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Seminal Microbiome Characterization and Body Mass Index Associations in a Clinical Male Cohort Using Full-Length 16S rRNA Long-Read Sequencing

Muñoz Alvarez, Silvia Juliana LU (2026) KMBM01 20261
Applied Microbiology
Biotechnology
Biotechnology (MSc)
Abstract
The seminal microbiome remains undercharacterised despite its potential role as a microbial reservoir influencing female partner reproductive health. This study applied Oxford Nanopore full-length 16S rRNA sequencing (V1–V9) with EMU v3.6.1 classification to characterise the seminal microbiome of 288 men enrolled in the couple-based Copenhagen Pregnancy Loss cohort. The seminal community was polymicrobial and highly variable, dominated by Finegoldia magna (mean 9.82%, prevalence 79.9%); VALENCIA nearest-centroid classification assigned 92.8% of samples to CST IV, confirming fundamental compositional divergence from vaginal reference profiles. A co-occurrence subnetwork comprising Gardnerella vaginalis and Lactobacillus iners, both... (More)
The seminal microbiome remains undercharacterised despite its potential role as a microbial reservoir influencing female partner reproductive health. This study applied Oxford Nanopore full-length 16S rRNA sequencing (V1–V9) with EMU v3.6.1 classification to characterise the seminal microbiome of 288 men enrolled in the couple-based Copenhagen Pregnancy Loss cohort. The seminal community was polymicrobial and highly variable, dominated by Finegoldia magna (mean 9.82%, prevalence 79.9%); VALENCIA nearest-centroid classification assigned 92.8% of samples to CST IV, confirming fundamental compositional divergence from vaginal reference profiles. A co-occurrence subnetwork comprising Gardnerella vaginalis and Lactobacillus iners, both hallmarks of non-optimal vaginal microbiota, was identified within the seminal community, consistent with the hypothesis that a subset of men harbour microbial profiles shaped by recurrent exposure to vaginal dysbiosis. Body mass index was the sole clinical variable significantly associated with alpha diversity (Shannon ρ = 0.170, p_adj = 0.006) and with colonisation probability of eight anaerobic taxa in multivariable modelling (MaAsLin3 prevalence sub-model, q < 0.05), a finding independently corroborated by Dirichlet Multinomial Mixture community typing. Species-level discrimination between L. crispatus and L. iners, taxa that are indistinguishable by short-read V4 approaches, was uniquely enabled by full-length sequencing. All primary findings were robust to reference database choice, confirmed by cross-validation against GTDB. Body mass index was the strongest detectable host correlate of seminal microbial diversity, and positioned body weight as a possible modifiable factor in male reproductive microbiome health. (Less)
Popular Abstract
What lives in semen and why it matters for couples trying to have a baby?
Semen is not sterile. Like the gut or the skin, it harbours a community of microorganisms, such as bacteria, that live in the male reproductive tract and are introduced into the female genital environment during intercourse. For a long time, science largely ignored this community, focusing instead on sperm quality and female reproductive factors. But growing evidence suggests that the microbial passengers in semen may matter more than previously thought, being important not only for the man's own reproductive health, but for his partner's as well.

This master's thesis examined the bacterial communities present in semen samples from 288 men enrolled in a Danish... (More)
What lives in semen and why it matters for couples trying to have a baby?
Semen is not sterile. Like the gut or the skin, it harbours a community of microorganisms, such as bacteria, that live in the male reproductive tract and are introduced into the female genital environment during intercourse. For a long time, science largely ignored this community, focusing instead on sperm quality and female reproductive factors. But growing evidence suggests that the microbial passengers in semen may matter more than previously thought, being important not only for the man's own reproductive health, but for his partner's as well.

This master's thesis examined the bacterial communities present in semen samples from 288 men enrolled in a Danish clinical study of couples experiencing pregnancy loss. Samples and clinical data were collected by medical personnel at Copenhagen University Hospitals as part of the ongoing cohort study. Using a cutting-edge DNA sequencing technology capable of identifying bacteria at the species level, the bacterial landscape of each sample was mapped.
The results revealed that no two men shared the same seminal bacterial community, and no single bacterium was universally present. Notably, two bacteria typically associated with an unhealthy vaginal environment, Gardnerella vaginalis and Lactobacillus iners, were found together in a subset of men's semen, raising the possibility that some men may carry microbial profiles that could influence their partner's vaginal health during sexual contact. This is particularly relevant given recent clinical trial evidence showing that treating male partners alongside women reduces the recurrence of vaginal bacterial imbalance.

The study also found that body weight (measured as body mass index) was the strongest factor linking a man's physical characteristics to the diversity and composition of his seminal microbiome. Heavier men tended to harbour a greater variety of bacteria, including several anaerobic species not typically associated with a healthy reproductive environment. No other lifestyle or clinical factor examined, including smoking or alcohol consumption, showed a comparable effect.

These findings position body weight as a modifiable factor in male reproductive microbiome health, and highlight the seminal microbiome as a biologically meaningful, and largely overlooked, component of couple reproductive biology. (Less)
Please use this url to cite or link to this publication:
author
Muñoz Alvarez, Silvia Juliana LU
supervisor
organization
course
KMBM01 20261
year
type
H2 - Master's Degree (Two Years)
subject
keywords
seminal microbiome, full-length 16S rRNA, Dirichlet Multinomial Mixture, host-microbiome associations, inter-partner microbial exchange, applied microbiology
language
English
id
9234544
date added to LUP
2026-06-10 14:54:20
date last changed
2026-06-10 14:54:20
@misc{9234544,
  abstract     = {{The seminal microbiome remains undercharacterised despite its potential role as a microbial reservoir influencing female partner reproductive health. This study applied Oxford Nanopore full-length 16S rRNA sequencing (V1–V9) with EMU v3.6.1 classification to characterise the seminal microbiome of 288 men enrolled in the couple-based Copenhagen Pregnancy Loss cohort. The seminal community was polymicrobial and highly variable, dominated by Finegoldia magna (mean 9.82%, prevalence 79.9%); VALENCIA nearest-centroid classification assigned 92.8% of samples to CST IV, confirming fundamental compositional divergence from vaginal reference profiles. A co-occurrence subnetwork comprising Gardnerella vaginalis and Lactobacillus iners, both hallmarks of non-optimal vaginal microbiota, was identified within the seminal community, consistent with the hypothesis that a subset of men harbour microbial profiles shaped by recurrent exposure to vaginal dysbiosis. Body mass index was the sole clinical variable significantly associated with alpha diversity (Shannon ρ = 0.170, p_adj = 0.006) and with colonisation probability of eight anaerobic taxa in multivariable modelling (MaAsLin3 prevalence sub-model, q < 0.05), a finding independently corroborated by Dirichlet Multinomial Mixture community typing. Species-level discrimination between L. crispatus and L. iners, taxa that are indistinguishable by short-read V4 approaches, was uniquely enabled by full-length sequencing. All primary findings were robust to reference database choice, confirmed by cross-validation against GTDB. Body mass index was the strongest detectable host correlate of seminal microbial diversity, and positioned body weight as a possible modifiable factor in male reproductive microbiome health.}},
  author       = {{Muñoz Alvarez, Silvia Juliana}},
  language     = {{eng}},
  note         = {{Student Paper}},
  title        = {{Seminal Microbiome Characterization and Body Mass Index Associations in a Clinical Male Cohort Using Full-Length 16S rRNA Long-Read Sequencing}},
  year         = {{2026}},
}