1. Biodiversity genomics research practices require harmonising to meet stakeholder needs in conservationElena Bužan, Christian de Guttry, Chiara Bortoluzzi, Nathaniel R. Street, Kay Lucek, Anna Rosling, Lino Ometto, Alice Mouton, Luísa S. Marins, María José Ruiz-López, José Melo-Ferreira, Elisabet Ottosson, Camila J. Mazzoni, Robert M. Waterhouse, 2025, izvirni znanstveni članek Opis: Biodiversity resilience relies on genetic diversity, which sustains the evolutionary potential of organisms in dynamic ecosystems. Genomics is a powerful tool for accurately estimating genetic diversity across genomes of species and populations. However, integration of genomic data into conservation efforts faces challenges due to the heterogeneity of approaches employed. Establishing common sets of standards for genomic data production and analysis is essential to consistently interpret results and clearly communicate outcomes to stakeholders. While the European Reference Genome Atlas (ERGA) community has contributed significantly to the standardisation of reference genome methodologies in synergy with other initiatives, there is now an urgent need to extend these principles to downstream analyses. ERGA aims to build on its experience to help establish harmonised approaches in applied biodiversity genomics research, aligned with ongoing efforts to define standardised metrics for measuring and reporting genetic diversity. Establishing consensus on best practices for genome-wide data generation methods and applications will substantially increase accuracy, interpretability, and comparability, together with enhanced stakeholder capacities. By identifying key opportunities and challenges, as well as conducting preliminary stakeholder mapping and examining case studies, the goal is to build an inclusive framework that ensures the relevance and widespread adoption of these best practices: fostering trust and confidence in genomics research practices to meet stakeholder needs in biodiversity conservation. We call upon the broader research community to join efforts in establishing these approaches, recognising the importance of participation of end-users, to foster the integration of genomic data into the toolkit for measuring and reporting genetic diversity.
Ključne besede: best practices, biodiversity genomics, genome-wide genetic diversity, stakeholder engagement, standardisation, whole genome resequencing data
Objavljeno v RUP: 16.01.2026; Ogledov: 1221; Prenosov: 6
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2. Methanobrevibacter smithii strain U29 whole genome sequence delineates M. smithii intermediate cell variantsIhab Malat, Vincent Bossi, Michel Drancourt, Ghiles Grine, Raymond Ruimy, 2025, izvirni znanstveni članek Opis: Background Methanobrevibacter smithii (M. smithii), the predominant methanogen in the human digestive tract, plays a key role in methane production. Despite its importance, the genomic diversity of M. smithii is poorly characterised, especially in extra-digestive sites such as the urinary and respiratory tracts, and the blood. Understanding this diversity would help unravel its potential role in human health and diseases. Results We report the genome of M. smithii strain U29, isolated from urine, expanding the known diversity of the species. The M. smithii U29 genome (scaffold level; 1̵822‒124-bp, 1745 protein-coding sequences) lacks Candidatus Nanopusillus sequences, unlike digestive tract strains. Comparative analysis has revealed a high similarity (99.86% ANI) with the reference M. smithii strain ATCC 35,061, although U29 contains 71 unique coding sequences including 12/71 (13 200-bp; 69% of the total extra-material size) with demonstrated Siphoviridae viral ancestry. Accordingly, M. smithii U29 has been identified as an intermediate M. smithii cell variant, exhibiting genomic traits potentially conferring adaptability to the urinary tract. Conclusion This study enhances our understanding of M. smithii genomic diversity and highlights the presence of viral sequences in the urinary tract M. smithii strain U29. These findings open up a hypothesis that viral integration may play a role in M. smithii mucosae colonisation and dynamics, underscoring the need for further investigations into the mechanisms underlying its tissue translocation and potential health implications.
Ključne besede: Methanobrevibacter smithii, Archaea, urinary tract, genome, cell variants
Objavljeno v RUP: 18.12.2025; Ogledov: 1046; Prenosov: 4
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