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Our Community

The Puerto Rico Center for Microbiome Sciences is a Proud member of the following consortia:

Global Microbiome Conservancy

Advancing Microbiome Science Equitably and Ethically:
The vision of the Global Microbiome Conservancy (GMbC) is to advance microbiome science through global conservation, capacity building, representation, and scientific innovation. GMbC works to preserve microbial diversity by sampling, culturing, and storing gut microbiomes from populations around the world, creating an open, non-profit repository of humanity’s microbial heritage. The organization strengthens research capacity by providing comprehensive scientific training and support to partner institutions, enabling consortium members to drive microbiome research within their own regions. GMbC also prioritizes equitable representation by collaborating closely with diverse and historically underrepresented communities, ensuring inclusivity in all aspects of its work. Through educational initiatives and the development of accessible scientific resources, GMbC contributes to the broader advancement of microbiome knowledge and helps address fundamental questions about the human microbiome.

https://microbiomeconservancy.org/

Microbiome Centers Consortium

The Microbiome Centers Consortium is a cooperative, inclusive and collaborative network of microbiome centers that aims to accelerate the understanding of all microbiomes. We share and develop intellectual, educational, and technical resources and promote common adoption of data standards and ethical guidelines as the field of microbiome science moves from discovery to translation.

https://microbiomecenters.org/

Publications

2025

Sepúlveda-Rivera V, Olivieri-Henry G, Morales-González H, Ruiz-Adames J, Herrero-Rivera C, Rentas-Echeverria A, Cardona-Berdecia V, Soler-Llompart C, Sala-Morales AC, Pérez-Montero G, Blanco-Ruiz E, Godoy-Vitorino F. Gut microbiota distinguishes aging hispanics with Alzheimer's disease: associations with cognitive impairment and severity. Sci Rep. 2025 Aug 5;15(1):28505. doi: 10.1038/s41598-025-13262-2. PMID: 40764790; PMCID: PMC12325907.

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Godoy-Vitorino F. Strengthening Integrative Microbiome Research Through Regional Leadership. Int J Environ Res Public Health. 2025 Aug 26;22(9):1322. doi: 10.3390/ijerph22091322. PMID: 41007466; PMCID: PMC12469662.

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Godoy-Vitorino F, Borrero M, Pérez-Santiago J, García-García R, Gomez-Manzano C. Connecting Innovation and Trust through Translational Sciences - A Need for a Community Focus and Effective Education Strategies. P R Health Sci J. 2025 Sep 18;44(3):185-188. PMID: 41026590.

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Pagán-Rivera LH, Godoy-Vitorino F, Meléndez-Vázquez NM, Ocasio-Rivera SE, Santiago-Gascot ME, Santiago JM, Salgado I, González V, Martínez-Guzmán O, Cáceres-Chacón M, Torrado-Tapias A, Miranda JD. The Effect of Cefazolin on the Gut Microbiome of Female Rats After Spinal Cord Injury. Microorganisms. 2025 Oct 7;13(10):2324. doi: 10.3390/microorganisms13102324. PMID: 41156784; PMCID: PMC12566097.

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Vélez-Torres LN, Bolaños-Rosero B, Godoy-Vitorino F, Rivera-Mariani FE, Maestre JP, Kinney K, Cavallin-Calanche H. Molecular and culture-based identification of Aspergillus species in water-impacted homes following Hurricane María in Puerto Rico. Sci Rep. 2025 Oct 14;15(1):35922. doi: 10.1038/s41598-025-19869-9. PMID: 41087584; PMCID: PMC12521471.

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Cáceres-Chacón M, Martínez-Guzmán O, Haddock-Martínez HA, Figueroa-Pérez A, Rodríguez-Rosado S, Suárez-Pérez J, Ramos-Sánchez RY, Godoy-Vitorino F, Sierra-Mercado D. Exposure to the herbicide glyphosate leads to inappropriate threat responses and alters gut microbial composition. Front Toxicol. 2025 Nov 5;7:1704231. doi: 10.3389/ftox.2025.1704231. PMID: 41267922; PMCID: PMC12626795.

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Rodriguez-Fernandez IA, Santiago-Rodriguez TM, Figueroa-Pratts PG, Cintrón-Berríos K, Rodriguez-Cornier ND, Toranzos GA. Gut microbial community structure of the adult citrus root weevil Diaprepes abbreviatus. Front Insect Sci. 2025 Oct 28;5:1676003. doi: 10.3389/finsc.2025.1676003. PMID: 41230492; PMCID: PMC12604102.

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Castelli L, García-Amado MA, Rudolf CA,Contreras M, Espinosa-Blanco AS and Godoy-Vitorino F (2025) Microbial diversity in the critically endangered Orinoco crocodile (Crocodylus intermedius): influence of body site and Helicobacter spp. on microbiota composition. Front. Microbiol. 16:1697111. doi: 10.3389/fmicb.2025.1697111

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Mendez, K.; Rosario-Santos, A.; Martínez-Ferrer, M.; Pérez-Rios, N.;Rivera-Torres, A.O.; Romaguera, J.; Godoy-Vitorino, F. Association of TLR-4 and TLR-9 Polymorphisms with HPV Infection and Cervical Dysplasia in Hispanic Women. Cancers 2025, 17, 3795. https://doi.org/10.3390/cancers17233795

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Projects

Check out the Research Projects sponsored by the COBRE Center:

  • Microbiome-driven social behavior adaptation in cavefish

     Roberto Rodríguez, Ph.D.

    - Instagram de su laboratorio: @brainsinthedark
    - ORCID ID: 0000-0002-7716-1342
    - LinkedIn: https://www.linkedin.com/in/roberto-rodriguez-morales/

    Biography

    Dr. Roberto Rodríguez is an Assistant Professor in the Department of Anatomy & Neurobiology at the University of Puerto Rico (UPR) School of Medicine. His research explores the mechanisms underlying social behavior adaptation using fish models. He earned his PhD in Anatomy at the UPR School of Medicine, where he investigated genetic mechanisms of sensory system regeneration in zebrafish, applying advanced tools such as CRISPR/Cas9 genome editing.

    As a postdoctoral fellow at Lehigh University under the mentorship of Dr. Johanna Kowalko, Dr. Rodríguez examined the repeated evolution of aggressive behavior in the blind Mexican cavefish, Astyanax mexicanus. His contributions as a trainee have been published in journals including Zebrafish, Gene Expression Patterns, and BMC Ecology and Evolution.

    In 2023, Dr. Rodríguez returned to UPR to establish his independent laboratory, focused on the intersection of sensory system function and social behavior in A. mexicanus. His program has been supported by multiple awards, including pilot project grants from the RCMI and COBRE Neuroplasticity Center at UPR, as well as an NIH R16 SuRE-First award from the National Eye Institute. He now also leads a research project within the Puerto Rico Center for Microbiome Sciences (COBRE Phase I), investigating how gut microbiome diversity shapes social behavior in cavefish. His mentor is Dr Riccardo Papa a Professor of Evolution at UPR Rio Piedras.

     Keywords

    • Mechanisms underlying sensory system adaptation (microbiota diversity, genetic diversity, etc.)
    • Sensory system plasticity (lateral line)
    • Sensory system regeneration (lateral line)

    Project summary

    Social behaviors are a hallmark of life across the animal kingdom, from insects like flies and ants to vertebrates such as fish, amphibians, rodents, and humans. Yet, the display of these behaviors varies widely: some species live in complex societies, while others are solitary. Even within the same species, populations may differ in how social they are. A striking example is the Mexican tetra (Astyanax mexicanus), which exists as two forms—highly social, river-dwelling surface fish and blind, cave-dwelling fish that have largely lost social behaviors. Our lab is interested in uncovering the biological mechanisms that drive this repeated loss of sociality in cavefish populations.

    One of our central projects, supported by the Puerto Rico Center for Microbiome Sciences, investigates how gut microbiome diversity influences social behavior adaptation. Using a resident–intruder assay, we focus on aggression and social hierarchy formation to address two key questions: (1) Do dietary changes or microbiome imbalances alter social dynamics in surface and cavefish? (2) Are specific microbiome signatures linked to dominance, subordination, or aggression? This work will clarify how the gut microbiome contributes to both social and asocial phenotypes in a unique natural model.

    In parallel, we study how blind cavefish have adapted through expansions of the mechanosensory lateral line—a superficial system of hair cells similar to those of the vertebrate inner ear. By investigating the developmental mechanisms that drive these expansions, we aim to identify genetic factors that promote sensory growth and test whether such compensations also influence social behavior.

    Fig. 1. The Mexican tetra, Astyanax mexicanus is a vertebrate fish that exists as two morphotypes: ancestral surface fish (top), and at least 30 populations of cave-adapted, blind cavefish (bottom). 

    Fig. 2. The resident-intruder assay is used to quantify aggressive interactions in fish dyads of the Mexican tetra. 

    Fig. 3. The mechanisms underlying social behavior adaptation are multifactorial, including natural genetic variation, and potentially gut microbiome diversity. 

    Meet Roberto’s Team: 

    Fabiola Pagán-Torres – This email address is being protected from spambots. You need JavaScript enabled to view it. - GRADUATE

    Alana del Coral López-Cruz – This email address is being protected from spambots. You need JavaScript enabled to view it. - GRADUATE

    Dhalma Bayron-Ho – This email address is being protected from spambots. You need JavaScript enabled to view it. - GRADUATE

    Julián Navarro-Pagán – This email address is being protected from spambots. You need JavaScript enabled to view it. - GRADUATE

    Angel Márquez-Otero – This email address is being protected from spambots. You need JavaScript enabled to view it. – LAB TECHNICIAN

    Paola Figueroa – This email address is being protected from spambots. You need JavaScript enabled to view it. - UNDERGRADUATE

    Alexander Figueroa – This email address is being protected from spambots. You need JavaScript enabled to view it. - UNDERGRADUATE

    Luis Perez – This email address is being protected from spambots. You need JavaScript enabled to view it. - UNDERGRADUATE

    Sofia Cuevas – This email address is being protected from spambots. You need JavaScript enabled to view it. - UNDERGRADUATE

    Jamilette Crespo – This email address is being protected from spambots. You need JavaScript enabled to view it. - UNDERGRADUATE

    Carlos Gonzalez – This email address is being protected from spambots. You need JavaScript enabled to view it. - UNDERGRADUATE

    Homar Cardona – This email address is being protected from spambots. You need JavaScript enabled to view it. - UNDERGRADUATE

    Adrian Rivera – This email address is being protected from spambots. You need JavaScript enabled to view it. - UNDERGRADUATE

    Axel Rodriguez – This email address is being protected from spambots. You need JavaScript enabled to view it. - UNDERGRADUATE

  • Microbiome responses to edelfosine in epilepsy

    Yancy Ferrer, Ph.D.

    Assistant Professor

    Dept Anatomy and Neurobiology, UPR School of Medicine

    - Instagram:

    - ORCID ID: https://orcid.org/0000-0001-6489-3272
    - LinkedIn: https://www.linkedin.com/in/yancy-ferrer-acosta-7b795667/
    - Google Scholar:
    https://scholar.google.com/scholar?hl=en&as_sdt=2007&q=%22Yancy+Ferrer-Acosta%22&btnG=

    -ResearchGate: https://www.researchgate.net/profile/Yancy-Ferrer?ev=hdr_xprf


    Biography:

    Dr. Yancy Ferrer-Acosta is an Assistant Professor and researcher whose career integrates neuroscience, cancer biology, and translational science. She earned his B.S. in Biology from the University of Puerto Rico (UPR)–Río Piedras, followed by a Ph.D. in Biology (specialty in Neuroscience) in the same Campus, where she investigated mechanisms of tau aggregation in neurodegenerative diseases. She then pursued postdoctoral training at the UPR, Rio Piedras Campus and the MSRC, focusing on the field of cancer and immunology.

    Dr. Ferrer has built a research program centered on neuroprotection and lung cancer therapies. Her work explores nanoparticle-based drug delivery across the blood–brain barrier in an in vivo epilepsy model, natural neuroprotective compounds such as tobacco-derived cembranoids in stroke, and the role of immune receptors in neuroinflammation. In parallel, she investigates therapeutic strategies for non-small cell lung carcinoma, including the use of natural compounds and targeted nanotechnology-based approaches.

    With extensive teaching and training experience, Dr. Ferrer is committed to mentoring the next generation of biomedical scientists. She has received research funding, authored peer-reviewed publications, and actively participates in national and local scientific meetings. Her long-term goal is to translate laboratory findings into innovative therapies for neurological disorders and cancer.

    Keywords: Neuroprotection and cancer therapeutics using natural products and nanotechnology

    Project summary

    Current antiepileptic drugs are often ineffective for about 30% of patients and cause significant side effects, underscoring the need for new treatments. Recent research links gut dysbiosis to epilepsy, showing that disrupting the gut microbiome increases seizure susceptibility and affects cognition and behavior. Positive outcomes have been observed in epilepsy patients by altering the gut microbiota through probiotics, diet changes, or fecal matter transplants. Gut microbiota may protect against epilepsy by modulating neuroimmune interactions and reducing neuroinflammation. Probiotic treatments have shown promise in increasing GABA and neurotrophic factors, reducing inflammatory cytokines, and decreasing seizures. However, the impact of treatments on the epileptic gut microbiome remains poorly understood.

    Our study, in collaboration with Dr. Yamixa Delgado’s laboratory aims to address this gap by testing Edelfosine (Ef), an FDA-approved investigational anti-neoplastic drug and HIV-1 latency reversal agent, as a novel epilepsy treatment. Our research reveals that the synthetic lysophospholipid edelfosine (Ef), delivered via a brain-targeted drug delivery system (Tf-SA-Ef-DDS), is an anti-inflammatory molecule and an effective anti-convulsant in a pilocarpine-induced epilepsy mouse model. This project explores whether Ef impacts the gut microbiota and metabolites following an epileptic insult. We will  do this by collecting fecal matter of naïve animals and epilepsy-induced animals before and after the seizure and analyzing their gut microbiota, its metabolites, and brain metabolites. We will compare the obtained data in Ef-treated and untreated mice. We hypothesize that Ef will promote an anti-inflammatory microenvironment within the gut by protecting the survival of butyrate-producing taxa such as Bifidobacteria and Lactobacillus after an epileptic insult.

    The Center for Microbiome Studies (CMS) 16S sequencing and metabolomic cores, together with the mentoring of Dr. Godoy and microbiome experts, our lab will be able to  delve into this new and exciting field, in our search for medications against epilepsy, that can treat brain and gut.

    Other Research Interests

    Our laboratory focuses on advancing research in neuroprotection and lung cancer through both synthetic and natural therapeutic strategies. In the area of neuroprotection, we investigate: 

    (1) Smart nanoparticles designed to cross the blood–brain barrier and deliver protective drugs, tested in epilepsy models and in vitro systems, and their effect on the gut microbiome.

    (2) Tobacco-derived cembranoids that naturally penetrate the blood–brain barrier and show promise in reducing stroke damage, explored through rat stroke models and mechanistic studies.

    (3) The role of the immunoreceptor TREM-Like Transcript-1 (TLT-1) in brain cells following neuroinflammation, by using immunofluorescence, histology, and molecular biology approaches. 

    In our lung cancer projects, we employ the Lewis Lung Carcinoma model to evaluate therapeutic strategies against non-small cell lung carcinoma (NSCLC), including the use of (1) natural products such as cembranoids to inhibit tumor growth, and (2) the development of targeted, biocompatible nanoparticles to deliver anti-tumor drugs. 

    Collectively, our work seeks to develop innovative therapies for neurological disorders and lung cancer, emphasizing natural compounds, nanotechnology, and immune-related mechanisms.

    Link: https://md.rcm.upr.edu/anatomyneurobiology/dt_team/yancy-ferrer-phd/

    Meet the Ferrer Lab Team

    Banner prepared by my students

  • Immunological changes associated with antibiotic use in oropharyngeal cancer

    Stephanie Dorta-Estremera, Ph.D.

    Associate Professor

    Dept. Microbiology and Immunology, UPR School of Medicine

    - Instagram: https://www.instagram.com/dortalab?igsh=OWx3YXVsZjBxaXFz
    - ORCID ID: https://orcid.org/0000-0003-4440-6806
    - LinkedIn: https://www.linkedin.com/in/stephanie-dorta-estremera-1a621a87/
    - Google Scholar: https://scholar.google.com/citations?hl=en&tzom=240&user=lvzur3QAAAAJ
    - Página web de su laboratorio
    https://md.rcm.upr.edu/micro/dt_team/dr-stephanie-m-dorta/

    Biography

    Dr. Dorta-Estremera is a basic and translational immunology researcher who has focused her career on characterizing immune mechanisms modulating the pathogenesis of different diseases such as HIV, autoimmune diseases, and cancer, as well as treatment responses for these diseases.  She obtained her B.S. in Biology at the University of Puerto Rico, Rio Piedras Campus. She did a post-baccalaureate training at the National Institutes of Health and obtained a Ph.D. in Immunology from the University of Texas Health Sciences Center MD Anderson Cancer Center.  Her doctoral degree focused on characterizing the immune-mediated mechanisms involved in the development of lupus. Her postdoctoral training at MD Anderson Cancer Center focused on cancer immunology research and identifying immune correlates for the protection of novel immunotherapies and for chemoradiation in mouse preclinical models and cancer patients. Now, as an assistant professor at the UPR-Medical Sciences Campus and UPR Comprehensive Cancer Center, she is developing a research program to dissect immunological mechanisms involved in treatment resistance on HPV-related cancers, to understand the interaction between microbiota and immune cells in mucosal tissues, and to identify immune and microbial biomarkers that could be targeted to improve current therapies, especially in the Puerto Rican population. 

    Keywords

    • Cancer Immunology
    • HPV-related cancers
    • Microbiome and host interactions
    • Immune monitoring by flow cytometry

    Project summary

    Patients with oropharyngeal cancer (a type of throat cancer) are often prescribed antibiotics to prevent infections after surgery; however, antibiotics can reduce the diversity of good bacteria in the gut and the oral cavity, which may weaken the immune system and lower the effectiveness of cancer treatments like chemotherapy and immunotherapy.

    Some studies show that antibiotic use increases the risk of death in patients with head and neck cancers who receive immune checkpoint therapy. However, not all antibiotics act the same way, posing the question of which antibiotics may be better or worse in terms of their impact on the oral and gut microbiota, immune responses, and response to cancer therapies in oropharyngeal cancer. Therefore, we hypothesize that different antibiotics decrease gut and oral microbial diversity and differentially impact anti-tumor immune responses and oropharyngeal cancer development. 

    This research project has two goals:

    1. Test antibiotics in mouse models of oropharyngeal cancer to see how oral and topical (on the tongue) antibiotics affect tumor growth, immune responses, and cancer treatment responses.
    2. Study the effects of antibiotics on oral bacteria and inflammation in Hispanics at high risk for cancer, to see how antibiotics change oral bacteria and inflammatory markers related to oral cancer risk.

    The long-term goal is to understand which antibiotics harm or help cancer patients so doctors can make better treatment choices and improve survival.

    Other projects in the laboratory:

    1. Identification of immune and microbial biomarkers associated with cancer treatment responses
      1. Díaz-Rivera J, Rodríguez-Rivera MA, Meléndez-Vázquez NM, Godoy-Vitorino F, Dorta-Estremera SM. Immune and Microbial Signatures Associated with PD-1 Blockade Sensitivity in a Preclinical Model for HPV+ Oropharyngeal Cancer. Cancers (Basel). 2024 May 30;16(11):2065. doi: 10.3390/cancers16112065. PMID: 38893183; PMCID: PMC11171047.
      2. Colbert LE, El Alam MB, Wang R, Karpinets T, Lo D, Lynn EJ, Harris TA, Elnaggar JH, Yoshida-Court K, Tomasic K, Bronk JK, Sammouri J, Yanamandra AV, Olvera AV, Carlin LG, Sims T, Delgado Medrano AY, Napravnik TC, O'Hara M, Lin D, Abana CO, Li HX, Eifel PJ, Jhingran A, Joyner M, Lin L, Ramondetta LM, Futreal AM, Schmeler KM, Mathew G, Dorta-Estremera S, Zhang J, Wu X, Ajami NJ, Wong M, Taniguchi C, Petrosino JF, Sastry KJ, Okhuysen PC, Martinez SA, Tan L, Mahmud I, Lorenzi PL, Wargo JA, Klopp AH. Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring. Cancer Cell. 2023 Nov 13;41(11):1945-1962.e11. doi: 10.1016/j.ccell.2023.09.012. Epub 2023 Oct 19. PMID: 37863066; PMCID: PMC10841640.

    Figure 1. In this aim, we will determine the biological effect of oral and topical antibioticson cancer treatment responses in preclinical models of oropharyngeal cancer

    Figure 2. In this aim, we will identify the impact of antibiotic use on the oral microbiota and inflamation in individuals with a high risk of developing cancer

    Meet Stephanie’s team:

    Michael Rodríguez Rivera – This email address is being protected from spambots. You need JavaScript enabled to view it., Ph.D. Microbiology

    Aryanne Torres Ventura – This email address is being protected from spambots. You need JavaScript enabled to view it., Ph.D. Microbiology

    Liz Velázquez Rivera – This email address is being protected from spambots. You need JavaScript enabled to view it., Ph.D. Microbiology

    Andy González Hernández – This email address is being protected from spambots. You need JavaScript enabled to view it., Postbac REPMIC Program

    Emmanuel Colón Rodríguez – This email address is being protected from spambots. You need JavaScript enabled to view it., Research Assistant

    Nicolle Colón Ortiz – This email address is being protected from spambots. You need JavaScript enabled to view it., Postbac

    Isabel Colón – This email address is being protected from spambots. You need JavaScript enabled to view it., Postbac CREPS Program

    Joshua Meléndez Calderon – This email address is being protected from spambots. You need JavaScript enabled to view it., Laboratory Manager

    Mónica Cintrón Santiago - This email address is being protected from spambots. You need JavaScript enabled to view it., Dental Medicine Degree (DMD) Student UPR-MSC













Leadership

  • Filipa Godoy-Vitorino, PhD

    Principal Investigator and Program Director

    Filipa Godoy-Vitorino, PhD, is a microbial ecologist by training and is Professor and Chair of the Department of Microbiology at the University of Puerto Rico School of Medicine. Originally from Portugal, she earned her B.Sc. in Cellular Biology from the University of Porto and her Ph.D. in Microbial Ecology from the University of Puerto Rico, followed by postdoctoral training in metagenomics at the DOE Joint Genome Institute. Her career centers on microbial biodiversity, community dynamics, and dysbiosis in human and animal microbiomes, pioneering metagenomic and bioinformatic approaches across the Caribbean.

    Her research integrates basic laboratory science with translational and clinical microbiome studies. She has led landmark work characterizing cervicovaginal and oral microbiomes in Hispanic and Caribbean populations, identifying microbial features linked to high-risk HPV persistence and cervical cancer. Her group was the first to show the predominance of Lactobacillus iners in Puerto Rican vaginal microbiomes and to link high-risk HPV with Malassezia yeasts, uncovering microbial and metabolic biomarkers of cervical disease. She has co-discovered bacterial phyla, characterized microbiomes across systems on a global scale, and forged collaborations across Puerto Rico and world institutions in the US, Latin America, and Europe.

    Dr. Godoy-Vitorino is Principal Investigator of the NIH/NIGMS-funded Puerto Rico Center for Microbiome Sciences (COBRE). She has held key roles across multiple NIH initiatives focused on cancer prevention and health disparities. As an international ambassador for applied and microbial ecology groups, including ISME and AMI, she collaborates globally while mentoring over 100 trainees in the past years. Her leadership emphasizes inclusion, scientific rigor, and workforce diversification. Her publications can be found here.

    Orcid ID: https://orcid.org/my-orcid?orcid=0000-0003-1880-0498    

    GoogleScholar: https://scholar.google.com/citations?user=vkcHVwEAAAAJ&hl=en&oi=ao

    My NCBI bibliography: https://www.ncbi.nlm.nih.gov/myncbi/1HkRwEN9HRXko/bibliography/public/

    Researchgate: https://www.researchgate.net/profile/Filipa-Godoy-Vitorino

    Instagram Dr Godoy’s lab: @thegodoylab

    Find a summary of the Godoy Lab research, at the-microbiologist.com:

    Web: https://md.rcm.upr.edu/micro/dt_team/filipa-godoy-vitorino/ 

  • Dr. María A. Sosa

    Professor and Chair of the Department of Anatomy & Neurobiology

    Administrative Core Director

    Dr. María A. Sosa is a Professor and Chair of the Department of Anatomy & Neurobiology at the University of Puerto Rico (UPR) Medical Sciences Campus, where she has led an active research program for more than 26 years. She earned her B.S. in Chemistry from the Pontifical Catholic University of Puerto Rico, followed by a Ph.D. in Neuroscience from the University of Florida, and completed postdoctoral training at the UPR Institute of Neurobiology.

    Dr. Sosa’s research explores the neural mechanisms underlying interactive behaviors in invertebrates and examines how environmental contaminants impact the nervous system of aquatic and terrestrial species. Her laboratory has made significant contributions to understanding synaptic physiology, sensory system development, biogenic amine signaling, and the effects of anthropogenic stressors on behavior and neural circuitry. She has served as PI, Co-I, or Subproject PI on multiple NIH and NSF grants, including projects focused on environmental neuroscience, synaptic mechanisms, and research infrastructure renovation.

    In addition to her scientific work, Dr. Sosa has held key administrative and leadership roles, including Interim Associate Dean for Biomedical Sciences and Interim Director of the Institute of Neurobiology. She has mentored over 15 faculty researchers and has overseen major laboratory renovation and infrastructure projects, contributing substantially to the growth of neuroscience research in Puerto Rico.

    Orcid ID:  https://orcid.org/0000-0003-2547-2875

    GoogleScholar: https://scholar.google.com/citations?user=NTiUGoQAAAAJ&hl=es&oi=ao 

    My NCBI bibliography: https://www.ncbi.nlm.nih.gov/sites/myncbi/maria.sosa.2/bibliography/40601172/public/?sort=date&direction=ascending

  • Dr. Mark Miller

    Professor in the Department of Anatomy & Neurobiology at the University of Puerto Rico Medical Sciences Campus

    Director Faculty Development Core

    Dr. Mark Miller is a Professor in the Department of Anatomy & Neurobiology at the University of Puerto Rico Medical Sciences Campus and an internationally recognized neuroscientist whose career spans more than four decades of research on neural circuit structure and function. He earned his B.A. in Psychology from the University of Pennsylvania and his M.S. and Ph.D. in Neuroscience from the University of Connecticut, followed by postdoctoral training in neurophysiology and animal behavior in Hawaii, Jerusalem, and UCLA. His work has advanced fundamental understanding of neuromodulation, neural plasticity, neuropeptide signaling, and central pattern generator networks, using both vertebrate and invertebrate model systems.

    Since joining UPR in 1992, Dr. Miller has led multiple large-scale collaborative programs, including an NSF Undergraduate Research Mentoring program, the NSF CREST Center in Environmental Neuroscience, and an NSF PIRE program on neural mechanisms of reward and decision-making. He has also played key leadership roles in the NIGMS-funded COBRE Center for Neuroplasticity, serving as Interim Director of Phase I and current Director of the Administrative Core. His research group recently expanded into parasitology–neurobiology interfaces, examining how schistosome infection alters snail host neural systems and behavior.

    A dedicated mentor and scientific leader, Dr. Miller has provided extensive guidance to early-career investigators and continues to support UPR’s advancement as a competitive biomedical research institution.

Administrative Peronnel

  • Kreshlya De La Paz Rodríguez

    Program Coordinator

    Mrs Kreshlya De La Paz Rodríguez is a public health professional with over five years of experience managing large-scale federal health programs and infrastructure projects exceeding $200 million. She specializes in project coordination, compliance, data-driven analysis, and interagency collaboration. As a Public Health Analyst with HRSA, she administered $215 million in federal funds for 165 beneficiaries, led contractor teams, and developed SOPs that significantly improved operational efficiency. Previously, she served as a CDC Quarantine Public Health Officer and coordinated NIH research programs. She holds master’s degrees in Public Health and Forensic Criminal Studies and is certified in project management and emergency response.

  • Dr. Nydia L. Rivera-Rivera, PhD

    Dr. Nydia L. Rivera-Rivera, PhD is a neuroscientist and educator with over a decade of experience in higher education, research, and faculty development in Puerto Rico. She earned her PhD in Cellular and Molecular Biology from the University of Puerto Rico, Río Piedras, with a research focus on neuroscience and developmental biology. From 2013 to 2024, she served as Assistant Professor at the University of Puerto Rico, Bayamón Campus, where she taught courses in neuroscience, human anatomy and physiology, microbiology, immunology, and developmental biology. Dr. Rivera-Rivera is highly experienced in curriculum design, laboratory instruction, student mentorship, and research ethics, and has served on multiple institutional committees, including IRB and biosafety. Her work reflects a strong commitment to undergraduate and graduate education, interdisciplinary research, and the professional development of future scientists. She is the COBRE Microbiome Sciences Outreach, Education and Logistics Coordinator.

Brenda Carrucini

Administrative support
Microbiology Dept. 787-758-2525 ext 1308

Vivian Santos

Administrative support
Anatomy Dept. 787-758-2525 ext 1500

External Advisory

Jack Gilbert

External Advisory Committee members

  • Professor
  • Department of Pediatrics and
  • Scripps Institution of Oceanography
  • Associate Vice Chancellor for Marine Science
  • Deputy Director for Scripps Institution of Oceanography

Biography

Professor Jack A. Gilbert (he/him) earned his Ph.D. from Unilever and Nottingham University, UK in 2002, and received his postdoctoral training at Queens University, Canada. From 2005-2010 he was a senior scientist at Plymouth Marine Laboratory, UK; and from 2010-2018 he was Group Leader for Microbial Ecology at Argonne National Laboratory, a Professor of Surgery, and Director of The Microbiome Center at University of Chicago. In 2019 he moved to the University of California San Diego, where he is a Professor in Pediatrics and Scripps Institution of Oceanography, Associate Vice Chancellor for Marine Science, and Director of the Microbiome and Metagenomics Center. Dr. Gilbert uses molecular analysis to test fundamental hypotheses in microbial ecology. He cofounded the Earth Microbiome Project and American Gut Project. He has authored more than 450 peer reviewed publications and book chapters on microbial ecology. He is the founding Editor in Chief of mSystems journal. In2014 he was recognized on Crain’s Business Chicago’s 40 Under 40 List, and in 2015 he was listed as one of the 50 most influential scientists by Business Insider, and in the Brilliant Ten by Popular Scientist. In 2016 he won the Altemeier Prize from the Surgical Infection Society, and the WH Pierce Prize from the Society for Applied Microbiology for research excellence. In 2017 he co-authored “Dirt is Good”, a popular science guide to the microbiome and children’s health. In 2018, he founded BiomeSense Inc. to produce automated microbiome sensors. In 2021 Dr Gilbert became the UCSD PI for the National Institutes of Health’s $175M Nutrition for Precision Health program. In 2023 he became President of Applied Microbiology International, and won the 2023 IFF Microbiome Science Prize. His publications can be found here.

Director of the Microbiome and Metagenomics Center
UC San Diego School of Medicine

https://gilbertlab.ucsd.edu/home

https://scripps.ucsd.edu/profiles/jagilbert

Janet Jansson

External Advisory Committee members

Chief Scientist/Laboratory Fellow (Retired) at Pacific Northwest National Laboratory – PNNL

Biography

Janet Knutson Jansson is an American biological scientist and internationally recognized leader in microbial ecology. She currently serves as Chief Scientist for Biology at the Pacific Northwest National Laboratory (PNNL), where she investigates the structure, function, and environmental resilience of complex microbial communities in soils and the human gut. Jansson is a key contributor to the Phenotypic Response of the Soil Microbiome to Environmental Perturbations Science Focus Area and is a Fellow of the American Society for Microbiology. She was the first to use molecular techniques such as genome sequencing to understand the human gut, gaining insight about the types of microbes that were involved in health and disease

Jansson spent much of her early career in Sweden at the Swedish University of Agricultural Sciences, where she served as researcher, lecturer, professor, and Chair of Environmental Biology. After returning to the United States in 2007, she joined Lawrence Berkeley National Laboratory as a senior staff scientist and held joint appointments at the University of California, Berkeley, and the University of Copenhagen.

Since joining PNNL in 2014, Jansson has pioneered multi-omics approaches to study how climate change affects soil and permafrost microbiomes, as well as how drought alters grassland ecosystems. She is also widely recognized for her groundbreaking use of molecular techniques to characterize the human gut microbiome, providing new insights into how diet and disease shape microbial communities. Jansson has served in several scientific leadership roles She served as President of the International Society for Microbiology. She was appointed to the National Academy of Sciences committee on Soil Sciences in 2020. She is currently on the Scientific Advisory Board of Seed.

https://scholar.google.com/citations?user=-G4QxjIAAAAJ&hl=en

https://www.researchgate.net/profile/Janet-Jansson

Martin J Blaser

External Advisory Committee members

  • Henry Rutgers Chair of the Human Microbiome 
  • Professor of Medicine and Pathology & Laboratory Medicine – RWJMS
  • Director, Center for Advanced Biotechnology and Medicine
  • Rutgers University

Biography

Martin J. Blaser holds the Henry Rutgers Chair of the Human Microbiome at Rutgers University, where he also serves as Professor of Medicine and Pathology & Laboratory Medicine, and as Director of the Center for Advanced Biotechnology and Medicine.  Previously, he served as Chair of the Department of Medicine at New York University. A physician and microbiologist, Dr. Blaser has been studying the relationships we have with our persistently colonizing bacteria. His work over 30 years focused on Campylobacter species and Helicobacter pylori, which also are model systems for understanding the interactions of residential bacteria with their hosts. Over the last 20 years, he has also been actively studying the relationship of the human microbiome with health and important diseases including asthma and allergy, obesity, diabetes, neurological conditions, and cancer. Dr. Blaser has served as the advisor to many students, post-doctoral fellows, and junior faculty. He holds 28 U.S. patents and has authored over 600 original articles. He wrote Missing Microbes, a book targeted to general audiences, now translated into 20 languages.

https://cabm.rutgers.edu/profile/martin-j-blaser

Internal Advisory Committee

Debora H. Silva Díaz - MD, FAAP, MEd

  • Dean
  • Professor
  • Department of Pediatrics
  • School of Medicine
  • University of Puerto Rico
  • Pediatric Hospital Medicine 
  • University Pediatric Hospital
  • Medical Center of Puerto Rico and the Caribbean

https://wfme.org/people/dr-debora-h-silva-diaz/ 

Karen Martínez González - MD, MSc

  • Professor
  • Director, Center for the Study and Treatment of Fear and Anxiety
  • Chair Department of Psychiatry
  • Principal Investigator, Hispanic Clinical and Translational Research Education and Career Development (HCTRECD) program (R25MD007607)
  • Web: Link
  • Bibliography: Link

https://www.cccupr.org/investigacion/investigadores/karen-martinez-gonzalez-md-msc/

Microbiome Core Lab

Filipa Godoy-Vitorino, Ph.D.

Core Lab Director

Education

  • Postdoctoral Fellow, Metagenomics, US NSF & DOE Joint Genome Institute (JGI), 2009–2012
  • Ph.D. Biology (Microbial Ecology), University of Puerto Rico Rio Piedras, 2009
  • EU Socrates Erasmus Fellow, Univ. of Las Palmas, Spain (ULPGC), 2002
  • B.S. Biology (Licentiate), University of Porto, Portugal (FCUP), 1998–2002

Mariam Vázquez, Ph.D

Project Coordinator

  • Postdoctoral Researcher, Institute of Neurobiology – UPR Medical Sciences Campus, 2018-2025
  • Complutense University of Madrid - Ph.D. in Neuroscience, 2016
  • Complutense University of Madrid - Master’s Degree in Psychopharmacology and Drugs of Abuse, 2008
  • Princeton University - B.A. in Psychology, 2004

Bio Dr Vazquez

Dr. Mariam Vázquez Berríos is the Project Coordinator for the RCM-COBRE Microbiome Center. She was able to acquire an extensive background in several disciplines including behavior, biochemistry, and molecular biology throughout her college and graduate career and research experience. From cognitive psychology to different aspects of alcohol addiction, this interdisciplinary experience has been crucial to her formation as a scientist.

Dr. Vázquez obtained a bachelor’s degree in Psychology from Princeton University. She pursued a Master’s Degree in Psychopharmacology and Drugs of Abuse, where she began her career as a scientist at Universidad Complutense de Madrid. She then continued to earn her PhD degree at the School of Medicine of Universidad Complutense de Madrid by focusing on the link between the endocannabinoid system and alcoholism. After, she continued her training as a postdoctoral researcher at the Institute of Neurobiology at Recinto de Ciencias Médicas.

As Project Coordinator, she is interested in supporting and furthering microbiome research through the COBRE Center to improve scientific research and, by extension, public and environmental health.

Jaleniz Suarez, B.S.

Miss Suarez is a research associate and bioinformatician with a  Bachelor’s Degree in Science with a major in Environmental Sciences, mentored by Dr. Filipa Godoy-Vitorino. Her research focuses on microbial ecology and applied microbiome science across environmental and clinical contexts with a strong interest in data-driven research and translational science. She contributes to projects examining the microbial community structure in a variety of settings across Puerto Rico. In the COBRE Center she supports data generation, bioinformatics analyses, project organization, and interdisciplinary collaborations. 

787-758-2525, ext 1323 (A376)

Irmarie Cotto, Ph.D

Adjunct Professor

Education

  • Ph.D. in Civil and Environmental Engineering
    Northeastern University, Boston, MA, 2022
  • M.S. in Civil Engineering (Environmental Engineering)
    University of Puerto Rico at Mayagüez, 2015
  • B.S. in Chemical Engineering University of Puerto Rico at Mayagüez, 2011

    Biography

    Irmarie Cotto, Ph.D. is an Adjunct Professor in Bioinformatics at the COBRE Puerto Rico Center for Microbiome Sciences. She earned her Ph.D. in Civil and Environmental Engineering from Northeastern University and completed an NSF ASEE Postdoctoral Fellowship at the University of Washington. Her previous research focused on environmental microbiology, wastewater treatment, and the application of metagenomics and bioinformatics to study microbial communities and antimicrobial resistance in environmental and human-associated systems.

    Dr. Cotto’s work has addressed critical challenges at the intersection of water quality, sanitation, and public health, including nitrogen removal in wastewater systems and environmental drivers of antimicrobial resistance in vulnerable populations. She has published peer-reviewed research in leading journals such as Water Research and Environmental Science & Technology and collaborated with interdisciplinary teams spanning engineering, microbiology, epidemiology, and public health.

    In her role at the COBRE Puerto Rico Center for Microbiome Sciences, Dr. Cotto contributes to bioinformatics training, student mentorship, and collaborative research initiatives that advance microbiome science and data-driven approaches in Puerto Rico.

    Zoila Alvarez-Aponte, Ph.D

    Adjunct Professor

    Education

    • Ph.D. in Microbiology, University of California, Berkeley, 2025
    • B.S. in Industrial Biotechnology, University of Puerto Rico, Mayagüez, 2019

    Biography

    Dr. Zoila Alvarez Aponte is an Adjunct Professor of Metagenomics at the COBRE Puerto Rico Center for Microbiome Sciences (COBRE-PRCMS). Her work has spanned diverse microbial systems, including vaginal, gut, plant-associated, and soil microbiomes, with a unifying focus on how microbial interactions shape community structure and function—and, ultimately, their surrounding environments.

    Dr. Alvarez Aponte obtained her PhD at UC Berkeley, where she investigated nutrient-sharing interactions among soil bacteria using a model nutrient approach. By integrating genomic analyses with molecular and experimental approaches in microbial ecology, she developed a predictive framework for understanding cooperative and competitive interactions within bacterial communities.

    In her role at COBRE-PRCMS, Dr. Alvarez Aponte supports bioinformatics training initiatives and contributes her expertise in data analysis to a range of collaborative research projects. She is deeply committed to interdisciplinary research, mentorship, and serving the people of Puerto Rico and the Caribbean through scientific knowledge.

    Our Philosophy & Vision

    Our Philosophy

    At the Puerto Rico Center for Microbiome Sciences, we believe that scientific discovery thrives in a culture of collaboration, curiosity, and inclusion. Our philosophy is grounded in the understanding that microbiomes play essential roles in human health, disease, behavior, and environmental resilience—and that advancing this field requires interdisciplinary expertise and shared access to cutting-edge technologies.

    We are committed to cultivating an environment where researchers at all career stages can innovate, learn, and grow. By fostering strong partnerships across clinical, basic, and computational sciences, we support rigorous, ethical research that expands knowledge and empowers the next generation of scientists. Our Center values diversity of ideas, mentorship, teamwork, and open scientific dialogue as the foundations of transformative microbiome research.

    Our Vision

    Our vision is to establish Puerto Rico as a leader in microbiome science within the Caribbean and the broader global research community. The PR-CMS aims to drive impactful discoveries, expand research capacity across the UPR system, and strengthen the scientific workforce through integrated training, state-of-the-art core facilities, and support for innovative investigators.

    We aspire to create a sustainable, collaborative research ecosystem that accelerates microbiome-driven solutions to pressing biomedical challenges. As members of national microbiome research networks, we envision Puerto Rico as a hub for excellence, shaping the future of microbiome science through rigorous research, technological innovation, and community engagement.

    Take a look at Dr. Godoy-Vitorino’s vision for what became the Puerto Rico Center for Microbiomes in a Trends in Microbiology ArticleTrends in Microbiology Article:

    What We Do

    🔬 Build Microbiome Research Capacity in Puerto Rico

    PR-CMS accelerates and expands microbiome research at the University of Puerto Rico Medical Sciences Campus by creating an innovative, collaborative platform for discovery, training, and data-driven science

    🧬 Advance Cutting-Edge Microbiome Science

    We support state-of-the-art microbiome research spanning data generation, sequencing, and advanced analyses—establishing the first microbiome research core facility of its kind in the Caribbean

    👩🏽‍🔬 Develop the Next Generation of Scientists

    PR-CMS fosters the growth of early-career investigators into competitive, independent researchers through mentorship, infrastructure, and professional development support

    🤝 Promote Interdisciplinary & Translational Collaboration

    We bring together basic, clinical, and data scientists to address microbiome-driven biomedical challenges and to strengthen interdisciplinary collaborations across campus and beyond

    🧪 Provide Shared Research Infrastructure

    PR-CMS is supported by three integrated cores:

    • Administrative Core – leadership, infrastructure, and faculty development
    • Microbiome Research Core – data production, sequencing, and analysis
    • Research Support Core – sustained support for junior research project leaders

    🌎 Connect Puerto Rico to National Microbiome Networks

    We are an active member of the Microbiome Centers Consortium, contributing to shared resources, data standards, and ethical research practices across the U.S. microbiome community