About

Silvia Restrepo is an adjunct professor at the School of Integrative Plant Science, specializing in Plant Pathology and Plant-Microbe Biology. She is the President of the Boyce Thompson Institute (BTI), where she is involved in research related to plant diseases, with a particular focus on cassava and potato diseases. Her interests include bioinformatics and computational biology, and she is engaged in education, mentoring, and interdisciplinary collaboration to advance understanding in her field.

Research topics

• Biology
• Evolutionary biology
• Ecology
• Computer Science
• Pathology
• Medicine
• Sociology
• Social Science
• Zoology
• Chemistry
• Geography
• Chromatography
• Virology
• Immunology
• Environmental planning
• Botany
• Biotechnology
• Environmental health
• Genetics

Selected publications

• Genomic and Functional Diversity of Pseudoalteromonas Associated with the Tropical Bivalve Anadara Tuberculosa

  Microbial Ecology · 2026-04-24

  articleOpen access

  Members of the genus Pseudoalteromonas are ecologically versatile marine bacteria involved in nutrient cycling, chemical signaling, and competition for resources via bioactive compound production. Here, we characterize the genomic and functional diversity of 19 Pseudoalteromonas isolates from the bivalve Anadara tuberculosa to elucidate ecological strategies enabling coexistence in host-associated environments. Whole-genome sequencing and phylogenomic inference revealed extensive genomic diversity, with most isolates affiliated with recognized taxa and two genomically distinct lineages representing candidate novel species. Functional profiling with Traitar identified 67 traits related to enzymatic activity, substrate utilization, and environmental tolerance, revealing a bimodal structure: one assemblage (Pseudoalteromonas maricaloris, Pseudoalteromonas xiamenensis, Pseudoalteromonas piscicida) exhibited diverse biosynthetic pathways consistent with chemical competition strategies, while a second assemblage including the two candidate species displayed broader carbohydrate utilization with streamlined biosynthetic capacity. Notably, unique non-NRPS siderophore clusters in Pseudoalteromonas gelatinilytica and one candidate species suggest alternative iron acquisition strategies adapted to host-associated niches. Principal coordinate analysis revealed two distinct ecological assemblages, indicating that functional differentiation through niche partitioning rather than direct competition enables coexistence of phylogenetically related populations within the bivalve microbiome. Comparative genomic metrics (ANI, AAI, dDDH) support the proposal of Pseudoalteromonas pianguae sp. nov. and Pseudoalteromonas iscuandensis sp. nov., expanding the known diversity of this ecologically important genus. This genome-informed approach provides mechanistic insight into bacterial diversification in tropical bivalve holobionts and establishes a foundation for exploring Pseudoalteromonas-mediated interactions in marine invertebrate microbiomes.

  PublisherDOI

• Deciphering the phenol degradation metabolic pathway in <i>Scedosporium apiospermum</i> HDO1

  Applied and Environmental Microbiology · 2025-07-10 · 1 citations

  articleOpen access

  ABSTRACT The filamentous fungus Scedosporium apiospermum is a microorganism capable of phenol degradation. Phenol is a petroleum-derived pollutant and a compound widely used in several industries. As a result of its widespread use, phenol is commonly discarded and accumulated in soils and water bodies. In this study, overexpressed and repressed genes that produce enzymes involved in phenol metabolism were identified in S. apiospermum HDO1 when the fungus grows in the presence of phenol. The fungus was grown with either glucose (control) or phenol as the sole carbon source to achieve this. RNA from the mycelium was extracted and sequenced using the Illumina Hiseq-4000 platform, with paired-end libraries. Eighteen genes coding for enzymes related to catechol ortho-cleavage, catechol meta-cleavage, and hydroquinone pathways were annotated from the assembled transcriptome. In the differential gene expression analysis, 11 genes coding for phenol 2-monooxygenase, catechol 1,2-dioxygenase, 3-oxoadipate enol lactonase, hydroxyquinol 1,2-dioxygenase, and aldehyde dehydrogenase were overexpressed. In contrast, one gene coding for protocatechuate 3,4-dioxygenase was repressed. We show for the first time that phenol degradation in S. apiospermum occurs through one of the catechol routes, the catechol-ortho ring cleavage pathway, and through the hydroquinone A pathway. These findings are important because they improve the understanding of how eukaryotic microorganisms with the potential for bioremediation degrade organic pollutants such as phenol. IMPORTANCE In recent years, bioremediation has emerged as one of the solutions to eliminate pollutants from the environment. Scedosporium apiospermum is one of the fungi capable of tolerating and degrading common pollutants such as phenol. This ability is of great interest as it highlights its potential for use, but also as an important eukaryotic model in contaminant metabolism. S. apiospermum has been widely studied for its clinical significance, but little is yet known about its role in natural environments and its capacity for removing organic pollutants. Using previously published biochemical data together with our differential gene expression results, we validated and completed the proposed phenol metabolic pathways.

  PublisherDOI

• The XopAE Effector from <i>Xanthomonas phaseoli</i> pv. <i>manihotis</i> Targets HSP20-like p23 Cochaperone to Suppress Plant Basal Immunity

  Molecular Plant-Microbe Interactions · 2025-01-01 · 1 citations

  articleOpen access

  Pathogenic bacteria use Type 3 effector proteins to manipulate host defenses and alter metabolism to favor their survival and spread. The non-model bacterial pathogen Xanthomonas phaseoli pv. manihotis ( Xpm) causes devastating disease in cassava. The molecular role of Type 3 effector proteins from Xpm in causing disease is largely unknown. Here, we report that the XopAE effector from Xpm suppresses plant defense responses. Our results show that XopAE is a suppressor of basal defenses such as callose deposition and the production of reactive oxygen species. XopAE targets a small heat shock protein ( Mep23-1 cochaperone) in cassava and its homolog Atp23-1 in Arabidopsis. XopAE localizes to the nucleus and in scattered points throughout the cell border, whereas Mep23-1 shows a nucleocytoplasmic localization. Upon interaction, XopAE hijacks Mep23-1 to the scattered points throughout the cell border, and they also interact in the nucleus. Our results indicate that the interaction between XopAE and Mep23-1 is essential for suppressing basal plant defense. This study is one of the first to address the molecular mechanisms deployed by Xpm to cause disease in cassava, a non-model crop plant. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

  PublisherDOI

• Microscopical and molecular characterization of the infection cycle of <i>Phytophthora betacei</i> during disease development on tree tomato ( <i>Solanum betaceum)</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-17

  preprintOpen accessSenior authorCorresponding

  Abstract Phytophthora betacei is a recently described oomycete plant pathogen closely related to Phytophthora infestans sensu stricto . This plant pathogen naturally infects tree tomato ( Solanum betaceum ) but has not been reported on tomatoes and potatoes, the primary hosts of P. infestans . The aim of this study was to characterize the infection cycle of P. betacei using microscopy and molecular approaches. Several strains were inoculated in susceptible tree tomato plants and disease progression was monitored via six epidemiological parameters. Although different P. betacei strains displayed a highly variable disease phenotype, the most aggressive one was chosen for further plant inoculations. Samples at different time points of the infection cycle were analyzed at the cellular level via light and scanning electron microscopy (SEM) and at the molecular level via qRT-PCR of infection-stage-specific markers. The infection cycle of P. betacei differed from that of P. infestans in having a longer biotrophic stage, larger lesions, and higher sporulation capacity. Additionally, P. betacei transcriptomic profiles were monitored along the infection cycle via RNAseq and evidenced a changing expression landscape that supports an elongated hemibiotrophic transition and a clear distinction from what is being expressed in the mycelium or the sporangia. This study provides novel insights into the interaction between P. betacei and S. betaceum .

  PublisherOA PDFDOI

• Genetic diversity and comparative genomics across Leishmania (Viannia) species

  Communications Biology · 2025-06-14 · 3 citations

  articleOpen access

  Leishmaniasis is an important public health problem worldwide, with a broad spectrum of clinical and epidemiological features partly associated with the diversity and complex life cycle of the Leishmania parasites. This study analyzes genomic data from 205 Leishmania (Viannia) samples, including 65 newly sequenced clinical isolates. It also provides chromosome-level genome assemblies for 10 isolates representing different species and populations. The observed distribution of Leishmania genomic diversity across the sampling locations suggests rapid adaptation to different ecosystems. The phylogenomic analysis provides new hypotheses challenging the current delimitation of species. Pangenomic analysis of high-quality assemblies shows consistent copy number variation between species for different gene families. Larger and more diverse amastin gene families were observed in the assembled genomes compared to previous reports based on the analysis of short-read data. This work provides genomic resources and helpful information regarding central problems in the biology of Leishmania spp, including species diversification, transmission dynamics, and the evolution of virulence mechanisms.

  PublisherOA PDFDOI

• Novel nanoparticle‐mediated plasmid delivery in bacteria for difficult applications

  Journal of Chemical Technology & Biotechnology · 2025-09-18 · 1 citations

  articleOpen access

  Abstract BACKGROUND This study presents the development and application of magnetite/silver‐pDMAEMA‐PEG‐BUFII nanobioconjugates as an advanced plasmid delivery system in bacteria. These nanobioconjugates demonstrated superior efficiency compared to traditional methods in four challenging applications: (i) genomic editing in Gram‐positive bacteria; (ii) CRISPR/Cas9‐mediated antibiotic resistance control; (iii) large plasmid delivery; and (iv) transformation in complex environmental matrices such as soil. RESULTS Functionalization with pDMAEMA improved plasmid loading, while PEGylation enhanced stability, dispersity, and cellular uptake. The system enabled high‐efficiency transformation in Streptomyces JH010 , overcoming low conjugation efficiency observed with conventional approaches. In Escherichia coli , the nanobioconjugates facilitated effective CRISPR /Cas9‐based resensitization to antibiotics, achieving higher transformation and genome‐editing efficiencies than traditional competent‐cell methods. Furthermore, the nanobioconjugates achieved large plasmid delivery without requiring conjugation or phage‐based methods, thereby simplifying transformation procedures. In soil environments, plasmid transfer was significantly enhanced compared to transformation in chemically/competent cells, demonstrating potential for bioremediation and environmental applications. Characterization confirmed successful multi‐functionalization, enhanced colloidal stability, and low toxicity across bacterial models. The magnetic properties of the nanoparticles further enable potential recovery and reuse, reducing environmental impact. CONCLUSION These findings highlight the versatility and robustness of nanobioconjugate‐mediated plasmid delivery, providing an effective alternative for bacterial genetic engineering in medical, industrial, and environmental settings. Future research should focus on optimizing delivery conditions for diverse bacterial species, scaling up for industrial applications, and assessing long‐term impacts in complex biological systems. © 2025 The Author(s). Journal of Chemical Technology and Biotechnology published by John Wiley &amp; Sons Ltd on behalf of Society of Chemical Industry (SCI).

  PublisherOA PDFDOI

• Mefenoxam Sensitive Isolates of <i>Phytophthora infestans</i> Can Quickly Acquire and Lose Resistance to This Fungicide

  Plant Disease · 2025-09-05

  articleSenior author

  Phytophthora infestans is an oomycete that causes late blight disease in multiple solanaceous crops, including potato and tomato. This makes it a worldwide concern for farmers, given the level of crop loss and its explosive epidemic potential. Although fungicides have traditionally been used for managing this disease, populations of P. infestans resistant to fungicides have been documented. Furthermore, it has been shown that isolates considered originally sensitive to mefenoxam acquire resistance to it after a single exposure in vitro to low concentrations of this widely used fungicide. Previous studies have measured such resistance in terms of mycelial growth. However, there is still much unknown regarding how this phenomenon is triggered. Here, we explored the dynamics of how this resistance is gained and lost, in terms of both mycelial growth and sporangial production. Isolates that acquired resistance to mefenoxam (i) did not sporulate significantly more than they did before, (ii) were not affected by repeated exposures to a high concentration of mefenoxam, (iii) lost the acquired resistance after a single passage through medium without mefenoxam, and (iv) reacquired the resistance after a single re-exposure to a low concentration of mefenoxam. Such dynamic behavior aligns well with the pleiotropic drug resistance mechanism that has been proposed as the molecular process behind the acquired resistance phenomenon, as well as with an epigenetic mode of regulation. This study narrows our knowledge gap on this phenomenon and reinforces the importance of deciphering whether it could be an issue under field conditions. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

  PublisherDOI

• Fungal endophytes of cactus ( <i>Stenocereus</i> spp.) as a potential alternative to alleviate drought stress in juveniles of <i>Theobroma cacao</i> L. ICS95

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-09-17

  preprintOpen accessSenior authorCorresponding

  Abstract Theobroma cacao , one of Colombia’s most economically and socially significant crops, faces productivity challenges due to drought. This stress can reduce growth, leaf area, and stomatal conductance (Ks), and generate reactive oxygen species (ROS). Therefore, exploring solutions to enhance drought tolerance is crucial. This study aimed to evaluate the use of fungal root endophytes from Stenocereus spp. to induce drought tolerance in T. cacao genotype ICS95. In vitro drought tolerance screening identified five fungal isolates that exhibited the highest biomass production and less than 20% biomass loss under drought compared to non-drought conditions. The soil of juvenile T. cacao plants was inoculated with these isolates, and physiological and morphological parameters were assessed, including leaf water potential (Ψ L ), stomatal conductance (Ks), proline content, and growth. The results showed a significant decrease in Ψ L and Ks in juveniles under drought stress, which was observed across all five fungal isolates tested. However, juveniles inoculated with Phoma sp. exhibited less negative Ψ L and lower Ks than non-inoculated controls, suggesting that this fungus may be a potential inducer of drought tolerance in T. cacao ICS95. One intriguing result was that plants inoculated with this fungus accumulated less proline during the drought treatment. Under non-drought conditions, juveniles inoculated with Acrophialophora sp., Ectophoma sp., Fusarium sp., and Phoma sp. exhibited an increase in mean leaf area. These findings suggest that fungal endophytes associated with Stenocereus spp. could provide a potential alternative for alleviating drought stress and may also mediate growth promotion under non-drought conditions in cacao. Importance Theobroma cacao is among the world’s most valuable crops, yet its productivity is increasingly threatened by fluctuating rainfall and prolonged drought. Identifying sustainable strategies to mitigate these impacts is therefore critical. Xerophilic plants, such as Stenocereus spp., harbor diverse fungal endophytes adapted to arid environments, representing a promising source of microorganisms capable of enhancing stress tolerance in commercial crops. Our study demonstrates that cactus-derived endophytes could improve drought resilience in juvenile cacao by modulating physiological responses such as stomatal conductance and leaf water potential. Furthermore, under favorable conditions, some endophytes could promote growth by increasing leaf area compared to non-inoculated plants. These findings underscore the potential of fungal endophytes from arid ecosystems as biotechnological tools for sustainable cacao production, offering an environmentally friendly alternative to mitigate drought stress while enhancing plant performance.

  PublisherOA PDFDOI

• El papel actual de la mujer en el desarrollo de la ciencia, una mirada desde mi experiencia

  Naturaleza y Sociedad Desafíos Medioambientales · 2025-03-07

  articleOpen access1st authorCorresponding

  In this essay, Silvia Restrepo reflects on the role of women in science, highlighting the historical and current challenges women face in this field. Drawing from her personal experience as president of the Boyce Thompson Institute, Silvia discusses the importance of diversity in scientific and professional teams, arguing that the inclusion of women is crucial for innovation and success. She criticizes policies that seek to eliminate diversity, equity, and inclusion initiatives, and instead proposes preventing negative actions that perpetuate discrimination. Additionally, she suggests concrete actions to make the work of female scientists more visible and to foster role models for girls and young women interested in science.

  PublisherOA PDFDOI

• Prevalence and risk factors of Campylobacter jejuni and Campylobacter coli in fresh chicken carcasses from retail sites in Bogotá, Colombia

  Heliyon · 2024-02-01 · 9 citations

  articleOpen accessSenior authorCorresponding

  Campylobacter is one of the most common causes of foodborne gastroenteritis. The objective of this study was to estimate the prevalence and risk factors associated with Campylobacter jejuni and Campylobacter coli species in fresh chicken carcasses for human consumption from farmers' markets and small food stores in seven localities of Bogotá, Colombia. Ninety-one samples of fresh chicken carcasses were collected from farmers’ markets and small food stores at seven localities in Bogotá. Samples were tested for Campylobacter using the real-time polymerase chain reaction (real time PCR) and isolation by plating. To analyze possible risk factors associated with Campylobacter spp. contamination in retail chicken carcasses, information was collected using a structured questionnaire and a univariate logistic regression analysis (α = 0.05) was used. Forty-two positive samples were obtained for Campylobacter spp., given a prevalence of 46.2%, of which 54.8% were to C. jejuni, 9.52% to C. coli and 35.7% to joint contaminations. C. jejuni was the most prevalent species. Risk factors found included poor cleanliness, in frequency of disinfection, type of establishment, and direct contact of chickens with other food. This study is the first report in the country on the prevalence and risk factors of Campylobacter in retail chicken.

  PublisherOA PDFDOI

Frequent coauthors

• Adriana Bernal

  Universidad de Los Andes

  67 shared

• Giovanna Danies

  Universidad de Los Andes

  48 shared

• Valérie Verdier

  Institut de Recherche pour le Développement

  47 shared

• Martha Cárdenas

  Universidad de Los Andes

  42 shared

• Javier F. Tabima

  Clark University

  31 shared

• Diego Riaño-Pachón

  Universidade de São Paulo

  31 shared

• Camilo López

  Universidad Nacional de Colombia

  27 shared

• Romain Guyot

  École Normale Supérieure de Lyon

  23 shared

Labs

• Silvia RestrepoPI

Education

• Docteur, Plant Pathology

  Université Pierre et Marie Curie

  1999

• Diplome d'études approfondies, Plant Pathology

  Université Pierre et Marie Curie

  1994

• Maitrise de Biologie cellulaire mention génétique, Cellular and Molecular Biology

  Université Pierre et Marie Curie

  1993

• Bachelor of Science, Biological Sciences

  Universidad de los Andes

  1992