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LEfSe specifications


Unique identifier OMICS_07818
Name LEfSe
Alternative name Linear discriminant analysis effect size
Interface Web user interface
Restrictions to use None
Input data The specifications of the biological hypothesis under, the high-dimensional data obtained experimentally, and, optionally, prior knowledge from literature or databases used to define known relationships between features or samples.
Output data The effect sizes of differences observed among mucosal/non-mucosal communities, the phylogenetic distribution of these differences based on the Ribosomal Database Project (RDP) bacterial taxonomy, and the raw data driving these effects.
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Curtis Huttenhower

Publication for Linear discriminant analysis effect size

LEfSe citations


Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum

PMCID: 5952429
PMID: 29764499
DOI: 10.1186/s40168-018-0472-x

[…] % false discovery rate (ad modum Benjamini-Hochberg) are reported.At deeper taxonomic levels (biomarkers from phylum to genus level), we performed linear discriminant analysis (LDA). Here, we applied LEfSe [] with default parameters (alpha value for Wilcoxon tests was set at 0.05, the logarithmic LDA score threshold set at 2.0) to identify taxonomic biomarkers that characterise the differences bet […]


The effect of the timing of exposure to Campylobacter jejuni on the gut microbiome and inflammatory responses of broiler chickens

PMCID: 5948730
PMID: 29753324
DOI: 10.1186/s40168-018-0477-5
call_split See protocol

[…] s were made using single-factor ANOVA with < 0.05 used as the level significance. For microbiota data sets, non-parametric Mann-Whitney tests were performed. Linear discriminant analysis effect size (LEfSe) was used to identify differentially abundant OTUs (available at https://bitbucket.org/nsegata/lefse/overview) using a minimum cutoff of 0.05% []. Analysis of similarity (ANOSIM) with the Benjam […]


Different rearing conditions alter gut microbiota composition and host physiology in Shaoxing ducks

Sci Rep
PMCID: 5943461
PMID: 29743727
DOI: 10.1038/s41598-018-25760-7

[…] dict the functions of microbial communities. In addition, differentially abundant functional components across different intestinal sections and under different rearing conditions were analyzed using LEfse algorithm. Differences with liner discrimination analysis scores >2.5 and p-value < 0.05 were considered statistically significant. […]


Gut microbiomes of wild great apes fluctuate seasonally in response to diet

Nat Commun
PMCID: 5934369
PMID: 29725011
DOI: 10.1038/s41467-018-04204-w

[…] ng-term seasonal trends and average daily rainfall over the 30 days prior to the date of collection for each sample, used to adjust for the lag phase for vegetation response and any yearly anomalies. LEfSe was used to examine variations in WLG fecal microbiota over the two wet seasons and two dry seasons defined by decadal rainfall patterns (Fig. ), as well as more discrete wet and dry periods, de […]


Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging

Front Microbiol
PMCID: 5943489
PMID: 29774014
DOI: 10.3389/fmicb.2018.00862
call_split See protocol

[…] dence analysis (CCA) and constrained principal coordinate analysis (CPCoA) were used to visualize the data. The differential abundances of OTUs between healthy controls and OSCC were determined using Linear discriminant analysis Effect Size (LEfSe) (Segata et al., ). A heatmap was obtained using R scripts with the clustering distance of “correlation” and clustering method of the “ward.D2” settings […]


The relationships between faecal egg counts and gut microbial composition in UK Thoroughbreds infected by cyathostomins

PMCID: 5946844
PMID: 29432771
DOI: 10.1016/j.ijpara.2017.11.003
call_split See protocol

[…] nal Analysis of Multivariate Dispersions (PERMDISP) through the ‘betadisper’ function (). Differences in the relative abundances of individual microbial species between groups were assessed using the Linear discriminant analysis Effect Size (LEfSe) workflow (), by assigning FEC/timepoint ‘groupings’ as the comparison class. All statistical analyses were repeated on a sub-group of horses with FEC ≥ […]

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LEfSe institution(s)
Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA; Microbial Sequencing Center, The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, MA, USA
LEfSe funding source(s)
Supported in part by grant DE017106 from the National Institute of Dental and Craniofacial Research, NIH grants AI078942 and Burroughs Wellcome Fund, and by NIH 1R01HG005969.

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