A standards perspective on genomic data reusability and reproducibility

Frontiers in Bioinformatics, Journal Year: 2025, Volume and Issue: 5

Published: March 10, 2025

Genomic and metagenomic sequence data provides an unprecedented ability to re-examine findings, offering a transformative potential for advancing research, developing computational tools, enhancing clinical applications, fostering scientific collaboration. However, effective ethical reuse of genomics is hampered by numerous technical social challenges. The International Microbiome Multi’Omics Standards Alliance (IMMSA, https://www.microbialstandards.org/ ) the Consortium (GSC, https://gensc.org hosted 5-part seminar series “A Year Data Reuse” in 2024 explore challenges opportunities reproducibility across disparate domains genomic sciences. Addressing these will require multifaceted approach, including common metadata reporting, clear communication, standardized protocols, improved management infrastructure, guidelines, collaborative policies that prioritize transparency accessibility. We offer strategies enable responsible technically feasible reuse, recognition challenges, emphasizing importance cross-disciplinary efforts pursuit open science data-driven innovation.

Language: Английский

Two-year follow-up of gut microbiota alterations in patients after COVID-19: from the perspective of gut enterotype

Microbiology Spectrum, Journal Year: 2025, Volume and Issue: unknown

Published: April 10, 2025

ABSTRACT Gut microbiota dysbiosis plays a role in the pathogenesis of post-acute coronavirus disease (COVID-19); however, long-term recovery gut following SARS-CoV-2 infection remains insufficiently understood. In this study, 239 fecal samples were collected from 87 COVID-19 patients during acute phase, and at 6 months, 1 year, 2 years post-discharge. An additional 48 non-COVID-19 controls also analyzed. enterotypes determined through 16S rRNA sequencing, dynamic changes phase assessed. Correlations between clinical characteristics examined. Two distinct identified: Blautia-dominated enterotype (Enterotype-B) Streptococcus-dominated (Enterotype-S). Species diversity richness significantly higher Enterotype-B. Enterotype-S, associated with inflammation, was more prevalent phase. Six months post-discharge, ratio Enterotype-B to Enterotype-S approached normal levels. Patients admission had incidence severe cases hospitalization longer duration nasopharyngeal viral shedding compared those Furthermore, residual pulmonary Computed Tomography (CT) abnormalities common (55%) than (20%, P = 0.046). index, B/S, representing Blautia Bifidobacterium Streptococcus, introduced found correlate closely characteristics. The is inflammation appears influence both severity illness cardiopulmonary recovery. IMPORTANCE This study sheds new light on intricate process rehabilitating disruptions caused by COVID-19. Our approach, which examines dynamics vantage point enterotypes, reveals rapid previously reported, majority rebounding within 6-month timeframe. our findings underscore importance as marker health, pivotal mitigating risk progression lingering effects post-SARS-CoV-2 infection. By scrutinizing these we can now foresee potential aftermath COVID-19, offering valuable tool for prognosis intervention.

Language: Английский

Development of reference-based model for improved analysis of bacterial community

Food Research International, Journal Year: 2025, Volume and Issue: unknown, P. 116380 - 116380

Published: April 1, 2025

Language: Английский