What the Genital Microbiome Reveals After Sex

After sexual intercourse, both partners leave behind more than just DNA.

A new study published in iScience by researchers at Murdoch University, has found that sexual partners leave traces of their unique genital microbiome that can be detected even after intercourse. These microbial signatures could provide a new forensic tool for identifying perpetrators in sexual assault cases, particularly when conventional DNA evidence is unavailable.

The limitations of DNA evidence in sexual assault cases

Sexual assault investigations often rely on biological evidence to establish whether sexual contact has occurred. One of the primary forensic techniques involves identifying the perpetrator’s DNA, typically through the detection of sperm cells in vaginal swabs. This method has proved incredibly valuable, helping link suspects to crimes and supporting survivor testimony in court. However, it comes with significant limitations.

One major issue is the short window for sperm detection. Research has shown that sperm can degrade or be washed away within hours of an assault, with forensic guidelines suggesting the likelihood of successfully retrieving sperm from vaginal samples drops significantly after 24 to 48 hours​. This narrow timeframe means that sexual assault survivors who delay reporting the crime may be left without crucial forensic evidence.

Even when forensic examinations are conducted promptly, DNA analysis can be challenging. Vaginal swabs often contain an overwhelming amount of the victim’s own DNA, which can overshadow or dilute the perpetrator’s genetic material​. To separate male and female genetic contributions, forensic scientists use a technique called differential DNA extraction. However, this method is far from perfect – it is time-consuming, prone to errors and can lead to degradation of the male DNA – further complicating analysis​.

Another limitation arises in cases where no sperm is present, such as when the perpetrator wears a condom. In these cases, standard forensic techniques struggle to establish whether sexual contact occurred, making it easier for perpetrators to deny involvement. Similarly, in sexual assault cases where ejaculation does not occur, or where assailants remove physical evidence through post-assault hygiene practices, traditional DNA analysis may fail to provide conclusive results.

These challenges highlight the urgent need for alternative forensic tools that can detect sexual contact even when sperm is absent.

The discovery of the "sexome"

Led by Dr. Brendan Chapman, a senior lecturer in forensic science, and Ruby Dixon, PhD candidate, at Murdoch University, the research team introduced a new forensic concept called the "sexome" in their latest study – a unique microbial signature exchanged between sexual partners.

“This research is based on the forensic concept that every contact leaves a trace,” said Chapman.

The team recruited 12 monogamous heterosexual couples and asked them to abstain from sex for 2–14 days before participating in intercourse. Before and after sex, each participant collected genital microbiome samples using swabs. The researchers then analyzed these samples using full-length 16S rRNA gene sequencing, a method capable of identifying bacterial strains down to the sub-species level​.

While forensic microbiology has been explored in crime scene analysis – such as tracking bacterial signatures on objects and surfaces – this study is among the first to investigate the potential of genital microbiomes in a forensic context​.

The results showed clear evidence of microbial transfer between sexual partners. In every couple, the bacterial profile of one partner was detectable in the other post-intercourse, confirming that genital microbiomes intermingle during sexual contact.

The study also found that specific bacterial genera were more likely to transfer between partners, with Lactobacilli frequently moving from females to males, while Staphylococci and Corynebacteria were commonly transferred from males to females. Surprisingly, this bacterial exchange occurred even when a condom was used, albeit with some variation in transfer patterns.

“We suspect that broadly speaking, how the condom is fitted and what activities took place prior to that might be acting as a vector to transfer the bacteria,” Chapman told Technology Networks.

“When a condom was used, the majority of transfer occurred from the female to the male. This shows promise for a means of testing a perpetrator post-assault and means there may be microbial markers that detect sexual contact even when a condom was used,” said Dixon​.

The researchers observed that microbial traces persisted for some time after intercourse, suggesting that forensic detection might be possible even beyond the typical sperm-detection window. Each couple also had distinct microbial transfer patterns, reinforcing the idea that bacterial signatures could serve as unique forensic identifiers in sexual assault cases.

The study also explored whether external factors influenced bacterial transfer. The researchers found that circumcision status and the presence of pubic hair had little to no effect on microbial exchange. However, menstruation altered the vaginal microbiome, potentially influencing forensic analyses​.

Some bacterial strains detected post-intercourse were not originally present in the genital microbiome but may have been introduced from other body sites during sexual contact, such as through oral or skin-to-skin interactions.

Applications and challenges in forensic science

“Until now, few studies have explored the vaginal and penile microbiomes within a forensic context. This research demonstrates that we can observe microbial traces from heterosexual couples’ genital microbiomes following sex,” said Chapman.

The team hopes microbial analysis could complement DNA-based forensic techniques, particularly in cases where DNA evidence is absent, degraded or inconclusive. The ability to detect bacterial signatures transferred during sexual contact, even in condom-protected assaults, offers a novel way to establish physical contact between a victim and a suspect. This could be especially valuable in legal cases where perpetrators deny involvement and traditional forensic evidence is lacking.

“We would never intend for this type of analysis to replace the current techniques that identify human DNA because there are well established databases and the techniques are incredibly robust. Instead, we propose that the sexome can be used as another tool in the forensic DNA toolkit, to either strengthen the validity of human DNA findings or to be used when that technique comes up short,” said Chapman.

However, challenges remain before microbial forensics can be reliably implemented in casework. One hurdle is understanding the stability of microbial transfer over time. While the study confirmed that genital bacteria persist post-intercourse, further research is needed to determine how long these bacterial signatures remain detectable and whether they can survive external influences such as washing, personal hygiene or environmental exposure.

“Often following sexual assault, it is many hours, sometimes days, before a victim is seen by a sexual assault physician. Our understanding of how long we can delay sampling is limited at this stage, so we are building that dataset in our current work,” said Chapman.

While the study found that circumcision status and pubic hair did not significantly impact bacterial transfer, other variables including hormonal changes, antibiotic use and individual microbiome diversity, may complicate forensic interpretation.

“The application of the sexome in sexual assault casework is still in its infancy. It’s important to completely understand the external factors that may have an impact on the microbial diversity of both males and females, and this is something we plan to continue studying,” said Dixon.

“We often get asked why we’re looking at heterosexual couples and the reality is that by far the largest proportion of sexual assaults in Australia are female victims with male offenders. Without diminishing the impact or importance of other combinations, we needed to start somewhere and it makes sense to tackle the largest cohort first. We certainly wish to extend this study to same-sex and gender-diverse combinations along with a range of transfers that aren’t just penile-vaginal intercourse,” Chapman added.

While microbial forensics does not aim to replace conventional DNA analysis, it represents a promising new avenue for forensic science. If further research can address these challenges and establish robust forensic standards, the sexome could become a powerful tool for identifying perpetrators in sexual assault cases – offering justice to survivors where traditional forensic methods fall short.

About the interviewee:

Dr. Brendan Chapman is a forensic scientist with expertise in the fields of forensic genetics and DNA, homicide and sex crime investigation, clandestine grave site recovery and cold case review. He is the director of the Cold Case Review at Murdoch initiative. Chapman’s research is focused on the enhancement of molecular capabilities for national security and unsolved cases using cutting-edge DNA sequencing techniques and high-sensitivity analysis. Having worked for over 10 years in Western Australian state government departments in both the forensic DNA laboratory and with law enforcement at crime scenes, Chapman has attended thousands of major crime scenes and been involved in countless investigations associated with high profile homicides.  

Reference: Dixon R, Egan S, Payne M, Mullally C, Chapman B. Bacterial transfer during sexual intercourse as a tool for forensic detection. iScience. 2025. doi: 10.1016/j.isci.2025.111861

This article is a rework of a press release issued by Cell. Material has been edited for length and content.