Edwin Omar Rivera-López

All Publications

• Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic Escherichia coli O157:H7 Rivera Lopez, E. O., et al BioRxiv. 2026

  Abstract

  The outermost surface layers of Gram-negative bacteria determine phage access to terminal receptors, yet their genetic basis has been mapped almost exclusively in laboratory strains that lack them. Here we apply genome-wide RB-TnSeq fitness profiling to four Escherichia coli O157:H7 strains from distinct phylogenetic clades sharing the O157 O-antigen, using 38 phages with terminal receptors previously mapped in E. coli K-12 strain. RB-TnSeq fitness landscapes across all four pathogenic backgrounds were mostly similar, and dominated by surface-associated loci, including the gfc-etk group 4 capsule operon, O-antigen biosynthesis genes, LPS core assembly genes and outer membrane proteins. Disruption of gfc-etk abolished infection in 11 genetically diverse myoviruses, establishing the O-antigen capsule as a widespread required primary recognition substrate. O-antigen loci generated two classes of fitness score patterns. For 10 phages, disruption increased infectivity, indicating it is a barrier to receptor access; for 3 others, disruption abolished infectivity, demonstrating it can also be a primary recognition substrate. Outer membrane protein receptor identity was conserved across laboratory and pathogenic backgrounds, with the same proteins recognized in both K-12 and O157:H7, while glycan layer state determines whether these receptors are reached. These results demonstrate that outer surface glycan layers can act as primary and optional recognition substrates for phage infection, or as physical barriers preventing terminal receptor access. Extending the ability to probe phage-targeted receptors beyond outer membrane proteins provides a framework for incorporating glycan layer state into predictive models of phage-host interactions.

• Regulatory Landscape and the Potential of Bacteriophage Applications in the United States' Food Industry. Journal of food protection Rivera-Lopez, E. O., Tirko, N. N., Dudley, E. G. 2025; 88 (6): 100510

  Abstract

  Bacteriophages are promising tools for mitigating bacterial contamination because of their specificity for bacterial cells. The food industry can enhance food safety and quality by applying bacteriophages in various settings, from farms to ready-to-eat (RTE) products. Renewed interest has been driven by recent advancements in research and the increasing need for sustainable alternatives in food safety. However, understanding the regulatory requirements for using bacteriophages in food and agriculture in the United States is essential. These complex and varied regulations impact the approval and implementation of bacteriophage-based solutions. Addressing these regulatory requirements is crucial to ensure that bacteriophage applications comply with safety and legal standards. This review synthesizes the evolving regulatory framework governing bacteriophage use in the United States food industry, providing a clear understanding of the evaluation and approval processes, while highlighting recent changes and addressing challenges and opportunities for effective integration into food processing.

  View details for DOI 10.1016/j.jfp.2025.100510

  View details for PubMedID 40268121

  View details for PubMedCentralID PMC12146206

• Metagenomic libraries data sets from the hypersaline benthic microbial mats of the Fraternidad Lagoon, Puerto Rico, using an indirect DNA extraction method. Microbiology resource announcements Nieves-Morales, R., Quiles-Pérez, C. J., Rivera-Lopez, E. O., Torres-Zapata, I., Rodriguez-Ramos, J., Rios-Velazquez, C. 2026; 15 (4): e0150425

  Abstract

  Microbial mats are biofilm formations that reflect early Earth ecosystems. To investigate their microbial diversity, an indirect DNA extraction method was applied to benthic ephemeral microbial mats from Fraternidad Saltern Lagoon during rainy and dry seasons. This approach yields high molecular DNA, suitable for metabolic and diversity analysis.

  View details for DOI 10.1128/mra.01504-25

  View details for PubMedID 41758007

  View details for PubMedCentralID PMC13064099

• Prokaryotic communities profile from metagenomic libraries of the brown rock sea cucumber (Holothuria glaberrima) intestinal system. Microbiology resource announcements Nieves-Morales, R., Paez-Diaz, J. A., Rivera-Lopez, E. O., Rodríguez-Ramos, J., Rios-Velazquez, C. 2025; 14 (10): e0073125

  Abstract

  Environmental rDNA profiling enables the identification of unculturable microbial communities. To access prokaryotic diversity in the metagenomic libraries of sea cucumber's intestinal environment, 16S rDNA sequencing was performed to provide insight into the libraries' taxonomic composition, unraveling microbial groups potentially associated with biomedical, environmental, and biotechnological applications.

  View details for DOI 10.1128/mra.00731-25

  View details for PubMedID 40853285

  View details for PubMedCentralID PMC12509550

• Whole-genome sequence of 19 Listeria monocytogenes, isolated from municipal wastewater in State College, Pennsylvania. Microbiology resource announcements Horack, E., Acosta, A., Jones, M., Feng, J., Rivera-Lopez, E. O., M'ikanatha, N. M., Kovac, J., Dudley, E. 2025; 14 (10): e0052325

  Abstract

  Eight wastewater samples were collected from three sites in State College, Pennsylvania, during June and July 2024. Nineteen Listeria monocytogenes were isolated and sequenced. Three isolates were ≤9 SNPs different from human cases deposited in GenBank, highlighting the potential for wastewater-based surveillance to monitor L. monocytogenes outbreaks.

  View details for DOI 10.1128/mra.00523-25

  View details for PubMedID 40911002

  View details for PubMedCentralID PMC12509671

• Characterization of prokaryotic communities in Puerto Rican caves using 16S rDNA amplicon sequencing. Microbiology resource announcements Pérez-Santos, N., Borrero-Villabol, S. J., Nieves-Morales, R., Paez-Díaz, J. A., Rivera-Lopez, E. O., Rodríguez-Ramos, J., Nieves-Rivera, A. M., Ríos-Velazquez, C. 2025; 14 (7): e0035425

  Abstract

  The cave ecosystems host microbial communities adapted to extreme environments. This study utilized 16S rDNA to investigate the prokaryotic diversity across seven caves in Puerto Rico's northern limestone karst belt. Microbial profiling revealed distinct subterranean communities, enhancing our understanding of cave microbiology and potential applications in environmental conservation and microbial research.

  View details for DOI 10.1128/mra.00354-25

  View details for PubMedID 40492773

  View details for PubMedCentralID PMC12243483

• Intestinal microbiome profile of the brown rock sea cucumber (Holothuria glaberrima) using ITS and 16S rDNA amplicons from direct mechanical, enzymatic, and chemical metagenomic extraction. Microbiology resource announcements Nieves-Morales, R., Paez-Diaz, J. A., Rodriguez-Carrio, S. M., Melendez Martinez, G., Rivera-Lopez, E. O., Rodríguez-Ramos, J., García-Arrarás, J. E., Rios-Velazquez, C. 2025; 14 (7): e0029325

  Abstract

  Using direct mechanical, enzymatic, and chemical extraction methods, the intestinal microbiome of the marine invertebrate Holothuria glaberrima was obtained. ITS and 16S rDNA regions were sequenced to enrich and investigate the prokaryotic and fungal diversity profiles from different anatomical regions within the sea cucumber's intestinal biology.

  View details for DOI 10.1128/mra.00293-25

  View details for PubMedID 40434086

  View details for PubMedCentralID PMC12243471

• Characterization of fungal communities in Puerto Rican caves using internal transcribed spacer sequencing. Microbiology resource announcements Nieves-Morales, R., Paez-Diaz, J. A., Rivera-Lopez, E. O., Pérez-Santos, N., Borrero-Villabol, S. J., Rodríguez-Ramos, J., Nieves-Rivera, A. M., Rios-Velazquez, C. 2025; 14 (6): e0002225

  Abstract

  Cave ecosystems harbor unique and diverse microbial ecology, with fungal communities playing important roles. This study utilizes internal transcribed spacer across seven caves in the northern limestone karst belt area of Puerto Rico to investigate fungal composition. This enhances scientific understanding of subterranean microbial dynamics and supports conservation efforts.

  View details for DOI 10.1128/mra.00022-25

  View details for PubMedID 40401940

  View details for PubMedCentralID PMC12160506

• Characterization of intestinal fungal communities through ITS amplicon from metagenomic libraries of sea cucumber (Holothuria glaberrima). Microbiology resource announcements Paez-Diaz, J. A., Nieves-Morales, R., Melendez-Martinez, G., Rivera-Lopez, E. O., Rodríguez-Ramos, J., Rios-Velazquez, C. 2025; 14 (3): e0132024

  Abstract

  The brown rock sea cucumber (Holothuria glaberrima) microbiome is vital for understanding its ecological dynamics. This study focuses on the microbial composition and abundance of fungi across different intestinal regions of H. glaberrima, giving insights into host-microbe interactions and supporting future ecological and comparative studies on their regeneration capabilities.

  View details for DOI 10.1128/mra.01320-24

  View details for PubMedID 39936895

  View details for PubMedCentralID PMC11895485

• Characterization of the microbial communities in paddy soils in Lajas, Puerto Rico using 16S rRNA gene. Microbiology resource announcements Rivera-Lopez, E. O., Huertas-Miranda, J., Rios-Velazquez, C. 2025; 14 (1): e0100824

  Abstract

  The microbiota in the paddy soils of the Lajas Agricultural Experimental Station at the University of Puerto Rico (LAES-UPR) plays a crucial role in agricultural ecosystems. Despite being at an experimental station, these soils represent natural environments supporting rice cultivation. Microbial diversity was evaluated during pre-harvest and post-harvest periods.

  View details for DOI 10.1128/mra.01008-24

  View details for PubMedID 39655923

  View details for PubMedCentralID PMC11737171

• Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing. Data in brief Rivera-Lopez, E. O., Nieves-Morales, R., Melendez-Martinez, G., Paez-Diaz, J. A., Rodriguez-Carrio, S. M., Rodriguez-Ramos, J., Morales-Valle, L., Rios-Velazquez, C. 2024; 54: 110421

  Abstract

  The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.

  View details for DOI 10.1016/j.dib.2024.110421

  View details for PubMedID 38690316

  View details for PubMedCentralID PMC11058721

• First Report of Salmonella Typhimurium Bacteriophages Infecting Multiple Serovars from a Wastewater Treatment Plant in Puerto Rico Caribbean J. of Science Cerezo, M., Rivera-Lopez, E. O., Olivo-Natal, B. K., Ramos-Lugo, C. M., Saldaña-Lopez, D., Rios-Velazquez, C. 2024