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.22177154 · W7204722797
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This Python code analyzes paired endometrioma and eutopic endometrium samples from eight patients using 16S rRNA sequencing to assess microbial diversity, composition, and differential abundance.

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This resource provides the Python analysis code used to process 16S rRNA sequencing data from eight patients with endometrioma and eutopic endometrium. The scripts perform paired analyses, calculate R² for PERMANOVA, screen for contamination, and conduct diversity analyses using repeated rarefaction. Additionally, the code summarizes BLAST search results for representative sequences, evaluates family-level composition, and assesses genus-level differential abundance with multiple comparison corrections. This paper is centrally about endometriosis — specifically the microbial profiling of endometrioma lesions compared to 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 (182 Bytes) | Name | Size | Download all | |---|---|---| | md5:91bc03948a1c147dfb359855cfbeedbb | 182 Bytes | Preview Download |

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