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In the summer of 2015, two intruders broke into Jose Lopez鈥檚 home in Hollywood, Florida, and stole a TV. But this was far from your standard-issue burglary. The 鈥渢hieves鈥� were deputies from the local sheriff鈥檚 office, and Lopez, a biologist at Nova Southeastern University, was in on the whole thing as part of a project to see whether police can identify criminals from the microbes they leave at the scene. 听

Having analysed microbial traces left on surfaces and isolated bacterial DNA, the researchers could match them to the deputies. But when they tried to pick the intruders out of a database of 10,000 microbiome samples, the signatures proved insufficiently unique. The technique, they concluded in a , 鈥渃annot be used as a reliable trace evidence standard for criminal investigations鈥�. 听
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Let鈥檚 call that cause for reasonable doubt. Forensic scientists have long argued that the billions of bacteria, viruses and fungi in and on our bodies could become a valuable source of evidence. The problem has been proving that 鈥渕icrobiome forensics鈥� is reliable enough for real investigations. 听

In recent years, however, researchers have refined their techniques, working with police to better establish what these methods can and can鈥檛 tell us. They have also developed a way to analyse the post-mortem microbiome to estimate time of death 鈥� an approach that is being explored in relation to a controversial murder case in Italy. 听

鈥淚t鈥檚 a massive frontier in forensic science right now,鈥� says at Chaminade University of Honolulu in Hawaii. The question is which of these techniques will prove useful 鈥� and whether the evidence they produce will ever stand up in court. 听

What is forensic microbiology?

It鈥檚 not difficult to see why forensic scientists see the human microbiome as an untapped source of information. 鈥淚magine if I told you that there was a type of physical evidence that was guaranteed to be associated with every death scene 鈥� no matter where it was, when it was,鈥� says Carter, alluding to the many cases where fingerprints and DNA aren鈥檛 retrievable. In those circumstances, the microbes we constantly shed onto other people and any surfaces we come into contact with could provide important clues because the ecosystems on our skin, for instance, vary enormously from person to person. 听

The field of forensic microbiology has really only existed since the 1990s, when advances in sequencing technology transformed what was possible in terms of analysing microbial DNA to isolate signature bacterial species. As sequencing got faster and cheaper, researchers could start testing the idea that the highly individual mixture of microbes we carry around 鈥� our microbial 鈥渇ingerprints鈥�, in forensic parlance 鈥� might be useful in identifying people. 听

For a study published in 2010, for example, , now at the University of California, San Diego, and his colleagues showed that the cocktail of bacteria deposited on a personal keyboard or mouse . Other studies, meanwhile, showed that people leave a unique microbial signature in their homes.听

All of which seemed promising. Yet when researchers tested the 鈥渢ouch microbiome鈥� approach under more realistic conditions 鈥� including in those mock burglaries 鈥� it fell well short of the reliability required of forensic evidence. 听

The results prompted , then director of the Microbiome Center at the University of Chicago, who had led the burglary studies and others, to warn the US Department of Justice against adopting the technique in 2018. 鈥淚 stipulated that I had no confidence that this could be used to identify individuals with enough rigour to definitively state that it was them and not somebody else,鈥� says Gilbert. 鈥淚 cannot prove, without a shadow of a doubt, that the bacteria that I found didn鈥檛 come from another human being.鈥� 听
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The setback didn鈥檛 end interest in forensic microbiology, though. And other researchers have since been exploring not only the extent to which better sequencing techniques and larger datasets can make a difference, but also whether other forms of microbiome analysis might play a role in criminal investigations. 听

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, a forensic scientist at the University of Lancashire, UK, is investigating one such possibility. She argues that touch microbiome techniques might already hold 鈥渋nvestigative intelligence鈥� that could give police crucial clues in cases where conventional forensic evidence is missing. 听

Her current research project began with the frustrations of Andy Nixon, a veteran crime-scene specialist for West Midlands Police in the UK, who is often confronted with murder cases where there is what he calls a 鈥渇orensic void鈥�. Many of the most vexing cases involve strangulation, says Nixon, because 鈥渢he neck is too soft and elastic to preserve conventional fingerprints, and touch alone rarely leaves usable fragments of DNA 鈥� even when attackers use such extreme violence鈥�. 听

Microbial fingerprints

To see whether microbial traces might help, in 2025, Procopio and Nixon recruited 100 new officers from West Midlands Police to test how reliably their touch microbiomes could be traced back to them. The participants pressed their fingers onto acetate sheets, which were then left around for days or weeks inside a room where passers-by could walk through, as real-world microbial fingerprints might be. To start with, Procopio and her colleagues focused on rare bacterial species, which sometimes identified individuals but often became undetectable through sequencing within 48 hours, which is likely to be because they are overwhelmed by other species from the environment. 听

Next, the researchers analysed the structure of the microbial community in the samples, rather than focusing solely on rare species, to see whether it could offer a more reliable signature. 鈥淢aybe we have the same bacteria, but I have more of that, less of that, something unique,鈥� says Procopio. In yet-to-be-published research, they found that this allowed them to match the sample to the individual with much greater accuracy, and that this signal remained a month later.

Crucially, Procopio isn鈥檛 claiming that such techniques will be a replacement for DNA analysis, sufficient alone to place a suspect at a crime scene. Instead, she sees them as 鈥渃omplementary鈥� additions to the investigative toolkit. In fact, she agrees with Gilbert that 鈥渋t will be very difficult, at least at this stage, to achieve the type of statistical weight typically associated with human DNA identification鈥�. But in cases where investigators draw a forensic blank, they might get a lead if the overall structure of a microbial community matches the sample taken from a known suspect.

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Knight says this reflects how forensic evidence is often used in practice. The most common form of forensic finding is not one conclusive method of identification, but 鈥渃lass evidence鈥� that narrows the suspect pool. Knight points to a 1982 case involving child murders in Atlanta, Georgia, where investigators found a mixture of microscopic fibres 鈥� yellowish-green nylon and violet acetate 鈥� on several murder victims and also in an unusual carpet owned by suspect Wayne Williams. They were able to explain to a jury the long odds of such a carpet being found in a suspect鈥檚 home: . 鈥淣o individual fibre was conclusive, but the aggregate was very convincing,鈥� says Knight. 鈥淭reating microbes in this context is reasonable.鈥澨�

Microbial traces might ultimately have a similar role. 鈥淎 technique doesn鈥檛 have to be perfect to be useful,鈥� says Knight. 鈥淚t鈥檚 about stacking multiple class characteristics so that the probability of a false match approaches zero.鈥澨�

The microbial communities we carry around with us might also point in directions that investigators weren鈥檛 looking. That鈥檚 because our microbiomes are shaped to a great extent by our lifestyles and our interactions with others over the course of our lives, from where we live and who we spend time with to the foods we eat. In 2023, for instance, Procopio and her colleagues showed that , Lombardy and Piedmont, based on their oral microbiome. 鈥淭his is definitely something that can be useful,鈥� says Procopio. 听

The challenge here has to do with reference data. For the moment, we don鈥檛 have datasets of diverse individuals鈥� microbiomes that are sufficiently large to draw useful conclusions. As with DNA, big databases make better insights possible. But Procopio reckons we could eventually use microbiome profiling to reveal clues about the lifestyle of an unknown murderer, for instance 鈥� whether they work in an office or on a farm, say, whether they have particular health problems or even whether they have pets. 听

Then again, for all the intrigue around efforts to use microbes to identify perpetrators from a crime scene, the most promising way to use the microbiome in forensics is in revealing when 鈥� and by extension how, in some cases 鈥� someone died.听听

Estimating time of death

Procopio is among a group of researchers seeking to use the bacteria that come and go as bodies decompose to develop microbial clocks that could offer a reliable estimate of the time since death, days or even weeks after a body is discovered. Few illustrate the potential better than one of the most controversial recent murder investigations in Italy: the case of Liliana Resinovich. 听

In January 2022, almost a month after the 63-year-old was reported missing, Resinovich鈥檚 body was found on the grounds of a former psychiatric hospital in Trieste. She was found with plastic bags around her head and body, yet forensic pathologists found no obvious signs she had been attacked; their first report concluded that she had died, possibly by suicide, within the previous 48 hours. 听

But later, following protests by Resinovich鈥檚 family, her body was re-examined. This new forensic assessment concluded not only that she had been killed by asphyxiation, owing to the identification of signs of trauma on the face and head, but also that Resinovich had been killed around the time of her disappearance 鈥� citing evidence including the undigested contents of her last known meal from the morning she vanished.听

鈥淪omeone says she was dead for 48 hours, then the next forensic expert said she鈥檇 been dead for 23 days,鈥� says Procopio. 鈥淚t鈥檚 a massive gap.鈥� And crucially, it leaves open the question of what really happened: did Resinovich die two days before her body was found, as the first report suggested? Or was she killed around the time she went missing and kept somewhere cold, possibly even frozen, before her body was moved to the place where she was discovered 鈥� a hypothesis proposed to explain why it appeared unusually well preserved for a body left outdoors for three weeks?听

Despite what detective dramas might suggest, conventional forensic tools can pinpoint the time of death only when a body is discovered quickly. For the first 24 hours, a forensic pathologist can usually calculate a reliable 鈥減ost-mortem interval鈥� using a temperature reading from a rectal thermometer, says Procopio, while colouration, rigor mortis and cues from insects that lay eggs in the body鈥檚 orifices can help in the first few days. But uncertainty increases as the body enters more advanced states of decay, she adds, especially if it is outdoors.听

This is precisely the kind of uncertainty that microbial clocks are designed to address, says Procopio. In the past decade, studies on human remains at 鈥渂ody farms鈥� across the US have shown that . And by tracking these microbial changes, researchers can estimate how long a body has been decomposing, potentially unearthing vital clues about when 鈥� and how 鈥� someone died. 听

In the Resinovich case, a mouth swab taken around the time of her body鈥檚 discovery preserved a snapshot of her oral microbiome. If her body had been frozen or kept somewhere cold before it was found, the microbial community in that sample should contain evidence of . 鈥淚t would leave a detectable signature,鈥� says Knight. Procopio adds that other clues might come from insects, because a showed that they introduce certain decomposing microbes to a body at different times depending on whether it was exposed outdoors from the moment of death or was moved, from inside to outside, later.听

Will microbial evidence ever stand up in court?

In Procopio鈥檚 view, the microbiome can resolve the uncertainty between the freezer hypothesis and the suicide hypothesis. All the evidence so far is 鈥渃learly going in one direction and not in the other鈥�, she says. But for the evidence to be admissible in court, judges require compelling proof that microbial clocks are reliable. Which is why Procopio and her colleagues are now recreating the two scenarios at a body farm in northern Michigan, where climatic conditions resemble those in northern Italy. There, four donated cadavers are kept under different conditions, allowing the researchers to track how their microbiomes change over time with a view to presenting a clear and admissible finding to the public prosecutor in charge of the Resinovich case. 听

On the broader question of whether microbiome forensics will ever produce evidence that leads to a criminal conviction, the answer depends on the application. In most countries, judges act as gatekeepers, with the power to decide if a new form of scientific evidence should be allowed in courts, often following guidelines similar to those set down in the US starting in 1993. Under the Daubert standard, as it became known, judges consider whether a technique has been independently tested and peer-reviewed and has a known error rate before admitting it as evidence.听

On all counts, microbial clocks to estimate time of death appear ready to be used in court, says Carter. Research led by Jessica Metcalf at Colorado State University shows that , though that gets larger the longer someone has been dead. 鈥淚 feel that it meets those criteria, but it would really be a judge that would determine that,鈥� says Carter. 听

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The prospects for using microbiome analysis to identify suspects are more uncertain. To offer an alternative to DNA matching in the identification of suspects, it would have to achieve similarly exacting evidentiary standards 鈥� roughly a million-to-1 chance of a false match. The difficulty here is that the skin microbiome remains such a dynamic and ever-changing ecosystem that Gilbert doubts it will be useful any time soon. 鈥淭he microbiome contains 500 species, maybe 5000 to 6000 strains that are constantly fluctuating in abundance, constantly undergoing genetic evolution, constantly shifting in the proportional representation and constantly being exchanged between people,鈥� says Gilbert. 鈥淵ou鈥檙e dealing with biology, and biology is horribly complex.鈥� 听

Others are more optimistic. Knight argues that sequencing technology has moved on in critical ways since 2018. More advanced methods can detect less obvious genetic differences between microbes, he says, revealing 鈥減ersonalised and persistent strains鈥� that older approaches could not. 鈥淚 wouldn鈥檛 give up on the trace evidence topic,鈥� says Knight. 鈥淚t鈥檚 challenging, but technology is advancing rapidly.鈥澨�听