Novel Autochthonous Strains from Cyprinus carpio as Candidates for Probiotic Use and Microplastic-Degrading Properties

In the modern era, identifying and characterizing novel bacterial strains with possible probiotic potential and environmental bioremediation capabilities is an emerging focus in microbiology and biotechnology. This study analysed the cultivable gut microbiota of the freshwater fish, Cyprinus carpio, and identified six different bacterial genera, including Citrobacter, Serratia, Bacillus, Enterococcus, and Kocuria. Among these, two novel autochthonous strains—Hafnia alvei UUNT_MP41 and Hafnia paralvei UUNT_MP29—were isolated and selected for further investigation due to their promising probiotic traits and potential to degrade microplastics in aquatic ecosystems. Both strains were evaluated for antibacterial activity against pathogens and susceptibility to a broad spectrum of antibiotics. Whole-genome analysis using next-generation sequencing (NGS) revealed the presence of genes potentially associated with probiotic properties, such as ClpB, as well as genes potentially involved in the biodegradation of common microplastics, including the tesA gene, a homolog of the PpEst gene from the genome of Pseudomonas pseudoalcaligenes, and the lipR gene, a homolog of the EstC9 gene from the genome of Acidocella sp. Here, we performed a more in-depth analysis of the similarity between the genes/proteins we identified as potentially involved in plastic biodegradation and previously described ones. Notably, the identified strains' potential to degrade microplastics under conditions relevant to the human gastrointestinal system positions them as candidates for a new generation of dual-function probiotics, supporting both human health and microplastic detoxification. These findings lay the groundwork for future development of multifunctional probiotic formulations with environmental and therapeutic benefits.