Forensic Human Identification through Microbial Signatures: The Value and Needed Expansion in Africa

Today’s guest blog is written by Yahaya Sumara Sulley, Snr. Research Assistant, Department of Forensic Sciences, University for Development Studies, Ghana. Reposted from the ISHI Report with permission.

Introduction

The skin is the largest organ in humans and some animals by weight and surface area. It serves as a protective barrier between internal organs and the external environment. A diverse community of microorganisms collectively known as microbiomes reside on and in the skin, as well as other parts of the human microbiome ecosystem. Even though several factors affect the composition of the microbiome on the skin, there remains a fairly stable group of microbes that may remain stable for up to 3 years within every microbiome population.

Microbiomes adapt to their host environment and are found in and or on diverse areas like hands, armpits, mouth and private parts. Skin microbiomes are inherently stable on human skin as a result of genetics. The environment may contribute directly to the microbial landscape of the human skin. The dynamic nature of microbiomes and their complexities may also be influenced by external pressures from the diet, antibiotic use and lifestyle choices (1).

Initially, skin microbiome studies provided insights in the area of cosmetology to dermatology (2). Today, however, the skin microbiome is showing promise in the field of forensic human identification (1). The primary goal of forensic individualization is to determine the source of biological evidence found at crime scenes (3–5). In situations where human DNA is of low quantity and/or quality forensic biologists may be able to rely on the potential of skin microbiome as an alternate DNA source (1).

Skin microbiomes are known to outnumber the ratio of human cells even though recent studies suggest a closer ratio of 1 to 1 (6). Notwithstanding, skin microbiomes exhibit high diversity and they constantly seek a state of equilibrium. Despite varying in their genetic makeup, a high probability exists for individuals to share similar microbiomes with close family members, spouses, pets, and roommates. However, living in the same environment does not guarantee an identical set of microbiomes within a population group due to a variety of influences.

Skin microbiome is also an abundant source of DNA (7). A skin swab would typically contain human DNA and also enough microbial DNA to enable high-resolution human host identification that could standalone or be used to complement human DNA profiling. While some microbes are naturally stable across all human skin, their genetic makeup can vary. This inherent diversity emphasizes the role of genetic factors in shaping the microbial communities present in and or on an individual. Ancestry informative markers are a shared approach in population genetics to establish evolutionary relationships and have been employed in forensic microbiome analysis due to the potential significance of microbial genomes in identifying individuals.

Skin microbiome analysis presents an innovative approach to human identification, offering a unique microbial fingerprint that is as distinctive as our human genetic code. Understanding these variations is crucial for accurate identification through microbiome analysis. By understanding the relationships within these microbial communities, forensic experts can unlock a new dimension in their quest to identify individuals involved in violent crimes, sexual assaults, high-volume crimes, and missing and unidentified individuals as a result of disasters.

Previously culture-based techniques have been employed in learning about microbes outside of their environment. While informative, they lacked the resolution necessary for individualization approaches. However, in recent times, the secrets of skin microbiomes are being unlocked with cutting-edge techniques, including microbial DNA profiling, that have propelled skin microbiome analysis into new frontiers. These advancements have helped scientists overcome previous limitations, refine the precision and increase the power of microbial profiling and also open doors to unforeseen possibilities in the realm of human identification.

There are several methods used in microbiome studies and the choice of approach, depends on the purpose of the study, the type of data required, questions that need to be answered, available limitations and the level of resources or funding a lab has. The rise of microbiomes metagenomics and concomitant bioinformatics approaches have also influenced advancements in the areas of sampling methods and microbial data analysis and have added a high level of efficiency to microbiome studies. Some of the methods used in microbiome studies include high-throughput cultivation-independent techniques, statistical methods that can account for the characterizations of microbiome data, detecting differentially abundant taxa across phenotype groups, identifying associations between the microbiome and covariates, and constructing microbiome networks to characterize ecological associations of microbes (8,9).

Currently, researchers may resort to one of three approaches: 16S rRNA (10–12), targeted sequencing of a selected number of markers (13) or whole-genome shotgun sequencing (WGS) (14). The use of these techniques to identify bacteria and other microbial communities complements traditional DNA analysis, by providing additional information about the diversity of an individual’s microbial profile. It enhances the forensic toolkit and provides a more comprehensive capability for accurate identification. These modern bioinformatic tools and techniques enable researchers to handle large amounts of data through high throughput technologies.

Even though the use of skin microbiomes in forensic identification is promising, it faces challenges tied to environmental influences and variability, standardization and validation. Establishing standardized methods and rigorous validation processes are crucial steps towards ensuring the reliability and accuracy of microbial profiling in forensic investigations.

Advancements in Skin Microbiome Research for Forensic Identification

In a study published by (15), researchers demonstrated the potential of microbiome analysis for forensic applications. A novel method, considering minor skin microbes, achieved remarkable success of 85% accuracy over two years on 66 samples, scaling to 78% on 837 samples from 89 individuals. Also, (16) linked skin-associated bacterial communities from touched objects (e.g., computer mice, keyboards) back to owners. In another study conducted by (17), analysis of pubic hair microbiomes was used to distinguish male and female subjects. Major findings included the identification of Lactobacillus spp. which may be unique to female participants. In a more recent study, stable, individual-specific genetic fingerprints in skin microorganisms were revealed, with 89.78% accuracy in donor identification across diverse skin sites as well as time points. Furthermore, bacterial communities from shoes usually resembled those from the skin of the individuals who wore them (18).

Bridging the Gap: Challenges and Opportunities in African Microbiome Forensic Studies

The realm of forensic microbiome research, with its promising implications for human identification, has yet to fully embrace the diverse landscapes of Africa. In regions like Africa, characterized by rich biodiversity and unique biology, challenges in expertise, resources, and research funding have hindered the spotlight on this critical field. Africa’s immense diversity, not only in terms of microbiomes but also in its genetic makeup, provides a unique opportunity for groundbreaking insights. Despite this potential, the disparities in research funding and resources have kept Africa from contributing significantly to the global discourse on forensic microbiome studies. While a few microbiome health studies have targeted African populations, the application of these technologies in forensic studies remains largely unexplored. Forensic microbiome studies can serve as a bridge between health, agriculture, and various other scientific domains, offering a holistic understanding of microbial ecosystems.

Funding the Invisible: A Call to Action

In Ghana, where our lab, The Quansah Lab, (The Qlab) has initiated background studies in this area for almost three years, we face the pervasive issue of lack of resources and research funding. Despite facing challenges in securing research funding for sophisticated molecular and bioinformatics processes, we’ve made significant strides using culture-based approaches. This limitation impedes our ability to fully characterize the African microbiome for forensic purposes.

Through this communication, we extend a call for international collaborations. Collaborative efforts can unlock the potential of a forensic human identification project centred on the African microbiome. Beyond contributing to SDG 16’s goal of justice, safety, and security, such collaborations hold the promise of enriching global microbiome studies across diverse scientific disciplines.

As the world acknowledges the transformative power of microbial signatures in forensic identification, let us ensure that Africa is not left in the shadows. The benefits of unravelling Africa’s microbial mysteries extend far beyond the realms of forensic science, resonating across numerous scientific contributions. It is time to invest in the untapped potential of Africa’s microbiome and pave the way for a more inclusive and comprehensive understanding of our shared human identity.

Conclusion

The application of skin microbiome analysis in forensic science presents a transformative capability in human identification, offering another powerful and versatile tool. The legal and ethical considerations surrounding this technology emphasize the importance of navigating issues related to consent and aligning with global ethical and legal frameworks. With the advancement of technology and increased cost-effectiveness, the highlighted studies demonstrate the feasibility of utilizing microbiomes for forensic purposes. The ongoing research in skin microbiome analysis holds exciting possibilities, promising enhanced reliability and applicability. When human and microbial markers are combined it likely will translate into higher typing success rates as it will substantially increase the capabilities of forensic scientists when they are working with low-quantity and/or low-quality human DNA samples that have limited information about human identity. There is also the potential for retrieving additional information in forensic-type cases, such as geolocation and drug network associations. These potential benefits further underscore the promising future of skin microbiome analysis in forensic human identification. However, for this field to advance to reach its full potential, community engagement and education are paramount, ensuring public trust and confidence in the science. Bridging gaps for forensic microbiome studies in Africa and other resource-deprived regions through international collaborations would also turn out to be a giant step in the right direction for the quantum leaps anticipated in this emerging frontier of human identification.

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