Analysis code for: Microbial profiling of endometrioma and eutopic endometrium using 16S rRNA sequencing

Kensaku Furui, Ayako Muraoka, Bayasula Bayasula, Takehiko Takeda, Tomomi Seki, Natsuki Miyake, Reina Sonehara, Tomoko Nakamura, Hiroaki Kajiyama
2026 · doi:10.5281/zenodo.22943668 · W7214218697
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This paper provides reproducible Python code for analyzing 16S rRNA sequencing data from endometrioma and eutopic endometrium samples to characterize microbial profiles in endometriosis patients.

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This resource provides the Python analysis code used to process 16S rRNA sequencing data from a study on microbial profiles in endometrioma and eutopic endometrium. The scripts handle paired analyses of eight patients, including PERMANOVA calculations, contamination screening, rarefaction for diversity metrics, and genus-level differential abundance testing with multiple comparison corrections. Input data consists of ASV tables and representative sequences derived from BioProject PRJDB40150, ensuring reproducibility through fixed random seeds. This paper is centrally about endometriosis — specifically the microbiome composition within endometriomas and normal endometrial tissue.

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Abstract

Python code used for the analyses reported in the manuscript. Covers the paired analysis of eight patients, the calculation of R² for PERMANOVA, contamination screening, repeated rarefaction for the diversity analyses, summarization of the BLAST search of all 146 representative sequences, family-level composition, genus-level differential abundance with correction for multiple comparisons, and the sensitivity analysis for the dominant Escherichia lineage. Input data are the ASV table and representative sequences generated from the 16S rRNA gene sequencing data deposited under BioProject PRJDB40150. The random seed is fixed, so the reported values are reproducible.
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Analysis code for: Microbial profiling of endometrioma and eutopic endometrium using 16S rRNA sequencing Description Python code used for the analyses reported in the manuscript. Covers the paired analysis of eight patients, the calculation of R² for PERMANOVA, contamination screening, repeated rarefaction for the diversity analyses, summarization of the BLAST search of all 146 representative sequences, family-level composition, genus-level differential abundance with correction for multiple comparisons, and the sensitivity analysis for the dominant Escherichia lineage. Input data are the ASV table and representative sequences generated from the 16S rRNA gene sequencing data deposited under BioProject PRJDB40150. The random seed is fixed, so the reported values are reproducible. Files endometrioma_16S_analysis_code.zip Files (22.5 kB) | Name | Size | Download all | |---|---|---| | md5:47a073c5440162974f907e7f45a3f564 | 22.5 kB | Preview Download |

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