LorMe: a unified framework for standardized microbiome analysis

Microbial ecology research is generating unprecedented amounts of data, and analyzing these datasets remains challenging. Researchers often need to combine multiple software tools, manually adjust numerous parameters, and reconcile different data formats before biological patterns can be effectively interpreted. These fragmented workflows increase technical complexity and make it difficult to achieve consistent and reproducible results across studies.

In a new study published in Microbiome and One Health, a research team has developed LorMe (Lightweight One-Line Resolving Microbial Ecology), an open-source R framework designed to provide a unified approach for standardized microbiome analysis. The researchers introduced an analytical platform that enables the transition from raw microbiome data processing to publication-ready visualization through a streamlined workflow.

LorMe is freely available through the Comprehensive R Archive Network (CRAN: https://cran.r-project.org/web/packages/LorMe) and GitHub (https://github.com/wangnq111/LorMe), allowing researchers from diverse fields, including agriculture, environmental science, and health-related microbiome studies, to adopt and further develop the framework.

“Microbial community analysis has become increasingly complex because researchers need to combine many different computational methods and software packages,” says first author Ningqi Wang from Nanjing Agricultural University. “To that end, LorMe was designed to reduce this technical burden by providing a common framework where different analytical approaches can work together while maintaining flexibility and transparency.”

Unlike conventional approaches that require researchers to work across separate analytical frameworks and data structures, LorMe allows seamless data exchange with widely used microbiome analysis packages, including phyloseq and microeco.

“This compatibility allows us to integrate diverse analytical approaches without repeatedly restructuring their datasets, providing a more consistent framework for microbiome data analysis,” says Wang. “The framework also introduces a one-command pipeline that performs major microbiome analyses, including microbial community profiling, identification of taxa associated with experimental conditions, co-occurrence network construction, and meta-network analysis integrating microbial associations with differential taxa.”

In a demonstration dataset containing approximately 22,000 microbial features, the complete workflow was completed within seconds on a standard laptop while generating figures, statistical results, and intermediate files required for reproducible research.

The researchers further evaluated LorMe using a real rhizosphere microbiome dataset from eggplants with contrasting resistance to bacterial wilt. “The analysis successfully reproduced biologically meaningful microbial patterns, demonstrating that the framework can support practical ecological investigations while providing a standardized analytical workflow,” adds Wang.

“By lowering technical barriers and improving reproducibility, we hope LorMe can help researchers focus more on understanding microbial ecological mechanisms rather than managing complicated computational workflows.” says senior and co-corresponding author Zhong Wei.

Contact the author:

Zhong Wei and Gaofei Jiang, Jiangsu Provincial Key Lab for Organic-based fertilizer development and its manipulation on soil health, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-saving fertilizers, Nanjing Agricultural University, Nanjing 210095, China. weizhong@njau.edu.cn and gjiang@njau.edu.cn

Funder:

This research was supported by the National Natural Scientific Foundation of China 42325704, the Natural Science Foundation of Jiangsu Province BK20230988, the National Natural Scientific Foundation of China W2431030, Anhui Provincial Postdoctoral Research Project (2024A778), the Jiangsu Province Excellent Postdoctoral Program (2024ZB584), the National Natural Science Foundation of China (32500093), the China Postdoctoral Science Foundation (2025M772497), and the National Key Research and Development Program of China (2024YFC3406003).

Conflict of interest:

The authors declare the following personal relationships which may be considered as potential competing interests: Zhong Wei is the Editorial Board Member of Microbiome and One Health and was not involved in the editorial review or the decision to publish this article. This paper was handled by the Editor-in-Chief.

See the article:

Ningqi Wang, Yaozhong Zhang, Xinrui Yangon, et al. LorMe: a streamlined and interoperable R framework for end-to-end microbiome analysis, Microbiome and One Health. 2026;1:100003. https://doi.org/10.1016/j.micoh.2026.100003