Postdoc position – Microbiome Signatures of Heavy Menstrual Bleeding

Sebibc; Madrid; Híbrido; EUR 37.000 - 45.000; Jornada completa

Descripción de la vacante

CBGP (UPM-INIA/CSIC) in Madrid invites a postdoctoral researcher to join the microbiome component of the MVS project, focusing on vaginal and menstrual-fluid microbiomes to understand heavy menstrual bleeding using shotgun and targeted metagenomics, single-cell data, and AI integration.

The position offers on-site with partial remote work, starts before December 2026, for 1.5–2 years, and an approximate gross salary of €41,000 per year.

Formación

• Experience in big-data metagenomic analysis.
• Fluency in HPC and Linux environments, processing pipelines and genomic data analysis.

Responsabilidades

• Metagenomic analysis of vaginal microbiome and menstrual-fluid samples (500 matched vaginal swabs + menstrual fluid): taxonomic and functional profiling (e.g. mOTUs, eggNOG-mapper).
• Development of bioinformatic pipelines and resources for metagenome data analysis.
• Host–microbiome AI integration: multimodal multi-instance learning integrating microbial data with host single-cell transcriptomics, genetic variants, clinical metadata and fluid volume.
• Metabolomic correlation and functional validation support (e.g. short-chain fatty acids), with follow-up in patient-derived endometrial organoids.
• Writing reports, attending international meetings, and supervising related work.

Conocimientos

Big-data metagenomic analysis

HPC environments

Bioinformatics pipelines

Genomic data analysis

Machine learning integration

Herramientas

mOTUs

eggNOG-mapper

Descripción del empleo

Postdoc position - Microbiome Signatures of Heavy Menstrual Bleeding

CBGP (UPM-INIA/CSIC), Madrid, Spain Hybrid (partial remote) Start expected before December 2026 1.5–2 years (depending on start date) ≈ €41,000 gross / year Apply by 1 September 2026 (or until filled)

The Comparative Genomics & Metagenomics Lab (CGMLab, https://cgmlab.org) at the Centre for Plant Biotechnology and Genomics (CBGP, Madrid) is seeking a postdoctoral researcher to join the microbiome component of the "Missed Vital Sign" (MVS) project.

About The Project

MVS is funded by the Wellcome Leap 'The Missed Vital Sign' programme, which is a 36-month collaborative initiative that is transforming the study and diagnosis of female reproductive health. The project uses vaginal and menstrual fluid as a non-invasive biological proxy to study heavy menstrual bleeding (HMB), a condition that affects over 30% of women of reproductive age but remains under-researched because traditional diagnostics rely on invasive biopsies or blood tests. Our multidisciplinary team, comprising experts in reproductive biology, generative AI, clinical gynaecology, and microbiome science, collects samples from 500 women using smart menstrual cups with integrated biosensors. We integrate single-cell RNA sequencing, spatial transcriptomics, genotyping, and microbial profiling with AI to identify the causal factors of HMB, stratify patients, and validate therapeutic targets in patient-derived endometrial organoids.

Our lab is leading the microbiome component, which involves understanding how microbial communities in the female reproductive tract correlate with host endometrial cells and contribute to HMB. However, menstrual-fluid microbiome analysis presents challenges due to low microbial biomass and an overwhelming presence of human host DNA. To overcome this, we combine regular shotgun sequencing with targeted metagenomic capture sequencing technology to achieve high precision, sensitivity, and phylogenetic resolution in low-biomass samples.

About Our Group

CGMLab studies the diversity and biological complexity of microbial communities through genomic sequencing and computational methods, developing bioinformatics tools and resources for metagenomics research. Learn more at https://cgmlab.org

Responsibilities

• Metagenomic analysis of vaginal microbiome and menstrual-fluid samples (500 matched vaginal swabs + menstrual fluid): taxonomic and functional profiling (e.g. mOTUs, eggNOG-mapper).
• Development of bioinformatic pipelines and resources for metagenome data analysis.
• Host–microbiome AI integration: multimodal multi-instance learning integrating microbial data with host single-cell transcriptomics, genetic variants, clinical metadata and fluid volume.
• Metabolomic correlation and functional validation support (e.g. short-chain fatty acids), with follow-up in patient-derived endometrial organoids.
• Writing reports, attending international meetings, and supervising related work.

Required

• Experience in big-data metagenomic analysis.
• Fluency in HPC and Linux environments, processing pipelines and genomic data analysis (all technical work is bioinformatic).

Valued

• Knowledge/experience in the human microbiome, particularly women's health (vaginal / reproductive tract).
• Strong data interpretation in clinical contexts; statistics; integration with omics data.
• Familiarity with genomic sequencing methods.

Conditions

• Postdoctoral position, ≈ €41,000 gross per year.
• Duration: 1.5–2 years depending on start date (expected before December 2026).
• Based at CBGP, Madrid. On-site presence required; partial remote work possible when tasks allow.