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I am a Postdoctoral Researcher at iBB-IST, focusing on algae microbiome and their secondary metabolites with potential biotechnological application. I am a Doctor in Microbiology by Ciências-ULisboa (2024), with my thesis on Mycobacterium tuberculosis complex under a One Health perspective, in particular, the environmental contamination as an indirect source of animal tuberculosis transmission and the need of a genomic surveillance system based on eco-epidemiological models by application of a phylodynamics framework. I also hold a Master's in Applied Microbiology (2017) and a Bachelor's in Biology (Cellular Biology and Biotechnology; 2015) both by Ciências-ULisboa. My main research areas are Infection Biology, Microbiome, Environmental Microbiology, Molecular and Cellular Microbiology, and Microbial Ecology. My work has been published in top-ranked multidisciplinary or specialized journals, featuring 17 articles with over 189 citations and a h-index of 8 (Web of Science metrics).
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Identification

Personal identification

Full name
André Conceição Pereira

Citation names

  • Pereira, André C.

Author identifiers

Ciência ID
591C-25AD-F68B
ORCID iD
0000-0003-4112-4037

Email addresses

  • andre.c.pereira@campus.ul.pt (Professional)
  • andre.conceicao.pereira@tecnico.ulisboa.pt (Professional)
  • andre.c.pereira94@gmail.com (Personal)

Telephones

Telephone
  • 218 417 00 (Professional)

Addresses

  • Av. Rovisco Pais, 1049-001, Lisboa, Lisboa, Portugal (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Microbiology
  • Medical and Health Sciences - Health Sciences - Infectious Diseases
  • Natural sciences - Biological Sciences - Cell Biology
  • Natural sciences - Biological Sciences - Molecular Biology
  • Medical and Health Sciences - Health Sciences - Epidemiology
  • Medical and Health Sciences - Health Sciences - Public and Environmental Health
  • Agrarian Sciences - Veterinary Sciences
  • Natural sciences - Biological Sciences - Ecology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
English Intermediate (B1) Intermediate (B1) Intermediate (B1) Intermediate (B1)
Spanish; Castilian Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2019/03 - 2024/04
Concluded
 Biologia (Doutoramento)
Major in Microbiologia
Universidade de Lisboa Faculdade de Ciências, Portugal
"Incorporating the genomic signature of environmental Mycobacterium bovis into transmission models of animal tuberculosis under a phylodynamics conceptual framework" (THESIS/DISSERTATION)
2023/09 - 2023/12
Concluded
 Risk prevention and laboratory safety (Outros)
Universidade de Lisboa Faculdade de Ciências, Portugal
2023/04 - 2023/04
Concluded
 Science Communication workshop (Outros)
Universidade de Lisboa, Portugal
2022/04 - 2022/04
Concluded
 FlowJo workshop - Intro to FlowJo and Advanced tools and plugins (Outros)
Instituto de Medicina Molecular, Portugal
2021/10 - 2021/10
Concluded
 Basics of Light Microscopy (Outros)
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2021/09 - 2021/09
Concluded
 Introduction to Image Analysis (Outros)
Universidade de Lisboa Faculdade de Ciências, Portugal
2020/08 - 2020/08
Concluded
 Summer School 2020: Global One Health – From Research to Practice (Outros)
Wageningen University and Research Wageningen Bioveterinary Research, Netherlands
2019/11 - 2020/03
Concluded
 Wildlife Epidemiology and Disease Control (Outros)
Instituto de Investigación en Recursos Cinegéticos, Spain
2019/04 - 2019/04
Concluded
 Survey for ArcGIS (Outros)
Instituto Nacional de Investigação Agrária e Veterinária, Portugal
2019/04 - 2019/04
Concluded
 Collector for ArcGIS (Outros)
Instituto Nacional de Investigação Agrária e Veterinária, Portugal
2019/02 - 2019/02
Concluded
 Introduction to R for Ecology and Evolutionary Biology (Outros)
Centro de Ecologia Evolução e Alterações Ambientais, Portugal
2018/12 - 2018/12
Concluded
 ArcMap 1: Iniciação ao SIG (Outros)
Instituto Nacional de Investigação Agrária e Veterinária, Portugal
2018 - 2018
Concluded
 Short course in Bionumerics (Outros)
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2015/09 - 2017/12
Concluded
 Microbiologia Aplicada (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Understanding the cross-talk between microbiota, host fitness, and the environment using Egyptian Mongoose (Herpestes ichneumon) as a model" (THESIS/DISSERTATION)
 18
2017/10/28 - 2017/10/29
Concluded
 Short Course in R language programming (Outros)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016/02 - 2016/03
Concluded
 Course in Chromatography Techniques (Outros)
Universidade de Lisboa Faculdade de Ciências, Portugal
2012 - 2015
Concluded
 Biologia (Licenciatura)
Major in Biologia Celular e Biotecnologia
Universidade de Lisboa Faculdade de Ciências, Portugal
"n/a" (THESIS/DISSERTATION)
 16
Affiliation

Science

Category
Host institution 		Employer
2024/09 - Current Postdoc (Research) Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
Universidade de Lisboa Instituto de Bioengenharia e Biociências, Portugal
2018/09 - 2024/08 Researcher (Research) Fundação para a Ciência e a Tecnologia, Portugal
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
(...)

Teaching in Higher Education

Category
Host institution 		Employer
2024/09 - Current Invited Adjunct Teacher (Polytechnic Teacher) Instituto Politécnico de Lisboa Escola Superior de Tecnologia da Saúde de Lisboa, Portugal
2016/09/15 - 2017/07/15 Tutor (University Teacher) Universidade de Lisboa Faculdade de Ciências, Portugal
Universidade de Lisboa Faculdade de Ciências, Portugal

Others

Category
Host institution 		Employer
2016/09/01 - 2018/08 Volunteer - supervision of Prof. Mónica Cunha (Dr.) - "Understanding the cross-talk between microbiota, host fitness, and the environment using Egyptian Mongoose (Herpestes ichneumon) as a model" Centro de Ecologia Evolução e Alterações Ambientais, Portugal
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
(...)
2016/02/01 - 2016/07/01 Volunteer - supervision of Leonor Silveira (Msc.) - "Salmonella Typhimurium and monophasic variant Salmonella 4,5,12:i:-" Instituto Nacional de Saúde Doutor Ricardo Jorge IP, Portugal
2015/10/01 - 2016/01/01 Volunteer - supervision of Sónia Abreu (PhD.) - "Biophysical evaluation of the AMP Pa-MAP1R3, derived from Pleuronectes americanus" Instituto de Medicina Molecular, Portugal
2015/01/01 - 2015/07/01 Volunteer - supervision Prof. Ana Rita Matos (PhD.) - "Lipid analysis of A. thaliana mutants" Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
Projects

Contract

Designation Funders
2024/09 - Current Pacto da Bioeconomia Azul
01/C05-i11/2024.PC644915664-00000026
Post-doc Fellow
Associação do Instituto Superior Técnico para a Investigação e Desenvolvimento, Portugal
Ongoing
2020/01/01 - 2024/12/31 Instituto de Biosistemas & Ciências Integrativas
UIDP/04046/2020
10.54499/UIDP/04046/2020
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal

Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal

Universidade do Minho, Portugal

Universidade de Trás-os-Montes e Alto Douro, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2020/01/01 - 2024/12/31 Centro de Ecologia, Evolução e Alterações Ambientais
UIDB/00329/2020
10.54499/UIDB/00329/2020
FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal

Universidade de Lisboa Centro de Ecologia Evolução e Alterações Ambientais, Portugal

Fundação Gaspar Frutuoso, Portugal

Universidade de Lisboa Faculdade de Ciências, Portugal

Universidade dos Açores, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2018/08 - 2021/08 COLOSSUS - ControlO de tubercuLOSe na interface bovinoS-faUna Silvestre com recurso a soluções inovadoras inspiradas na natureza
PTDC/CVT-CVT/29783/2017
Other
Centro de Ecologia Evolução e Alterações Ambientais, Portugal
 Fundação para a Ciência e a Tecnologia
Ongoing
Outputs

Publications

Conference poster
  1. Pinto, Daniela; Espregueira Themudo, Gonçalo; Pereira, André C.; Botelho, Ana; Cunha, Mónica V.. "Rescue of Mycobacterium bovis DNA obtained from cultured strains during official surveillance of animal tuberculosis". Paper presented in Microbiotec'23, 2023.
  2. Pereira, André C.; Reis, Ana C.; Lourenço, José; Espregueira Themudo, Gonçalo; Botelho, Ana; Cunha, Mónica V.. "Population structure and transmission dynamics of Mycobacterium bovis at the livestock-wildlife interface". Paper presented in Microbiotec'23, 2023.
  3. Pereira, André C.; Cunha, Mónica V.. "Population genomics and phylodynamics of Mycobacterium bovis at the livestock-wildlife interface, Portugal". Paper presented in VII International Conference on Mycobacterium bovis, 2022.
  4. Pereira, André C.; Tenreiro, Ana; Tenreiro, Rogério; Cunha, Mónica V.. "A new tool to uncover Mycobacterium bovis patterns and signature outside the mammal host". Paper presented in VII International Conference on Mycobacterium bovis, 2022.
  5. Pereira, André C.; Tenreiro, Ana; Tenreiro, Rogério; Cunha, Mónica V.. "Development of a novel FISH method coupled with flow cytometry to characterize Mycobacterium bovis from the environment". Paper presented in 6th cE3c Annual Meeting: Frontiers in E3, 2020.
  6. Pereira, André Conceição; Tenreiro, Ana; Tenreiro, Rogério; Cunha, Mónica Vieira. "Detection, identification, and sorting of viable environmental Mycobacterium bovis from soil and water samples". Paper presented in X RUSI, 2019.
  7. Pereira, André C.; Bandeira, Vítor; Fonseca, Carlos; Cunha, Mónica V.. "Microbiota intestinal de sacarrabos: diferenças taxonómicas e funcionais entre sexo e classe etária". Paper presented in Wildlife Game Management Summit, 2019.
  8. Pereira, André da Conceição; Bandeira, Vítor; Fonseca, Carlos; Cunha, Mónica Vieira. "Understanding the cross-talk between microbiota, host fitness, and the environment using Egyptian mongoose (Herpestes ichneumon) as a model". Paper presented in WAVES X International Symposium on Wild Fauna, 2017.
Journal article
  1. 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.
    10.1016/j.scitotenv.2024.176053
  2. André C. Pereira; Bernat Pérez de Val; Mónica V. Cunha. "Phylogenetic analysis of Mycobacterium caprae highlights past and present epidemiological links at the Iberian Peninsula scale". Microbes and Infection (2024): https://doi.org/10.1016/j.micinf.2024.105405.
    10.1016/j.micinf.2024.105405
  3. André C. Pereira; Daniela Pinto; Mónica V. Cunha. "First time whole genome sequencing of Mycobacterium bovis from the environment supports transmission at the animal-environment interface". Journal of Hazardous Materials (2024): http://dx.doi.org/10.1016/j.jhazmat.2024.134473.
    10.1016/j.jhazmat.2024.134473
  4. André C. Pereira; Mónica V. Cunha. "Flow Cytometry Coupled with Resuscitation Assays As a High-Resolution Tool to Inform Environmental Management and Disinfection of Settings Affected by Tuberculous Mycobacteria". Microorganisms (2024): https://doi.org/10.3390/microorganisms12061068.
    10.3390/microorganisms12061068
  5. André C. Pereira; José Lourenço; Gonçalo Themudo; Ana Botelho; Mónica V. Cunha. "Population structure and history of Mycobacterium bovis European 3 clonal complex reveal transmission across ecological corridors of unrecognized importance in Portugal". Microbiology Spectrum (2024): http://dx.doi.org/10.1128/spectrum.03829-23.
    10.1128/spectrum.03829-23
  6. Daniela Pinto; Gonçalo Themudo; André C. Pereira; Ana Botelho; Mónica V. Cunha. "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 (2024): https://doi.org/10.3390/ijms25073869.
    10.3390/ijms25073869
  7. André C. Pereira; Ana C. Reis; Mónica V. Cunha. "Genomic epidemiology sheds light on the emergence and spread of Mycobacterium bovis Eu2 Clonal Complex in Portugal". Emerging Microbes & Infections (2023): https://doi.org/10.1080/22221751.2023.2253340.
    10.1080/22221751.2023.2253340
  8. André C. Pereira; Daniela Pinto; Mónica V. Cunha. "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 (2023): http://dx.doi.org/10.1016/j.scitotenv.2023.164366.
    10.1016/j.scitotenv.2023.164366
  9. Pereira, André C.; Tenreiro, Ana; Tenreiro, Rogério; Cunha, Mónica V.. "Stalking Mycobacterium bovis in the total environment: FLOW-FISH & FACS to detect, quantify, and sort metabolically active and quiescent cells in complex matrices". Journal of Hazardous Materials 432 (2022): 128687. http://dx.doi.org/10.1016/j.jhazmat.2022.128687.
    10.1016/j.jhazmat.2022.128687
  10. Pereira, André C.; Tenreiro, Ana; Tenreiro, Rogério; Cunha, Mónica. "When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment". Science of The Total Environment 806 (2022): 150682-150682. http://dx.doi.org/10.1016/j.scitotenv.2021.150682.
    10.1016/j.scitotenv.2021.150682
  11. Ana C. Reis; Beatriz Ramos; Pereira, André C.; Mónica Cunha. "The hard numbers of tuberculosis epidemiology in wildlife: A meta-regression and systematic review.". Transboundary and emerging diseases (2020): https://doi.org/10.1111/tbed.13948.
    10.1111/tbed.13948
  12. Pereira, André C.; Cunha, Mónica V.. "An effective culturomics approach to study the gut microbiota of mammals". Research in Microbiology 171 8 (2020): 290-300. http://dx.doi.org/10.1016/j.resmic.2020.09.001.
    10.1016/j.resmic.2020.09.001
  13. Ramos, Beatriz; Pereira, André C.; Reis, Ana C.; Cunha, Mónica V.. "Estimates of the global and continental burden of animal tuberculosis in key livestock species worldwide: A meta-analysis study". One Health 10 (2020): 100169. http://dx.doi.org/10.1016/j.onehlt.2020.100169.
    10.1016/j.onehlt.2020.100169
  14. André C. Pereira; Beatriz Ramos; Ana C. Reis; Mónica V. Cunha. "Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches". Microorganisms 8 9 (2020): 1380-1380. https://doi.org/10.3390/microorganisms8091380.
    10.3390/microorganisms8091380
  15. Pereira, André C.. "Global trends of epidemiological research in livestock tuberculosis for the last four decades". Transboundary and Emerging Diseases (2020): http://dx.doi.org/10.1111/tbed.13763.
    10.1111/tbed.13763
  16. André C. Pereira; Victor Bandeira; Carlos Fonseca; Mónica V. Cunha. "Crosstalk Between Culturomics and Microbial Profiling of Egyptian Mongoose (Herpestes ichneumon) Gut Microbiome". Microorganisms 8 6 (2020): 808-808. https://doi.org/10.3390/microorganisms8060808.
    10.3390/microorganisms8060808
  17. Pereira, André C.; Bandeira, Victor; Fonseca, Carlos; Cunha, Mónica V.. "Egyptian Mongoose (Herpestes ichneumon) Gut Microbiota: Taxonomical and Functional Differences across Sex and Age Classes". Microorganisms 8 3 (2020): 392. http://dx.doi.org/10.3390/microorganisms8030392.
    10.3390/microorganisms8030392
  18. Pereira, André C.. "Animal tuberculosis: impact of disease heterogeneity in transmission, diagnosis, and control". Transboundary and Emerging Diseases (2020): http://dx.doi.org/10.1111/tbed.13539.
    10.1111/tbed.13539
Magazine article
  1. Pereira, André C.. "Zoonoses, um problema atual com ancestralidade: o caso da tuberculose animal", Jornal Crónico, 2020
  2. Cunha, Mónica Vieira; Reis, Ana C.; Pereira, André Conceição; Ramos, Beatriz; Albuquerque, Teresa; Botelho, Ana; Santos, Nuno. "Tuberculose animal: diagnóstico, epidemiologia, investigação e controlo", Vida Rural, 2019
Thesis / Dissertation
  1. "Incorporating the genomic signature of environmental Mycobacterium bovis into transmission models of animal tuberculosis under a phylodynamics conceptual framework". PhD, Universidade de Lisboa Faculdade de Ciências, 2023.
  2. Cunha, Mónica Vieira; Pereira, André da Conceição. "Understanding the cross-talk between microbiota, host fitness, and the environment using Egyptian mongoose (Herpestes ichneumon) as a model". Master, Universidade de Lisboa Faculdade de Ciências, 2017. http://hdl.handle.net/10451/30405.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/03/01 Who infects who? Genomic surveillance to infer transmission networks in the risk epidemiological area of animal tuberculosis 15th Jornadas Internacionais Hospital Veterinário Muralha de Évora
(Portugal)
2023/12/09 Breaking the Wall: Mycobacterium bovis transmission at the animal-environmental interface Microbiotec'23
(Portugal)
2023/11 A new understanding of the transmission landscape of Mycobacterium bovis boosted by single-cell analyses, genomics, and ecological modelling 3rd Symposium of the National Research Infrastructure for Genome Sequencing and Analysis
2023/11 An ecosystems view of animal tuberculosis powered by environmental genomics and phylodynamics 2nd Egas Moniz One Health Symposium
(Portugal)
2023/04 Real-time environmental monitoring of Mycobacterium bovis in a multi-host transmission scenario XVII Congress of the Iberian Society of Cytometry
(Spain)
2022/11 Research in animal tuberculosis in Landscape Epidemiology and Wildlife Diseases group of Centre for Ecology, Evolution, and Environmental Changes (ce3c) II Iberian Workshop on Animal Tuberculosis Research
(Spain)
2022/11 Environmental diagnosis of animal tuberculosis in applied research II Iberian Workshop on Animal Tuberculosis Research
(Spain)
2021/11 A new high-performance method to detect, identify, and sort metabolically active cells of environmental Mycobacerium bovis Microbiotec'21
(Portugal)
2020/08/28 Animal tuberculosis in Portugal: A One health perspective Summer School 2020: Global One Health – From Research to Practice
2019/12 Sex and age taxonomical and functional differences of Egyptian mongoose gut microbiota Microbiotec'19
Sociedade Portuguesa de Microbiologia e Sociedade Portuguesa de Biotecnologia (Coimbra, Portugal)
2019/04 Passado, Presente e Futuro da Investigação em tuberculose animal no INIAV, IP, em Portugal I Workshop Ibérico y II Nacional de Investigación en Tuberculosis Animal
2017/12/08 Understanding the cross-talk between microbiota, host fitness, and the environment using Egyptian mongoose (Herpestes ichneumon) as a model Microbiotec17
Sociedade Portuguesa de Microbiologia e Sociedade Portuguesa de Biotecnologia (Porto, Portugal)
2017/12 Deciphering the microbial landscape of an Iberian mammal: cross-talk between microbiota, host fitness and the environment Cycle of Seminars – Department of Bioengineering, Autumn Series

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023/09 - 2024/01 Exploring Fluorescence Microscopy, Culture Methods, and Viability PCR to Evaluate Cell Burden and Viability of Mycobacterium bovis
Co-supervisor
 Biologia (Degree)
Universidade de Lisboa Faculdade de Ciências, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2023/01/20 - 2023/01/20 COLOSSUS – Presentation of the project main results to stakeholders (2023/01/20 - 2023/01/20)
Seminar (Member of the Scientific Committee)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2019/06 - 2019/06 Wildlife Game Management Summit/Cimeira da Fauna e Gestão Cinegética (2019/06 - 2019/06)
Conference (Member of the Organising Committee)
 Instituto Nacional de Investigação Agrária e Veterinária, Portugal

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2022/10 - Current FICA – International Science Festival. Oeiras, Portugal.
Exhibition
Camara Municipal Oeiras, Portugal
2022/09 - Current International Microorganism Day
Exhibition
Universidade de Lisboa Faculdade de Ciências, Portugal
2020/01/31 - 2020/01/31 II Simpósio de Investigação em Tuberculose e Micobactérias Não Tuberculosas em Portugal
Symposium
 II Simpósio de Investigação em Tuberculose e Micobactérias Não Tuberculosas em Portugal
Universidade de Lisboa Faculdade de Farmácia, Portugal
2019/11 - 2019/11 International Microorganisms Day
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2017/09 - 2017/09 International Microorganisms Day
Centro de Ecologia Evolução e Alterações Ambientais, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2024/09 - Current Microbiologia Geral (General Microbiology) Saúde Ambiental (Licenciatura) Instituto Politécnico de Lisboa Escola Superior de Tecnologia da Saúde de Lisboa, Portugal
2019/04 - 2019/04 Young Creators: Biohacking and bio fabrication module (Outros)
2016/09 - 2017/07 Fundamentos de Biologia Molecular (Fundamentals of Molecular Biology) Biologia (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
2016/09 - 2017/07 Engenharia Genética (Genetic Engineering) Biologia (Licenciatura) Universidade de Lisboa Faculdade de Ciências, Portugal
Distinctions

Other distinction

2017 Academic Merit Certificate
Universidade de Lisboa Faculdade de Ciências, Portugal
2016 Academic Merit Certificate
Universidade de Lisboa Faculdade de Ciências, Portugal