Biology subjects

Dutra, L. A. L.

Publications and source records attributed to Dutra, L. A. L..

3 recordsLinked to original sources

bioRxiv2026

Detection and characterisation of alpha- and betacoronaviruses in rodents and bats from Germany, France, Belgium and Ireland

Recent zoonotic coronavirus outbreaks have sparked an interest in understanding coronaviruses circulating in animal reservoirs. While bats are recognised as major reservoirs for these viruses, coronaviruses have also been detected in a wide range of terrestrial small mammals, particularly rodents. However, coronavirus diversity in these mammals, specifically in Europe, is still poorly characterised. In this study, we detected and characterised coronaviruses in terrestrial small mammals and bats from Belgium, France, Germany, and Ireland. We screened tissue samples from rodents and shrews and environmental bat guano using pan-coronavirus real-time and conventional PCRs, with positive results confirmed by sanger sequencing. Among 2667 bat and 1152 terrestrial mammal samples, we detected 59 positive samples, 36 from bats and 23 from rodents, from which we recovered 60 coronavirus sequences, spanning both Alphacoronavirus and Betacoronavirus lineages. Through next generation sequencing we identified one Pipistrellus pygmaeus bat guano sample carrying two distinct alphacoronaviruses, representing Nyctacovirus and Pedacovirus subgenera. Among rodents, most coronavirus-positive samples originated from a zoo in Belgium, where several CoV lineages co-circulated. The identified rodent coronaviruses clustered among previously described rodent-associated lineages, some of which also include human and other mammal-derived coronavirus sequences. Consistent with previous studies, we found sarbecoviruses in horseshoe bats (particularly Rhinolophus ferrumequinum and R. hipposideros) and merbecoviruses in Plecotus auritus bats, and these viruses are distantly related to the human coronaviruses of the respective families. Similar to bat coronaviruses, some rodent coronaviruses strains seemed to be association with specific rodent species. In conclusion, our study enhances the understanding of coronaviruses in rodents and bats, revealing potential hotspots for these viruses and their implication for human and animal health. These findings underscore the necessity for continued surveillance of coronaviruses in wildlife reservoirs to mitigate future zoonotic spillover risks.

microbiology↗

bioRxiv2026

Mimicin, an antimicrobial protein encoded by mimivirus

Antimicrobial peptides (AMPs) are innate defense molecules found in all domains of life. Giant viruses of amoeba are known to thrive among complex microbial relationships within its hosts cells, hinting at the existence of virus-derived antimicrobial strategies. Here we show that viruses belonging to the Mimiviridae and Marseilleviridae families contain a higher density of in silico predicted AMPs per genome size than other viruses of amoeba. The investigation of potential AMPs led to the description of Mimicin, a taxonomically restricted 74 amino acid long protein coded by few mimiviruses. Mimicin contains three smaller predicted AMP sequences within it and has a broad in vitro antimicrobial activity against different bacteria, a yeast and two non-enveloped phages. In contrast, it has no activity against a marseillevirus, a mimivirus or human cell lines. When tested against bacterial endosymbionts co-cultured with Acanthamoeba terricola, Mimicin and its SIM-31 portion were able to control the attenuated Protochlamydia amoebophila but not the highly virulent Parachlamydia acanthamoebae. Based on deposited transcriptomic data, Mimicin is coded by an early gene more active during the beginning of the infection process. No structure could be predicted using Alphafold, while additional structural analysis indicate that Mimicin could be a highly disordered protein. In conclusion, we describe evidence of a biologically relevant antimicrobial activity derived from a giant virus. Mimicin highlights the relevance of AMPs from giant viruses for microbial ecology and opens the way for investigating their biotechnological and clinical potential.

microbiology↗

bioRxiv2022

Single-cell resolution genetic association analysis of heterogeneous bacterial communities by utilizing droplet digital PCR

Microbial communities often respond to environmental challenges, such as the presence of antibiotics, as a whole. Dissecting these community-level effects into separate acting entities requires the identification of organisms that carry functional genes for the observed feature. However, unculturable microbes are abundant in various environments, hence making the identification challenging. Moreover, while at present the development and application of single-cell tools for eukaryotic cells are enhancing, the comparable methodologies applicable for prokaryotic cells are still scarce and have not gained broad and solid status as tools for investigating microbial populations. Here, we present a cultivation-free technique that can be utilized to link functional genes with the carrying bacterial species at single-cell resolution. The developed protocol is relatively simple to use, utilizes commercially available droplet microfluidics devices, does not require toxic reagents, and eliminates invalid signals emerging from extracellular DNA. We validate the methodology by studying the conjugative transfer of antibiotic resistance plasmids in an environment challenged by antibiotics. Furthermore, the method can be customized for any given genetic trait to accurately identify its hosting subpopulation from a heterogeneous and potentially uncultivable bacterial community. ImportanceBacterial systems usually contain numerous different species that may harbor highly similar or identical genes that confer same phenotypic qualities for the community. To decipher the functions of these systems, we report the development of a novel methodology that enables investigating microbial communities at single-cell level. This user-friendly method utilizes droplet digital PCR (ddPCR) to find and identify carriers of specific genes potentially from various microbial sample types. By pinpointing gene carriers, such as those responsible for antibiotic resistance, this method can provide insights to the behavior of microbial communities and gene transfer therein. By strategically combining the use of common methods (ddPCR and amplicon sequencing), the workflow is highly accessible. Thus, it allows also the researchers without a background in single-cell techniques or access to special equipment to adopt the method for producing single-cell data to serve their own research, enabling new research avenues in microbial genetics and ecology.

microbiology↗