New method for extracting human DNA from the environment

New research suggests that it is now possible to sequence human DNA from minimal environmental sources such as water, sand, and air. This groundbreaking discovery allows scientists to extract valuable information about an individual’s genetic lineage, gender, and even potential health risks.

The basis for this method lies in the fact that every cell in our bodies contains DNA, which possesses a unique genetic code. Traditionally, medical professionals and researchers obtain human DNA through direct sampling methods like blood tests, swabs, or biopsies. However, it is important to note that all living organisms, including animals, plants, and microbes, constantly release DNA. These microscopic particles of biological material can be found in various environmental components such as water, soil, and even the air.

This shed DNA, known as environmental DNA or eDNA, has been extensively studied in the past few decades for monitoring biodiversity, wildlife populations, and disease-causing pathogens. By collecting and sequencing eDNA from soil or water samples, scientists have been able to effectively track and study rare or elusive endangered species, eliminating the need for invasive and unsuccessful traditional monitoring methods like observation or trapping.

While researchers typically focus on specific species when utilizing eDNA tools, it is important to recognize that humans also contribute to this environmental pool of DNA through shedding, coughing, and other activities. The recent findings from the Duffy Lab at the University of Florida, where a team of geneticists, ecologists, and marine biologists conducted their research, demonstrate that traces of human life can be detected almost everywhere except the most isolated locations.

The authors and their colleagues use environmental DNA to study sea turtles.

Animals, humans and viruses in eDNA

Our research team utilizes environmental DNA to study endangered sea turtles and their susceptibility to viral tumors. When hatchling sea turtles crawl along the beach en route to the ocean, they shed DNA, which can be found in the sand within their tracks. By analyzing this DNA, we can gain valuable insights into the turtles themselves, as well as the chelonid herpesviruses and fibropapillomatosis tumors that affect them. Similarly, collecting a liter of water from the tanks of sea turtles under veterinary care provides a wealth of genetic information without causing any stress to the animals.

Advancements in genetic sequencing technology have significantly improved in recent years, enabling us to easily decode the DNA of all organisms present in an environmental sample. We suspected that the sand and water samples we collected for our sea turtle research would contain DNA from various other species, including humans. What we didn’t anticipate was the level of valuable information we could extract from the human DNA.

To explore this further, we gathered samples from different locations in Florida, including urban and rural areas, beaches with varying levels of human activity, and even a remote island rarely visited by people. Surprisingly, we discovered human DNA in all the sampled locations, except for the remote island. The quality of these human DNA samples allowed for thorough analysis and sequencing.

We also conducted tests in Ireland, following a river’s path from a secluded mountaintop through small rural villages until it reached a larger town with a population of 13,000. In this case, we found human DNA everywhere along the river, except for the distant mountain tributary where human habitation was absent.

Additionally, we collected air samples from a room within our wildlife veterinary hospital in Florida. With the consent of the individuals present in the room, we retrieved DNA samples that matched the people themselves, the animal patients, and even common animal viruses that were present during the collection.

These findings demonstrate the broad scope and applicability of environmental DNA analysis, providing valuable genetic insights not only into endangered sea turtles but also into human presence and associated genetic information in various environmental settings.

Human eDNA can be collected and analyzed from a variety of sources. Credit: Liam Whitmore/Created with, CC BY-NC-ND

To our astonishment, the human environmental DNA (eDNA) discovered in the surrounding environment retained its integrity to a remarkable degree. This enabled us to identify disease-associated mutations and unveil the genetic ancestry of individuals residing in the region. Strikingly, even the DNA retrieved from footprints left by volunteers in the sand contained fragments of their sex chromosomes, adding an additional layer of genetic information.

The preservation and accessibility of human eDNA in the local environment opened up unprecedented possibilities for our research. By sequencing this genetic material, we were able to discern specific mutations linked to various diseases, shedding light on potential health risks within the population. Furthermore, we delved into the ancestral origins of the individuals living in the area, unearthing valuable insights into their genetic heritage.

Perhaps most intriguingly, the DNA obtained from footprints left by volunteers in the sand yielded segments of their sex chromosomes. This discovery showcased the sensitivity of our sequencing techniques, allowing us to discern not only broad genetic characteristics but also finer details related to an individual’s biological sex.

These findings highlight the immense potential of studying human eDNA in the environment. It provides a non-invasive and comprehensive means of understanding genetic traits, health risks, and ancestral backgrounds of individuals within a given geographical area. Such knowledge can contribute significantly to fields like population genetics, personalized medicine, and epidemiology.

Ethical implications of collecting human eDNA

Our research team has coined the term “human genetic bycatch” to describe the unintentional retrieval of human DNA from environmental samples. Recognizing the potential impact of this phenomenon, we are advocating for a thorough and comprehensive discussion on the ethical considerations surrounding the handling of human environmental DNA.

The utilization of human eDNA has the potential to drive significant advancements in a wide range of fields, including conservation, epidemiology, forensics, and agriculture. With proper management, human eDNA could aid archaeologists in locating undiscovered ancient human settlements, assist biologists in monitoring cancer mutations within specific populations, and provide valuable forensic information to law enforcement agencies.

Nevertheless, it is essential to address the numerous ethical implications associated with the inadvertent or intentional collection and analysis of human genetic bycatch. Extracting identifiable information from eDNA raises concerns regarding consent, confidentiality, and privacy. The level of detail that can be obtained about individuals or populations necessitates a responsible approach to ensure ethical standards are upheld.

As we explore the potential of human eDNA, it becomes imperative to engage in thoughtful dialogue to establish guidelines and frameworks that safeguard the rights and privacy of individuals involved. It is crucial to strike a balance between the remarkable opportunities that human eDNA offers and the ethical obligations that come with handling such sensitive genetic information. Only through comprehensive and informed discussions can we navigate this complex terrain and responsibly harness the potential of human environmental DNA research.

The researchers extracted identifiable genetic information from footprints in the sand. Credit: David Duffy, CC BY-ND

While our study adhered to ethical research guidelines and received approval from our institutional review board, it is crucial to acknowledge that not all individuals or organizations may treat this type of information ethically.

The presence of human environmental DNA raises numerous important questions that demand careful consideration. Determining who should have access to human eDNA sequences becomes a pivotal issue. Should this information be made publicly available, or should it be restricted to specific researchers or authorized individuals? Furthermore, the question of consent arises: should individuals provide explicit consent before their eDNA samples are collected, and if so, from whom should consent be obtained? Additionally, there is the matter of whether researchers should remove human genetic information from samples originally collected for the purpose of identifying other species.

To ensure the ethical and appropriate collection, analysis, and storage of human eDNA data, it is imperative to establish regulations and guidelines. Policymakers, scientific communities, and other stakeholders must take the matter of human eDNA collection seriously. Striking a balance between consent, privacy, and the potential benefits of studying eDNA is of utmost importance. By addressing these questions now, we can raise awareness about the capabilities of eDNA and allow sufficient time to develop protocols and regulations that safeguard the responsible use of eDNA techniques and the ethical handling of human genetic bycatch.

Leave a Comment