Firmino Maria de Oliveira, Forofontov Mykyta, Soares Ricardo, Louro Ricardo O, Martín-Rodríguez Alberto J, Ramirez Mário, Paquete Catarina M
Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
Instituto de Microbiologia da Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal.
Appl Environ Microbiol. 2025 Aug 13:e0118925. doi: 10.1128/aem.01189-25.
is an environmentally ubiquitous genus with significant roles in bioelectrochemical applications and human infections. However, identification problems involving , , and have been reported, potentially hindering research progress in these areas. In this study, we explored how to discriminate between these species. By comparing the genomes of spp. available in public databases with that of the newly sequenced strain DSM9451, we showed that this strain is a member of the species . Of the eight public genomes associated with this species, only two were correctly identified in public databases. Phenotypic analysis revealed distinct features of with respect to and . However, only differences in the intensity of biochemical reactions were observed between and . To discriminate between these closely related species and explore their diversity, a whole-genome multilocus sequence typing scheme was developed. The scheme distinguished related species and revealed significant diversity among and isolates, suggesting that both species may harbor isolates with significantly different metabolic properties. These differences are so wide within the clade that they may explain why these two species are difficult to distinguish. The identification of exclusive genes of each species allowed the design of a simple molecular method to differentiate from closely related species, which will help in clarifying its role in human infections and environmental processes.IMPORTANCEMisidentification within the genus, particularly between , , and , has been reported and misperceives scientific research on spp. in diverse fields, including both biotechnological applications and human infections. Near-complete 16S rRNA gene sequencing fails to correctly classify many species, and MALDI-TOF systems used in clinical microbiology laboratories are suboptimal for species-level identification. In this study, we identified phenotypic characteristics that can guide differentiation and classification, and building upon the identification of species-specific genes, we suggest an accurate and cost-effective molecular test as an alternative to genome sequencing. The proposed whole-genome multilocus sequence typing scheme allows the exploration of species and strain diversity, highlighting the limitations of generalizing results from studies of a single strain. As an emergent pathogen and biotechnological candidate, the proper identification by a single molecular test will enhance the insights about these species towards biotechnology development and public health safety.
是一种在环境中普遍存在的属，在生物电化学应用和人类感染中具有重要作用。然而，已经报道了涉及、和的鉴定问题，这可能会阻碍这些领域的研究进展。在本研究中，我们探索了如何区分这些物种。通过将公共数据库中可用的 spp. 基因组与新测序的菌株DSM9451的基因组进行比较，我们表明该菌株是物种的成员。在与该物种相关的八个公共基因组中，只有两个在公共数据库中被正确鉴定。表型分析揭示了相对于和的独特特征。然而，在和之间仅观察到生化反应强度的差异。为了区分这些密切相关的物种并探索它们的多样性，开发了一种全基因组多位点序列分型方案。该方案区分了相关物种，并揭示了和分离株之间的显著多样性，表明这两个物种可能都含有代谢特性差异很大的分离株。在进化枝内这些差异如此之大，这可能解释了为什么这两个物种难以区分。每个物种的专属基因的鉴定允许设计一种简单的分子方法来区分与密切相关的物种，这将有助于阐明其在人类感染和环境过程中的作用。重要性已报道在属内存在错误鉴定，特别是在、和之间，这误解了包括生物技术应用和人类感染在内的不同领域中对 spp. 的科学研究。近乎完整序列的16S rRNA基因测序未能正确分类许多物种，临床微生物实验室中使用的基质辅助激光解吸电离飞行时间（MALDI-TOF）系统在物种水平鉴定方面并不理想。在本研究中，我们确定了可以指导分化和分类的表型特征，并基于物种特异性基因的鉴定，我们建议一种准确且经济高效的分子测试作为基因组测序的替代方法。所提出的全基因组多位点序列分型方案允许探索物种和菌株多样性，突出了从单一菌株研究中概括结果的局限性。作为一种新兴病原体和生物技术候选物，通过单一分子测试进行正确鉴定将增强对这些物种在生物技术发展和公共卫生安全方面的认识。
