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Early Career Researchers �at Work Panel
Filipa Godoy Vitorino
P.I. Microbial Ecology and Genomics Lab ��
Inter American University of Puerto Rico,Metropolitan Campus
STM Spring Conference 2013, May 1 2013
Outline
• Background and Educa-on • Research Projects and Collaborators • Access to data: – My literature searches – Wri-ng papers with collaborators – Networking
• Journal Peer Review Process • Sugges-ons for improving Peer Review Process
Background • Educa-on and Training
• Research Interests
Use of next-‐genera-on sequencing technologies to study microbial communi-es in natural ecosystems, aiming at understanding the role of microbes in tree adapta-on and cellulose degrada-on in foregut fermen-ng ecosystems as well as in human pathologies.
• Selected Peer-‐reviewed Publica-ons (2011-‐2012)
INSTITUTION AND LOCATION DEGREE
YEARS FIELD OF STUDY
University of Porto, Porto, Portugal Licenciate (BSc+MSc) 1998-‐2002 Biology
University of Puerto Rico, San Juan, PR Ph.D. 2003-‐2009 Biology (Microbial Ecology)
US Department of Energy – Joint Genome Ins-tute (DOE-‐JGI), CA, USA
Postdoc 2009-‐2012 Metagenomics of Microbial Communi-es
University of Queensland (UQ), Brisbane, Australia
Visi-ng Academic 2012 Bioinforma-cs
Inter American University of Puerto Rico (IUPR), San Juan, PR
Research Professor and PI MEGL
Current Microbial Ecology
¢ Godoy-‐Vitorino, F., et al (2012) Compara-ve analyses of foregut and hindgut bacterial communi-es in hoatzins and cows. The ISME Journal, 6: 531-‐541 ¢ Godoy-‐Vitorino, F., et al. (2012) Differences in the structure of the crop bacterial community of hoatzins from different geographical
loca-ons. Research in Microbiology, 2012 Jan 21. [Epub ahead of print] ¢ De Jesús-‐Laboy, K.M.*, Godoy-‐Vitorino , F.*, et al (2011) Comparison of the fecal microbiota in feral and domes-c goats. Genes, 3,
1-‐18; doi:10.3390/genes3010001, ¢ García-‐Amado, M. A.*, Godoy-‐Vitorino, F*., et al (2011) Bacterial Diversity in the Cecum of the Capybara (Hydrochoerus
hydrochaeris). Microbial Ecology, DOI 10.1007/s00248-‐011-‐9963-‐z, published online Nov 15, 2011 ¢ Maldonado-‐Contreras, A. L.*, Goldfarb, K. C.*, Godoy-‐Vitorino, F., et al (2011). Structure of the human gastric bacterial community in
rela-on to Helicobacter pylori status. The ISME Journal, 5:574-‐579
• M.ecol. studies the microbial mechanisms and interac-ons biological processes
• “We’re seeing an unprecedented
rate of discovery. Everywhere we look, microbes seem to be involved.” Rob Knight in "The Washington Post", October 9 2011.
NATIONAL ACADEMY OF SCIENCES NATIONAL ACADEMY OF ENGINEERING INSTITUTE OF MEDICINE NATIONAL RESEARCH COUNCIL
Humankind has benefited enormously from the study of microbes since their
discovery in the 17th century. However, such benefits have come from
the study of just a miniscule fraction of the millions of species of microbes
in the environment. In addition, scientists are realizing the importance
of studying the collective properties of communities of microbes, which perform com-
plex tasks essential to the health of human beings and our planet. The emerging field of
metagenomics opens the door to exploring the vast array of microbes unstudied to date
and to investigating entire microbial communities. Through a deeper understanding of the
microbes that sustain life on Earth, the metagenomics approach offers the promise of an
incredible array of new benefits.
U N D E R S T A N D I N G O U R MICROBIAL PLANETT H E N E W S C I E N C E O F M E T A G E N O M I C S
Blaser, MJ, 2010 PNAS, 107, 14, 6125–6126 Filipa Godoy, Ph.D.
Microbes are everywhere -‐We are outnumbered by our microbial ‘mates’ by 10 to 1
Microbial Ecology and Genomics Lab ��
We use high-throughput sequencing technologies to characterize the community profiles and metagenomes of environmental/human body microbial ecosystems�
Microbial community contribuQons to stress adaptaQon and plasQcity in the tropical tree Tabebuia heterophylla
BioprospecQng for the lignocellulolyQc capabiliQes of herbivore crab guts associated to the Red Mangrove -‐ Rhizophora mangle in Puerto Rico
RelaQng the genital microbiota to HPV infecQons
in laQn women
Principal InvesQgator: Filipa Godoy, Ph.D.
Other internaQonal endeavors
• Hoatzin Projects: – Metagenomics – Ciliate single-‐cell – Bacterial collec-on – Fungal Diversity – with Inter Metro student G. Vargas
• EU Funded: Uncovering the life-‐style of Acidobacteria symbionts of marine sponges
• EU Funded: Cetaceans as marine ecosystem health senQnels • Bacteria in the red algae Chondrus crispus in Portuguese
rivers
A broad collaboraQve network
Access to data My literature searches
– Access to: • hYp://www.ncbi.nlm.nih.gov/pubmed • hYp://www.plos.org • scholar.google.com • www.asm.org • Sciencedirect.com • Wilsonweb-‐Ebscohost • Directly search in journals such as AEM, ISMEJ/Nature
– Very useful: • hYp://endnote.com
• IAUPR doesn’t have access to some educa-on journals that I look for for references (e.g. The ISME Journal) – collaborators, emails, socie-es,etc
• Need for Public access – peer
review process is free!
WriQng papers with collaborators
• Main author draqs out the MS star-ng with results and discussion (bullets). Figures and data analyses pipelines shared via e-‐mail/dropbox/googledrive
• References are shared via endnote travel library and storage drives
• Aqer every co-‐author agrees with the main message and result summary, main author writes the paper and the review process con-nues.
• Mee-ngs via SKYPE
Networking
• Linkedin.com – Collaborators post recommenda-ons and support skills – You can post news, links etc
• Research Gate – Pos-ng references and full texts
• ASM – Junior Adivisory Group (JAG) – I’ve been organizing workshops and have been Chair of some plenary sessions at the General Mee-ng of the ASM (~50,000 members, largest life science professional organiza-on in the world)
Journal Peer Review Process
• I am a reviewer for several journals: – 2013-‐present BioMed Research Interna-onal (Hindawi Corpora-on – Open access) – 2012-‐present Canadian Journal of Microbiology (NRC research press) – 2011-‐present Environmental Science & Technology (ACS Pubica-ons) – 2011-‐present Journal of Compara-ve Physiology – B (Springer) – 2011-‐present Microbial Ecology (Springer) – 2011-‐present Molecular Ecology (Wiley-‐Blackwell) – 2011-‐present FEMS Microbiology Ecology (Wiley-‐Blackwell) – 2010-‐Present The ISME Journal (Nature group) – 2009-‐Present Journal of Theore-cal Biology (Elsevier)
• Important to offer to review back manuscripts aqer suggested modifica-ons and also access all reviews in the second stage.
SuggesQons for improving Peer Review Process
• Journals (publishing groups) should grant access to all manuscripts from their group at least during the ~ 3 week review process.
• Journals (publishing groups) should facilitate review process, e.g. list manuscripts related to the submived ar-cle.
• Aqer review is submived, reviewers should be informed of the final decision and should have copy of the final manuscript. -‐ Editors don’t discuss with reviewers their final decision
• Reviewers should be able to refer authors to other more appropriate journals.
