LEfSe Differential Analysis

LEfSe Differential Analysis

LEfSe analysis refers to the LDA Effect Size analysis. LEfSe is used to discover high-dimensional biomarkers and reveal genomic characteristics, including genes, metabolism and classification. It can achieve the comparison between multiple groups so as to find species with significant differences in abundance between groups, and distinguish two or more biological groups. This method emphasizes the statistical significance and biological relevance, allowing researchers to identify features of different abundances as well as associated categories.

LEfSe results on human microbiomesFig. 1 LEfSe results on human microbiomes. (Segata N, et al. 2011)

Our Service Process

LEfSe has a powerful recognition function through biological statistical differences. To be specific, first use the non-parametric factorial Kruskal-Wallis (KW) sum-rank test to detect the significant differences in abundance, and find out the groups with significant differences in abundance. Then, LEfSe performs additional tests to assess whether these differences are consistent with expected biological behavior. Finally, LEfSe uses linear discriminant analysis (LDA) to estimate the impact of the abundance of each component (species) on the difference effect. The flowchart of the process is as follows,

The service process of LEfSe differential analysis – Creative Biogene

Service Offering

Our services in terms of LEfSe differential analysis include,

  • Data processing and analysis
  • The drawing of LDA value distribution histograms
  • The drawing of evolutionary branches
  • The drawing of biomarker abundance comparison graphs in different groups of samples

Tool Used

Analytical tools used in our LEfSe differential analysis service include LEfSe software and other related tools.

Turnaround Time

In general, our turnaround time is 2-6 weeks depending on the size of your project.

Advantages of Our Services 

  • We have rich experience in LEfSe differential analysis.
  • We can combine the needs of customers, and negotiate to determine the content of services.
  • We provide fast turnaround, high quality analysis reports at competitive prices to our global customers.
  • We regularly accept audits from our customers to ensure that we meet their high standards.

Creative Biogene is a forward-looking research institution and a leading customer service provider in the field of LEfSe differential analysis. We use advanced analysis platforms to provide you with results of good reproducibility. The service we offer is excellent in speed, accuracy and sensitivity. You can choose us with confidence.

If you are interested in our services, please contact us for more details.


  1. Segata N, et al. (2011). "Metagenomic biomarker discovery and explanation." Genome biology. 12.6: 1-18.
  2. Inserra A, et al. (2019). "Mice lacking Casp1, Ifngr and Nos2 genes exhibit altered depressive-and anxiety-like behaviour, and gut microbiome composition." Scientific reports. 9.1: 1-12.
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