New study could help prevent misidentification of bacteria
Oeiras, 09th September 2025
Bacteria with similar traits are often difficult to tell apart. This challenge is particularly evident with Shewanella species, which are found in a wide variety of environments, used for biotechnological purposes, and also associated with severe community- and hospital-acquired infections. Misidentifying these bacteria can lead to errors in diagnosis and treatment, and it can also misinterpret scientific research in the biotechnology field. In fact, Shewanella are of particular scientific interest because they can survive in harsh conditions. For this reason, researchers from ITQB NOVA’s Inorganic Biochemistry and NMR lab, led by Ricardo Louro, have been investigating their potential in wastewater treatment and energy production.
The new study was sparked by an unexpected case of misidentification. “It all started when a strain obtained from a national repository turned out to be misidentified”, explains Catarina Paquete, researcher at ITQB NOVA and the corresponding author of this work. “Around the same time, a distinct pathogen was identified in clinical samples from a Portuguese hospital”, she adds. Concerned about the clinical impact of such errors, the research team joined forces with the Molecular Microbiology and Infection Unit, headed by Mario Ramirez from Faculdade de Medicina from Universidade de Lisboa.
To address this issue, the researchers analyzed different Shewanella species, including pathogenic members, by evaluating their characteristics and sequencing their DNA. Their findings are now published in the journal Applied and Environmental Microbiology of the American Society for Microbiology, reveal a practical way to differentiate between species. “We identified a gene unique to Shewanella seohaensis, a pathogenic species. This marker can serve as a low-cost tool for laboratories to avoid misidentifications and as a reliable reference for both research and clinical diagnostics”, says Maria Firmino, PhD student at ITQB NOVA and first author of the paper. “We also observed a large diversity within each of these species, which shows that generalizing results obtained from a single Shewanella group to the whole species can lead to errors”, she concludes.
By improving the accurate identification of Shewanella species, this study not only supports better infection diagnosis but also helps protect aquaculture, where pathogenic Shewanella species are common, and strengthens environmental monitoring.
This study was developed in collaboration with Instituto de Microbiologia da Faculdade de Medicina da Universidade de Lisboa, the Department of Clinical Sciences, University of Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain, and the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
The financial support was provided by the following institutes and funding agencies with the respective projects specified: MOSTMICRO-ITQB base funding with references UIDB/ 04612/2020 and UIDP/04612/2020, LS4FUTURE Associated Laboratory (LA/P/0087/2020), and Portuguese Foundation for Science and Technology (FCT) with the project grant PTDC/BIA-BQM/4143/2021 and the PhD grant 2022.12339.BD for Maria de Oliveira Firmino (https://doi.org/10.54499/2022.12339.BD).
Original paper:
Applied and Environmental Microbiology | https://doi.org/10.1128/aem.01189-25
Polyphasic discrimination of Shewanella seohaensis from closely related species and a whole-genome multilocus (wgMLST) scheme for the evaluation of diversity within this Shewanella clade
Maria Firmino , Mykyta Forofontov, Ricardo Soares, Ricardo Louro, Alberto Martín-Rodríguez, Mário Ramirez, Catarina Paquete
