journal of Environmental Protection 03 01 (2012): 74-82. http://dx.doi.org/10.4236/jep.2012.31010.
    Published • 10.4236/jep.2012.31010
  23. Rigottier-Gois, Lionel; Alberti, Adriana; Houel, Armel; Taly, Jean-François; Palcy, Philippe; Manson, Janet; Pinto, Daniela; et al. "Large-Scale Screening of a Targeted Enterococcus faecalis Mutant Library Identifies Envelope Fitness Factors". PLoS ONE 6 12 (2011): e29023. http://dx.doi.org/10.1371/journal.pone.0029023.
    Published • 10.1371/journal.pone.0029023
  24. Pinto, D.; Almeida, V.; Almeida Santos, M.; Chambel, L.. "Resuscitation of Escherichia coli VBNC cells depends on a variety of environmental or chemical stimuli". Journal of Applied Microbiology 110 6 (2011): 1601-1611. http://dx.doi.org/10.1111/j.1365-2672.2011.05016.x.
    Published • 10.1111/j.1365-2672.2011.05016.x
Preprint
  1. Reis, Ana C.; Pinto, Daniela; Monteiro, Sílvia; Santos, Ricardo; Martins, João Vieira; Sousa, Alexandra; Páscoa, Rute; Lourinho, Rita; Cunha, Mónica V.. "Systematic SARS-CoV-2 S Gene Sequencing in Wastewater Samples Enables Early Lineage Detection and Uncovers Rare Mutations in Portugal". 2023. http://dx.doi.org/10.1101/2023.10.30.23297774.
    10.1101/2023.10.30.23297774
  2. Pinto, Daniela; Themudo, Gonçalo; Pereira, André C.; Botelho, Ana; Cunha, Mónica V.. "Rescue of Mycobacterium bovis DNA obtained from cultured strains during official surveillance of animal TB: key steps for robust whole genome sequence data generation". 2023. http://dx.doi.org/10.1101/2023.08.24.554648.
    10.1101/2023.08.24.554648
Thesis / Dissertation
  1. Pinto, Daniela. "Understanding resuscitation process of two foodborne pathogens: Escherichia coli and Listeria monocytogenes". PhD, 2013.
  2. Pinto, Daniela. "Caracterização de enterococos isolados de areias". Master, Universidade de Lisboa Faculdade de Ciências, 2007.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2025 Charting the Safe Zones: A Genomic Atlas for Circuit Integration in the Probiotic Lactobacillus acidophilus iMed.Ulisboa Meeting 2025
iMed.ULisboa (Lisboa, Portugal)
2024 PROSPERUS: Engineering Probiotics for Production and Delivery of Protein Drugs Weekly iMed.ULisboa Seminars
iMed.ULisboa (Lisbon, Portugal)
2020 How invisible organisms can be seen Anthropocene Campus Lisboa: Parallax
CIUHCT (Lisboa, Portugal)
2018 Signal transduction in bacteria: the special case of alternative sigma factors Altenberg Workshops in Theoretical Biology
Konrad Lorenz Institute for Evolution and Cognition Researc (Viena, Austria)
2017 Extracytoplasmic function sigma factors: from diversity to synthetic switches Institution Seminar Series
Radboud University (Neijmegen, Netherlands)
2016 Extracytoplasmic function sigma factor-based delay devices Institution Seminar Series
LOEWE-Zentrum für Synthetische Mikrobiologie (Marburg, Germany)
2013 Resuscitation of VBNC Listeria monocytogenes. Institution Seminar Series
Ludwig-Maximilians University (Munique, Germany)
2010 Unraveling the VBNC black-box in foodborne pathogens: what drives them in and out? Institution Seminar Series
Universidade de Lisboa (Lisboa, Portugal)
2010 Cell wall synthesis machinery in Bacillus subtilis: interaction and specific role of the PBP components Institution Seminar Series
Newcastle University (Newcastle, United Kingdom)
2010 Escherichia coli VBNC cells: variability in resuscitation factors Institution Seminar Series
Newcastle University (Newcastle, United Kingdom)
2007 Especiação e perfis de resistência a antibióticos de Enterococcus isolados das areias II Encontro Nacional de Pós-Graduações em Ciências Biológicas
(Porto, Portugal)

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2025/10 - Current Engineering Probiotics for Vaginal Health – The Candidiasis Case
Co-supervisor
Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2025/10 - Current Engineering Probiotics for Vaginal Health – The Bacterial Vaginosis Case
Co-supervisor
Biologia Humana e Ambiente (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2025/03 - 2025/07 Building a Stable Future: Engineering a Stable Lactobacillus acidophilus Chassis for Synthetic Biology and Clinical Applications
Co-supervisor
Universidade de Lisboa Instituto Superior Técnico, Portugal
2025/02 - 2025/07 Enhancing Phage-Based Therapies: Exploring Teichoicase-Endolysin Synergy Against Staphylococcus aureus
Co-supervisor
2023/09 - 2025/01 Epidemiology of Staphylococcus aureus at the Livestock-Wildlife Interface: Phylogenetic, Resistome, and Virulome Insights for One Health Application
Co-supervisor
Applied Microbiology (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/09 - 2024/12 Antimicrobial resistance and phylogenetic analyses of commensal and zoonotic bacteria at livestock-wildlife interfaces
Co-supervisor
Applied Microbiology (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2019 - 2020 Phylogenetic Insulation of Sigma Factors
Supervisor
Biologia Molecular e Genética (Scientific initiation)
Universidade de Lisboa Faculdade de Ciências, Portugal

Event organisation

Event name
Type of event (Role)
Institution / Organization
2023/01/20 - 2023/01/20 Final meeting to present the results of the COLOSSUS project. (2023/01/20 - 2023/01/20)
Meeting (Member of the Organising Committee)
Universidade de Lisboa Faculdade de Ciências, Portugal

Event participation

Activity description
Type of event
Event name
Institution / Organization
2025/12 - 2025/12 Conference "Microbiotec 25"
Conference
Microbiotec 25
Sociedade Portuguesa de Microbiologia, Portugal
2025/08 - 2025/12 Professional Certificate "Google Data Analytics" by Google on Coursera
2025/11 - 2025/11 Course "Share Data Through the Art of Visualization" by Google on Coursera
Other
Share Data Through the Art of Visualization
2025/11 - 2025/11 Course "Data Analysis with R Programming" by Google on Coursera
2025/10 - 2025/10 Course "Process Data from Dirty to Clean" by Google on Coursera
Other
Process Data from Dirty to Clean
2025/10 - 2025/10 Course "Analyze Data to Answer Questions" by Google on Coursera
Other
Analyze Data to Answer Questions
2025/09 - 2025/09 Course "Ask Questions to Make Data-Driven Decisions" by Google on Coursera
Other
Ask Questions to Make Data-Driven Decisions
2025/09 - 2025/09 Course "Prepare Data for Exploration" by Google on Coursera
Other
Prepare Data for Exploration
2025/08 - 2025/08 Course "Foundations: Data, Data, Everywhere" by Google on Coursera
Other
Foundations: Data, Data, Everywhere
2025/01 - 2025/01 Course "Computing skills for reproducible research: software carpentry" by EMBL
2023/12 - 2023/12 Conference "Microbiotec 23"
2023/09 - 2023/12 Course "Risk Prevention and Laboratory Safety" by Faculdade de Ciências da Universidade de Lisboa
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/09 - 2023/09 Outreach activity "European Researchers Night 2023"
2023/05 - 2023/05 Course "Data Visualisation For Biology Course 2023" by the European Molecular Biology Laboratory - European Bioinformatics Institute Data Visualisation For Biology Course 2023
European Bioinformatics Institute, United Kingdom
2022/11 - 2022/11 Conference "II Iberian workshop on Animal Tuberculosis"
Conference
II Iberian workshop on Animal Tuberculosis
Universidad de Córdoba, Spain
2022/10 - 2022/10 Outreach activity "FIC.A - International Science Festival 2022" FIC.A - International Science Festival 2022
Camara Municipal Oeiras, Portugal
2022/09 - 2022/09 Outreach activity "International Day of the Microorganism 2022" International Day of the Microorganism 2022
Ciência Viva, Portugal
2021 - 2021 Conference "World Microbe Forum"
Conference
World Microbe Forum
2021 - 2021 Conference "iMed.ULisboa Meeting 2021"
Meeting
iMed.ULisboa Meeting 2021
2021 - 2021 Conference "Microbiotec 21" Microbiotec 21
Sociedade Portuguesa de Microbiologia, Portugal
2021 - 2021 Outreach activity "Ciência Viva - Ocupação Científica de Jovens nas Férias 2021"
2020 - 2020 Conference "Anthropocene Campus 2020: Paralax" Anthropocene Campus 2020: Paralax
2019 - 2019 Conference "SMBE2019"
Conference
SMBE 2019
Society for Molecular Biology and Evolution, United States
2019 - 2019 Conference "Microbiotec 19"
Conference
Microbiotec 19
Sociedade Portuguesa de Microbiologia, Portugal
2019 - 2019 Course on “Machine Learning” by Stanford University on Coursera
Workshop
Machine Learning
Stanford University, United States
2018 - 2018 Workshop "The ground-floor of cognition: from microbes to animals and plants"
Workshop
37th Altenberg Workshop in Theoretical Biology
The Konrad Lorenz Institute, Austria
2018 - 2018 Conference "How microorganisms view their world"
Conference
How microorganisms view their world
2017 - 2017 Conference "SB7.0: the seventh international meeting on synthetic biology"
Conference
SB7.0: the seventh international meeting on synthetic biology
2016 - 2016 Course "BioBash Python"
Workshop
BioBash Python
2016 - 2016 Conference "VAAM general meeting"
Conference
VAAM General meeting
2016 - 2016 Conference "Mechanisms of gene regulation"
Conference
Mechanisms of Gene Regulation
2015 - 2015 Conference "VAAM general meeting"
Conference
VAAM General Meeting
2015 - 2015 Conference "CAS Conference Synthetic Biology II"
Conference
CAS Conference Synthetic Biology II
2014 - 2014 Course "Intellectual property rights for Marie-Curie fellows"
Workshop
Intellectual Property Rights for Marie-Curie Fellows
Europäisches Patentamt Patentinformationszentrum München, Germany
2014 - 2014 Conference "Mechanisms of gene regulation"
Conference
Mechanisms of Gene Regulation
2014 - 2014 Conference "VAAM general meeting"
Conference
VAAM General Meeting 2014
2013 - 2013 Conference "How dead is dead III: life cycles"
Conference
How dead is dead III: Life cycles
2011 - 2011 Conference "MicroBiotec'11"
Conference
MicroBiotec'11
2011 - 2011 Conference "Great wall symposium"
Conference
Great Wall Symposium 2011
2010 - 2010 Conference "FoodMicro"
Conference
FoodMicro
2009 - 2009 Course "Introductory bioinformatics"
Workshop
Introductory Bioinformatics
Instituto Gulbenkian de Ciência, Portugal
2009 - 2009 Conference "III international conference on environmental, industrial and applied microbiology"
Conference
III International Conference on Environmental, Industrial and Applied Microbiology
2008 - 2008 Course "Molecular methods to study complex microbial communities"
Workshop
Molecular methods to study complex microbial communities
Universidade de Aveiro, Portugal
2008 - 2008 Course "Proteomics data analysis"
Workshop
Proteomics Data Analysis
Instituto Gulbenkian de Ciência, Portugal
2008 - 2008 Conference "108th general meeting from american society for microbiology"
Conference
108th General Meeting from American Society for Microbiology
2007 - 2007 Conference "II encontro nacional de pós-graduações em ciências biológicas"
Conference
II Encontro Nacional de Pós-Graduações em Ciências Biológicas

Jury of academic degree

Topic
Role
Candidate name (Type of degree)
Institution / Organization
2025/11/24 Master thesis on "Peptide-conjugated nanoparticles as alternative approach for antibacterial therapy"
(Thesis) Main arguer
Xenia Jiovana Aroonslam Marques (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2025/11/17 Master thesis on "Targeted microbiome analysis in Human health and precision medicine"
(Thesis) Arguer
Henrique Simões Pinheiro (Master)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2025/09/24 Master thesis on "Not just Bugs: The Power of Gut Microbiota in Health"
(Thesis) Main arguer
Joana Catarino (Master)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2025/03/11 PhD first year examination on "Helicobacter and Campylobacter prophages: phage-bacteria interactions in vitro and in the gut"
(Thesis) Arguer
Luís Vitorino de Azevedo Godinho Pereira Tanoeiro (Other)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2024/03/08 Master thesis on "Development of Vibrio natriegens as a microbial chassis for plasmid production"
(Thesis) Main arguer
Guilherme Fernandes Mourato, (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/10/09 Master thesis on "Lysins encoded by prophages of Acinetobacter baumannii"
(Thesis) Main arguer
Maria Leonor Raposo Vieira da Silva (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/01/11 Master thesis on "Reappraising the use of beta-lactam antibiotics against tuberculosis: study of genes associated with beta-lactam susceptibility in mycobacteria"
(Thesis) Main arguer
Diana da Costa Mortinho (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020/12/17 Master thesis on "Microbiological assessment of polyether ionophorous and their derivatives against Gram-positive bacteria".
(Thesis) Main arguer
Mafalda De Azeredo Coelho Fernandes Da Silva (Master)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2019/12/18 Master thesis on "Phenol Stress Response in Corynebacterium glutamicum".
(Thesis) Main arguer
Miguel Ângelo da Costa Alves (Master)
Instituto Politécnico de Setúbal Escola Superior de Tecnologia do Barreiro, Portugal
2019/12/18 Master thesis on "Regulatory Functions of Sigma Factors of RNA Polymerase SigH and SigE in Corynebacterium glutamicum".
(Thesis) Main arguer
Ana Rita Mendes de Castro Coelho (Master)
Instituto Politécnico de Setúbal Escola Superior de Tecnologia do Barreiro, Portugal
2017/10/25 PhD thesis "Investigation of planctomycetal strategies to thrive - from cell biology to secondary metabolism"
(Thesis) Arguer
Olga Jeske (PhD)
Radboud Universiteit, Netherlands

Association member

Society Organization name Role
2022 - Current Graduate Women in Science
2009 - Current Sociedade portuguesa de microbiologia Member
2021 - 2022 European Society of Clinical Microbiology and Infectious Diseases Member
2014 - 2021 German association for general and applied microbiology Member
2019 - 2019 Society for Molecular Biology and Evolution Member

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2025/11/27 - 2025/11/27 Advanced Topics in Microbiology I - Synthetic Biology Microbiologia Aplicada (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2025/10/15 - 2025/10/15 Synthetic Biology - Synthetic Biology in Medicine (Licenciatura) Universidade de Lisboa Instituto Superior Técnico, Portugal
2025/10/02 - 2025/10/02 Advanced Topics in Microbiology I - Data Visualisation Seminar Microbiologia Aplicada (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2024/12/19 - 2024/12/19 Advanced Topics in Microbiology I - Data Visualisation Seminar Microbiologia Aplicada (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2024/11/18 - 2024/11/19 Biopharmaceutical Sciences - WGS data analysis class Ciências Biofarmacêuticas (Mestrado) Universidade de Lisboa Faculdade de Farmácia, Portugal
2024/02/29 - 2024/02/29 Advanced Topics in Microbiology II - Synthetic Biology Applied Microbiology (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2023/12/14 - 2023/12/14 Advanced Topics in Microbiology I - Data Visualisation Seminar Applied Microbiology (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2023/10/31 - 2023/10/31 Prokaryote Genetics - Phage Therapy & Phage Display class Biology (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2023/10/25 - 2023/10/27 Microbial Biotechnology - Phage Therapy & Phage Display class Biology (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2023/10/18 - 2023/10/20 Microbial Biotechnology - Synthetic Biology class Biology (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2023/10/17 - 2023/10/17 Prokaryote Genetics - Alternative Sigma Factors class Biology (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2023/03/28 - 2023/03/28 Advanced Topics in Microbiology II - Synthetic Biology Seminar Applied Microbiology (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal
2018/12/03 - 2018/12/14 Applied and synthetic biology (Master) Technische Universität Dresden, Germany
2017/12/04 - 2017/12/15 Bacterial gene expression and signal transduction (Master) Technische Universität Dresden, Germany
2016/11/07 - 2016/11/18 Bacterial gene expression and signal transduction (Master) Technische Universität Dresden, Germany

Journal scientific committee

Journal title (ISSN) Publisher
2025 - 2025 Antibiotics MDPI
2024 - 2024 Pharmaceuticals MDPI
2022 - 2024 BioTech MDPI
2020 - 2024 International Journal Of Molecular Sciences MDPI
2022 - 2022 Vaccines MDPI
2022 - 2022 Microbiology Research MDPI
2019 - 2019 Philosophical Transactions of the Royal Society B: Biological Sciences Royal Society Publishing
2018 - 2018 Microbiology (1350-0872) Microbiology Society

Mentoring / Tutoring

Topic Student name
2025/10 - Current Master project "Enhancing Phage-Based Therapies: Exploring Teichoicase-Endolysin Synergy Against Staphylococcus aureus" Mariana Nunes
2023/01 - 2023/07 Internship on "Searching for Mycobacteriophages infecting Mycobacterium bovis in environmental samples" Inês Mendes
2023/01 - 2023/02 Lab rotation from PhD program "Searching for Mycobacteriophages infecting Mycobacterium bovis in environmental samples" Ana Isabel Gouveia
2020 - 2021 Master project "Heteromeric endolysins encoded in a single gene: occurrence in Gram-positive targeting phages and relevance for lytic activity" Raquel Bastos Gonçalo
2014 - 2021 Master and PhD project "Regulation and function of ECF41 extracytoplasmic function sigma factors" Franziska Dürr
2015 - 2019 PhD project "Characterization of a novel group of C-terminal extension containing extracytoplasmic function (ECF) ECF42 sigma factor" Qiang Liu
2014 - 2019 PhD project "Streptomyces venezuelae: a source of ECF-sigma factors for genetic switches and a model for antibiotic resistance studies" Dayane Araújo
2015 - 2015 Bachelor project "Defining target promoters of extracytoplasmic function sigma factors" Frederike Froriep
2014 - 2015 PhD project "Classification and functional characterization of extracytoplasmic function (ECF) sigma factors from Planctomycetes and Actinobacteria" Xiaoluo Huang
2010 - 2010 Lab rotation project "VBNC state in food pathogens" Vânia Almeida
Distinctions

Award

2025 Best Poster on Health Biotechnology on Microbiotec25 conference
Sociedade Portuguesa de Microbiologia, Portugal

Sociedade Portuguesa de Biotecnologia, Portugal
2023 CEEC.IND Associate Researcher Level
Fundação para a Ciência e a Tecnologia, Portugal
2018 EMBO short-term fellowship
Gesellschaft zur Förderung der Lebenswissenschaften Heidelberg GmbH, Germany
2014 Marie Curie Intra-European fellowship
European Union, Belgium
2009 PhD scholarship
Fundação para a Ciência e a Tecnologia, Portugal
2005 Academic merit scholarship
Universidade de Lisboa Faculdade de Ciências, Portugal