About

The Medina Lab studies the ecology and evolution of host–microbe interactions, with a focus on cnidarian systems, using approaches that span genomics, developmental and cell biology, and organismal physiology.

Research topics

• Biology
• Genetics
• Computational biology
• Evolutionary biology
• Computer Science
• Ecology
• Astronomy
• Physics
• Nanotechnology
• Chemistry
• Data science
• Chromatography
• Materials science
• World Wide Web
• Library science

Selected publications

• Cassiopea xamachana microbiome across anatomy, development, and geography

  PLoS ONE · 2025-04-11 · 1 citations

  articleOpen accessSenior author

  The upside-down jellyfish holobiont, Cassiopea xamachana, is a useful model system for tri-partite interactions between the cnidarian host, the photosymbiont, and the bacterial microbiome. While the interaction between the host and photosymbiont has been well studied, less is understood of the associated bacterial community. To date, the bacterial microbiome of wild C. xamachana has remained largely uncharacterized. Thus, wild medusae (n=6) and larvae (n=3) were collected from two sites in the Florida Keys. Bacterial community composition was characterized via amplicon sequencing of the 16S rRNA gene V4 region. The medusa bacterial community was dominated by members of the Alphaproteobacteria and Gammaproteobacteria, while Planctomycetota, Actinomycetota, Bacteroidota, and Bacillota were also present, among others. Community composition was consistent between locations and across medusa structures (oral arm, bell, and gonad). The larval bacterial community clustered apart from the medusa community in beta diversity analysis and was characterized by the presence of several Pseudomonadota taxa that were not present in the medusa, including the Alteromonas, Pseudoalteromonas, and Thalassobius genera. A bacterial isolate library encompassing much of the amplicon sequencing diversity was also developed and tested via metabolic assays in a separate culture-dependent analysis of isolates from medusa bells, oral arms, and laplets. Most characteristics were not correlated with host sex or medusa structure, but gelatinase production was more common in laplet isolates, while lactose fermentation was more common in female oral arm isolates. The Endozoicomonas genus was dominant in both amplicon sequencing and in our isolate library, and was equally prevalent across all medusa structures and in both sexes. Understanding the bacterial component of the C. xamachana holobiont will allow us to further develop this important model cnidarian holobiont.

  PublisherDOI

• Scientific diasporas can accelerate the implementation of global biodiversity goals

  Nature Reviews Biodiversity · 2025-05-13

  articleSenior author
  PublisherDOI

• The mycobiome of Cassiopea xamachana as determined by culture-based and metagenomic sequencing

  Symbiosis · 2025-12-01

  articleSenior authorCorresponding
  PublisherDOI

• Speciation across depth gradients in reef corals

  Nature Communications · 2025-11-19 · 1 citations

  articleOpen access

  Ecological speciation through adaptation to different habitats can readily occur without strong geographic isolation when the same traits underlie both ecological divergence and reproductive isolation. In light-dependent corals with environment-mediated spawning, adaptation to varying light regimes across depths provides opportunities for such speciation. We show that depth-related distributions are common among sister lineages of corals within the photic zone. We then investigated molecular drivers of depth-associated adaptive divergence by analyzing sequence variation in proteins related to environmental sensing in depth-segregated and light-dependent lineages in the Orbicella species complex. Specifically, we analyzed 1) two genetically divergent ecotypes of Orbicella faveolata across a depth gradient, and 2) two depth-segregated sister species, O. annularis and O. franksi, with different spawning times following sunset. Genome-wide analyses indicate divergence across depths occurred through adaptation via positive selection on G-protein-coupled receptors (GPCRs). These molecules mediate chemo/photo/thermo-reception, enhancing physiological adaptation across environments, and are also involved in reproductive isolation via differences in spawning time. Our study proposes a molecular mechanism for the origin of depth-segregated coral species, common across anthozoans, in which ecological divergence operates at spatial scales smaller than their larval dispersal potential, and highlights avenues contributing to generating biodiversity in the sea.

  PublisherOA PDFDOI

• Protect US racial affinity groups

  Science · 2025-02-27 · 2 citations

  letterOpen access

  On its first day, the Trump administration released several executive orders terminating diversity, equity, and inclusion (DEI) programs, calling them “illegal,” “immoral,” and “discriminatory” (1, 2). DEI programs include racial affinity groups, which counter the systemic barriers to inclusion and advancement that Black, Indigenous, and People of Color (BIPOC) face in science, technology, engineering, and mathematics (STEM) disciplines (3, 4). These organizations provide a welcoming space for underrepresented scientists to give and receive culturally aware mentorship (5). Given that diverse teams produce more innovative science (6), racial affinity groups benefit not only BIPOC scientists but also their employers and the public. Racial affinity groups do not violate US antisegregation or antidiscrimination laws; they enable equitable access to resources that support academic advancement for all. To protect scientists and scientific output, US stakeholders must work to protect affinity groups from government interference.

  PublisherOA PDFDOI

• <i> Endozoicomonas</i> dominance and Vibrionaceae stability underpin resilience in urban coral <i>Madracis auretenra</i>

  PeerJ · 2025-04-15 · 5 citations

  articleOpen accessSenior author

  Coral resilience varies across species, with some exhibiting remarkable stability and adaptability, often mediated by their associated microbiomes. Given the species-specific nature of coral-microbiome interactions, investigating the microbiomes of urban-adapted corals provides critical insights into the health, dynamics, and functioning of coral holobionts. In this study, we examined the microbiome of Madracis auretenra , a Caribbean coral from Santa Marta, Colombia, across contrasting environmental conditions. Over two years, we compared the microbiomes of healthy and stressed coral colonies from two distinct reef habitats—urban and protected—using 16S rRNA gene sequencing (V4 region) to assess microbial diversity. Our findings revealed microbial richness and diversity were primarily influenced by seasonal and local factors rather than host-specific traits such as interaction with algae, health status, or microhabitat. These variations were not substantial enough to disrupt the overall microbial community structure, which remained stable across temporal and spatial scales. Dominant taxa included Endozoicomonas , along with Vibrionaceae and Rhodobacteraceae, which form dense ecological interaction networks. Notably, nutrient and oxygen levels emerged as key drivers of microbiome fluctuations, yet Vibrionaceae populations exhibited exceptional temporal stability. These findings highlight the presence of a well-structured and resilient coral microbiome with minimal seasonal variability, even in urban-influenced environments. We propose that the dominance of Endozoicomonas and the stability of Vibrionaceae populations play a pivotal role in maintaining microbiome balance, ultimately contributing to the ecological resilience of M. auretenra in dynamic reef habitats.

  PublisherDOI

• RNAseq sheds light on “who is doing what” in the coral <i>Porites lutea</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-09 · 1 citations

  preprintOpen access

  Abstract Global decline of coral reefs due to climate change necessitates nature-based protection strategies for these crucial ecosystems. Developing such strategies requires a thorough understanding of the complex roles and interactions occurring within the coral holobiont. Using RNAseq, we investigated the active microbiome of healthy stony coral Porites lutea , focusing on the coral tissue, the green endolithic algal layer ( Ostreobiu m layer), and the deeper coral skeleton. We identified distinct, metabolically active communities within these compartments and highlight substantial metabolic redundancy across carbon, nitrogen, and sulphur pathways. Our study provides first transcriptomic evidence of Ostreobium’s ability to transfer fixed carbon to other holobiont members and the coral host. Additionally, we highlight critical roles of diverse coral holobiont members in nutrient cycling and maintaining homeostasis through scavenging of reactive oxygen and nitrogen species. This study provides novel molecular-level understanding of the functional roles played by diverse coral holobiont members in their respective compartments and underscores that corals harbour distinct microbiomes with wide-ranging functions.

  PublisherDOI

• Water Quality Trends and Eutrophication Indicators in a Large Subtropical Estuary: A Case Study of the Greater Charlotte Harbor System in Southwest Florida

  Estuaries and Coasts · 2025-01-25 · 8 citations

  article1st authorCorresponding
  PublisherDOI

• Evaluation of full-length <i>16S</i> rRNA amplicon sequencing using Oxford Nanopore Technologies for diversity surveys of understudied microbiomes

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-21 · 1 citations

  preprintOpen accessSenior author

  ABSTRACT The use of long-read sequencing using portable Oxford Nanopore Technologies (ONT) is becoming increasingly popular in the study of host-associated microbiomes. However, its application has not yet been optimized for characterizing understudied microbiomes, such as those in marine environments. We evaluated the accuracy and consistency of ONT sequencing of full-length 16S rRNA genes for diversity surveys of symbiotic dinoflagellate (family Symbiodiniaceae) microbiomes. When comparing amplicon sequencing of the full-length bacterial 16S rRNA gene with only its V4 hypervariable gene region using a known microbial community, the former recapitulated the bacterial taxonomic composition more accurately. ONT sequencing was also highly consistent between sequencing runs and flow cells. Long-read sequencing technologies enable microbiome surveys using the full-length 16S rRNA gene, achieving higher accuracy and resolution. This work validates ONT long-read sequencing as a powerful tool for marine microbiome studies to catalyze advancements in the fields of ecology and evolution, resource management, and conservation.

  PublisherOA PDFDOI

• Genomic potential of crustose coralline algae-associated bacteria for the biosynthesis of novel antimicrobials

  Microbial Genomics · 2025-07-25 · 1 citations

  articleOpen access

  The global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from a CCA collected from Varadero Reef located in Cartagena Bay, Colombia. After performing antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 115 putative biosynthetic gene clusters (BGCs) and identified genes in relevant biosynthetic pathways across the three genomes. Nonetheless, we hypothesize that the biosynthesis of antimicrobial compounds results from the expression of undescribed BGCs. Further analysis revealed the absence of genes pertaining to the synthesis of coral larvae settling molecule tetrabromopyrrole, commonly produced by CCA-associated bacteria. We also discuss how differential representation of gene functions between the three isolates may be attributed to the distinct ecological niches they occupy within the CCA. This study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis, and highlights the potential of specialized marine environments like CCA.

  PublisherDOI

Recent grants

• RAPID: Coral robustness: lessons from an "improbable" reef

  NSF · $200k · 2016–2019

• CAREER: Coral Health Genomics: Transcriptome Analysis of two Caribbean Species and their Algal Symbionts

  NSF · $1.1M · 2007–2013

• BE/GENEN Coral Reef Genomics: A Genome Wide Approach to the Study of Cnidarian Symbiosis

  NSF · $740k · 2005–2009

• CAREER: Coral Health Genomics: Transcriptome Analysis of two Caribbean Species and their Algal Symbionts

  NSF · $51k · 2013–2014

• Collaborative Research: Ontogenic change in Cnidarian-algal symbioses: A genomic and ecologic perspective

  NSF · $258k · 2010–2013

Frequent coauthors

• Allen G. Collins

  Smithsonian Institution

  49 shared

• Roberto Iglesias‐Prieto

  Pennsylvania State University

  40 shared

• Cheryl M. Woodley

  National Oceanic and Atmospheric Administration

  35 shared

• Shinichi Sunagawa

  ETH Zurich

  33 shared

• Aki Ohdera

  33 shared

• Christian R. Voolstra

  International Coral Reef Society

  33 shared

• Ehsan Kayal

  Iowa State University

  28 shared

• Jeffrey L. Boore

  Institute for Systems Biology

  23 shared

Education

• Ph.D.

  The Pennsylvania State University

• B.S.

  The Pennsylvania State University