As a part of our microbiome research interview series, we spoke with Ms. Celia Díez López, a Ph.D. candidate from the Department of Genetic Identification, Erasmus Medical Centre Rotterdam, the Netherlands. Ms. Díez López is conducting research to identify novel uses of the human microbiome and other non-human components in forensic genetics.
How did you first get interested in science and microbiome research?
I got interested in science around the age of 12 when a vocational science teacher invited me to visit a laboratory for the first time. I remember myself becoming more and more enthusiastic about science with every visit to the lab, during which I was allowed to carry out my first biology- and chemistry-related experiments. My interest in microbiome came several years later, while I was working on my master’s thesis. I became fascinated by the human microbiome research and its multiple applications in several fields. Although some forensic-oriented microbiome research had already been conducted, in my opinion this was just the tip of the iceberg, with potentially many exciting applications to come in the study of the microbiome in forensics.
Can you give us a summary of the project you submitted for the Microbiome Awards?
The aim of my project is to develop a classification tool based on microbiome data and deep neural networks, together with a forensically suitable laboratory tool based on next-generation sequencing that can accurately identify the body site of origin of forensically-relevant human traces (such as semen, vaginal secretion, blood, saliva, skin and urine traces (1)).
In routine forensic investigations, the gold standard for identifying individuals is DNA profiling based on short tandem repeats (STRs). Through this profiling, a human biological trace found at a crime scene can be related to its donor, who may be a known suspect or an individual whose DNA profile is included in the (inter-)national criminal offender database(s). However, to evaluate the relevance of a trace and to reconstruct the events that took place at a scene, identifying the tissue-type to which a human biological sample belongs to is essential. Given that the microbial communities found on different human body sites (niches) are distinct from each other, these differences can be employed as the key for identifying human tissue-types.
This is especially relevant in alleged sexual assaults, where the suspect and victim co-habit or share common spaces. In this case, finding DNA from the people involved at the scene may not have strong evidential value, but identifying the tissue-type of a trace might have. In the context of a sexual assault investigation, differentiating semen from vaginal secretion, for example, can have considerable impact.
What is a typical day for you in the lab?
I would say that I have two kinds of typical days in the lab. There are periods in which I am pretty busy collecting samples, performing nucleic acids isolations, preparing libraries for sequencing, etc. On other days I spend the majority of my time sitting at my computer, performing data analysis and going through the current literature to come up with new project ideas and learn useful tips to further optimize my experimental plans.
What do you find most interesting about your project? What is the most interesting or surprising result you have found?
I find it very exciting that the microbes that naturally inhabit our bodies have the potential to answer challenging investigative questions. We have already published research on accurate classification of forensically relevant epithelial tissues, i.e., vaginal secretion, saliva and skin. It is very surprising to observe accurate results in mock casework forensic samples that contain minute microbial DNA biomass and have been stored at room temperature for many years under no special preservation conditions. This really highlights the implementation potential of the approach to real forensic casework.
What kind of microbiome research do you perform and how does it impact health and disease or the environment? Where do you see this heading in the next five years?
I am motivated to carry out this type of research because it provides society with a tool that can shed light on investigations that nowadays face difficulties when trying to answer some key forensic questions, such as ’which tissue(s) does a DNA sample belong to’.
I hope that the microbiome is proven to be a useful, reliable and powerful investigative tool in the next five years, not only in the forensic field but also beyond it. Conducting this research would be the first step in a long way until we reach its application in criminal and civil court cases.
What are your hobbies?
I love traveling, especially to places where I can get close to nature. I never miss the chance to go scuba diving and hiking. I also practice boxing; which is a great way to relieve stress.
What are the major challenges you face in your research with regards to sample collection, nucleic acid isolation and data analysis?
Some samples have low microbial biomass, which makes it very difficult to get high nucleic acid yields. This can lead to biases in our analysis and interpretation that must be taken into account. The large variety of references and data analyses pipelines available is a blessing on the one hand, good in terms of topic popularity and interest by researchers who strive to improve currently available microbiome analysis methods. But it can also lead to having no common consensus of what is the best approach for certain applications.
Which QIAGEN products do you use/have you used in the past and what did you like about the products?
For my ongoing projects, I use the DNeasy PowerSoil Kit and the AllPrep PowerFecal DNA/RNA Kit to perform nucleic acid isolation. What I like the most about these kits is their simplicity and efficiency.
What was your reaction when you found out you were a finalist in the Microbiome Awards?
I was very excited to be a finalist, especially with a forensics-oriented project.
1. Díez López C. et al. (2019) Novel taxonomy-independent deep learning microbiome approach allows for accurate classification of different forensically relevant human epithelial materials. Forensic Sci Int Genet. 41, 72–82.
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