PrimerBac: A Searchable Database of Taxon-specific Primers for Rapid Microbial Identification.

IF 4.7 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology Pub Date : 2026-09-21 DOI:10.1016/j.jmb.2026.170027

Yingjian Hou, Shuo Feng, Mao Gu, Zhengxing Song, Yingying Ding, Zitong Wang, Yijia Hou, Jing Li, Xingzhen Lao

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引用次数: 0

Abstract

Species-resolved PCR detection of gut microorganisms is challenged by within-species genomic diversity and sequence conservation among related taxa. We developed PrimerBac (https://primerbac.cn), a searchable database that integrates gut-focused reference collection, RefSeq pan-genome analysis, core-orthogroup marker selection, background screening, and assembly-level ePCR evaluation. The reference intestinal resource contains 1762 species, and complete pan-genome analyses were obtained for 1179 species. PrimerBac provides 1,148,644 primer pairs for 991 prokaryotic species and 611,077 pairs for 424 genera. Broad screening of 22,207 RefSeq reference/representative assemblies yielded 68.9% sensitivity. In a non-overlapping temporal panel of 4115 post-construction assemblies, 57 of 65 evaluable targets were detected (87.7% sensitivity; 95% CI, 77.5-93.6%), with 84.0% hit-defined macro precision. PrimerBac therefore provides a searchable and systematically evaluated resource for targeted microbial identification.

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PrimerBac：用于快速微生物鉴定的分类群特异性引物的可搜索数据库。

肠道微生物的种分辨PCR检测受到种内基因组多样性和相关分类群序列保守性的挑战。我们开发了PrimerBac (https://primerbac.cn)，这是一个可搜索的数据库，集成了以肠道为中心的参考资料收集、RefSeq泛基因组分析、核心-正类群标记选择、背景筛选和组装级ePCR评估。参考肠道资源包含1762个物种，并获得了1179个物种的完整泛基因组分析。PrimerBac为991种原核生物提供了1,148,644对引物，为424个属提供了611077对引物。对22207个RefSeq参考/代表性组合进行广泛筛选，灵敏度为68.9%。在由4,115个施工后组件组成的非重叠时间面板中，65个可评估目标中有57个被检测到（87.7%的灵敏度；95% CI, 77.5-93.6%），命中定义的宏观精度为84.0%。因此，PrimerBac为目标微生物鉴定提供了可搜索和系统评估的资源。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Molecular Biology 生物-生化与分子生物学

CiteScore

11.30

自引率

1.80%

发文量

412

审稿时长

28 days

期刊介绍： Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.