Young Investigator
October 16, 2023 | Human ID and Forensics

Young Investigator Meghna Swayambhu

On forensic applications of microbiome and metabolome analyses for body fluid identification
Meghna Swayambhu talks about establishing standard workflows for forensic body fluid identification using next-generation sequencing of 16S rRNA markers and metabolomics-based analysis of body-fluid metabolites. Meghna’s plan is to use machine learning tools to combine the discriminatory power of bacterial and metabolic markers to obtain prediction values for presentation in forensic case reports. This integrated microbial and metabolic workflow will potentially allow multiple tests from one sample.

The Young Investigator Community is an active group within the wider QIAGEN Investigator Community that focuses on forensic scientists who are working towards a PhD/MSc in a forensics or HID discipline or have received their PhD/MSc within the last five years. The New Investigator blog is a place to meet one of these talented researchers in a forum where they can share their achievements and aspirations with their peers, friends and colleagues. Read on to find out what attracted this month’s blogger to forensic science. Share with them the excitement of discovery that sustains a passionate commitment to their work.

This New Investigator blog introduces Meghna Swayambhu. Meghna is currently a Doctoral student working with Dr. Natasha Arora at the Institute of Forensic Medicine at the University of Zurich (ZIFM). Meghna’s research path explores forensic applications of microbiome analysis and body fluid identification using bacterial markers together with a metabolomics-based approach.

1. Tell us about your background and how you became interested in forensic science?

I have always been interested in studying biological systems in cells both human and microbial. In addition, I found research topics with a direct application to be most interesting and fulfilling. For my Bachelor’s degree, I studied Biotechnology at Bangalore University where I learned about molecular biology and cellular mechanisms in different organisms and the application of these insights in human health, forensics and food technology. I found the forensics modules most fascinating and was immediately drawn to the aspect of making a social contribution using concepts from basic science.

I focused on Forensic Science during my Masters at the University of Amsterdam where I learned about the various branches in forensics. After my Masters, I was determined to research in the field of forensic genetics in my doctoral studies. While looking for a fitting project, I got in touch with Dr. Natasha Arora (my current PhD supervisor) who gave me the opportunity to explore the analyses of biological evidence from a microbiome perspective.

In 2020, I received the Swiss Government Excellence Scholarship for conducting my doctoral research on body fluid identification (BFI) by combining both microbial and metabolic markers at the Zurich Institute of Forensic Medicine (ZIFM). My current project has brought together my interests in studying molecular biology as well as the direct application of research investigations.    

2. Can you provide a summary of the project you are working on?

My main research goal is to develop a novel method for BFI by combining microbial and metabolic markers. We aim to establish standard workflows for forensic BFI using next-generation sequencing techniques targeting the variable regions of the 16S rRNA gene in bacteria. In addition to bacterial markers, we employ an untargeted metabolomics-based approach for analyzing body-fluid characteristic metabolites.

Leveraging this data, I will use machine learning tools to combine the discriminatory power of both bacterial and metabolic markers for obtaining prediction values that can be presented in forensic case reports. Additionally, together with my colleagues, I aim to explore the application of these workflows in other forensic areas like human identification and Time since Deposition (TsD) to obtain more information from a single stain.

3. Please describe your typical day in the lab.

My days vary depending on the phase of my PhD and the stage of the project/s. On some days, I have a number of duties in the lab starting from collecting samples, extraction of DNA and metabolites, preparing for sequencing and metabolomics analyses. On other days, I assist in training new Masters students in the procedures for investigating both bacterial and metabolic markers. More recently, I spend my time working on optimizing data analysis strategies and publishing our results.

4. What do you find most interesting about your project? Have you seen any surprising results?

I find it rewarding to work on a project that has a direct application in forensic casework. I believe that the most exciting aspect of my project is to work in the Department of Forensic Genetics at ZIFM where there are staff working on casework. This gives me opportunities as a researcher to receive feedback and tailor my project to their needs in the field. It is also exciting to work with omics techniques that provide information not only on the bodily site but also the individual’s characteristics and behavior. I was surprised to see a distinct separation between body sites even though the human microbiome project highlighted differences in body sites based on the bacterial compositions. It was exciting to see promising results with the inclusion of previously underexplored forensically relevant biological fluids and their metabolites.

5. What are the benefits of your project?

Body fluid identification of biological evidence found in crime scenes is important for providing context on the type of crime and for reconstructing the crime-related events. Current methods are limited in sensitivity and specificity, especially in challenging cases with low biomass biological evidence or with complex mixtures of biological fluids. Therefore, a complementary method that combines information from two different sources such as bacteria and metabolites can be a powerful tool for BFI.

In addition, most of the existing methods destroy the starting sample and do not enable multiple tests on a single sample. Our integrated microbial and metabolic method is compatible with current workflows and will potentially allow multiple tests using DNA (human and microbial), RNA and metabolites, from one sample. We aim to use our BFI workflows for other forensic purposes like human identification and Time since Deposition (TsD), thereby improving the overall quality of forensic investigations. Furthermore, information about the microbial and metabolic compositions of underexplored biological fluids like seminal fluid, urine, menstrual blood among others, can be utilized in other applied fields like healthcare and diagnostics. 

6. What are the major challenges faced while working on your project and how do you overcome them?

One of the main challenges faced in forensic projects is to reliably and reproducibly bring research from controlled to forensic settings. Forensic evidence is usually found in trace amounts, aged conditions, samples deposited on different substrates and containing mixtures of different biological fluids and donors. Therefore, to understand the strengths and limitations of our novel method, we are extensively testing the reliability in simulated forensically relevant settings and on samples from forensic cases. Another challenge is the reporting of our findings in a manner that can be presented and accepted in court. To overcome this challenge, we are collaborating with other groups to test suitable models and reporting guidelines for our findings. Lastly, contamination is a constant challenge with microbiome work as bacteria are ubiquitous. In our protocols, we endeavor to minimize contamination by being meticulous with our protocols and by the inclusion of negative controls to keep track of all potential contaminants. 

7. Which QIAGEN products do you use and what do you like about the products?

Forensic applications require protocols that have been benchmarked and utilize standardized kits that perform reliably across runs and different laboratories. We use QIAGEN products for all the foundational steps in our bacterial sequencing protocols to ensure reliable, reproducible and good quality data. We use the Investigator Lyse&Spin Basket Kit by QIAGEN as part of our DNA extraction protocol. The Lyse&Spin Basket Kits enable us to minimize contamination as they are individually packed. In addition, these kits help us extract the biological material directly from swabs used in casework thereby increasing the compatibility of our methods with existing workflows. We use the QIAamp DNA Mini Kit with the QIAcube Connect instrument for standardized and automated DNA extractions as the instrument is reliable and time-efficient. I am able to process almost twice as many samples as I would with manual extractions and also minimize pipetting and contamination errors. Lastly, we use the MiSeq FGx Reagent Micro Kit for obtaining bacterial sequence data from different variable regions of the 16S rRNA gene. This kit offers the most suitable combination of read length and sequencing depth for our projects. I find QIAGEN products to be well suited for use in forensic research due to their reliability and trustworthy customer support.

8. Outside of forensic science, what are your hobbies?

I am originally from India and love spending time cooking Indian meals. I enjoy swimming, running and hiking with friends. I recently developed an interest in scuba diving which I try to combine with my love for traveling solo or with friends and family.