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27 May 2021

Study of 60 cities' microbes finds each has a signature microbial fingerprint

An international consortium, including a team from King’s Forensics, has reported the largest-ever global metagenomic study of urban microbiomes, spanning both the air and the surfaces of multiple cities.

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The international project sequenced and analysed samples collected from public transport systems and hospitals in 60 cities around the world, including on the London Underground. The study, published today in Cell with a companion paper in the journal Microbiome, features comprehensive analysis and annotation for all the microbial species identified—including thousands of viruses and bacteria and two archaea not found in reference databases.

The findings are based on 4,728 samples from cities on six continents taken over the course of three years, characterise regional antimicrobial resistance markers, and represent the first systematic worldwide catalogue of the urban microbial ecosystem. In addition to distinct microbial signatures in various cities, the analysis revealed a core set of 31 species that were found in 97% of samples across the sampled urban areas. The researchers identified 4,246 known species of urban microorganisms, but they also found that any subsequent sampling will still likely continue to find species that have never been seen before, which highlights the raw potential for discoveries related to microbial diversity and biological functions awaiting in urban environments.

The aim of the Metagenomics and Metadesign of Subways and Urban Biomes (MetaSUB) international consortium is to create metagenomic profiles of cities around the globe to improve city design, functionality and to monitor the impact on health. One important area of this research is to identify and track antimicrobial resistance markers (AMRs) as this is a global concern that threatens the ability to treat infectious diseases.

Another aim, one that is of high interest to King’s Forensics is to study the metagenome and its potential to provide forensic intelligence to aid criminal investigations, such as predicting where someone may have been or what they might have touched before, during or after a crime event.

The Analytical, Environmental and Forensic Sciences (AEFS) department from King’s founded MetaSUB London in 2017, adding London to the MetaSUB consortia and the worldwide metagenomic map. Since then, London MetaSUB has been sampling the London Underground network throughout the year. Professor Denise Syndercombe Court, Gabriella Mason-Buck and the King’s Forensics team have co-ordinated and conducted surface swabs from areas such as ticket machines, handrails and benches which support from researchers at the Imperial College London who co-ordinated and conducted air sampling.

King's Forensics is responsible for the recovery of surface and air samples across the London Underground as part of a global urban microbiome collection. The Cell and Microbiome publications detail the 2017 effort. The King's Forensics MetaSUB London Group, is particularly interested in the forensic and geolocation aspects of this ongoing annual DNA collection and the future research and funding opportunities enabled through analysis of our local collections.

Professor Denise Syndercombe Court, from the School of Population Health & Environmental Sciences

Gabriella Mason-Buck, from the School of Population Health and Environmental Sciences, said: “It's wonderful to see the hard work of the MetaSUB consortium coming together as publications in both Cell and Microbiome. This is an exciting and novel project to be a part of and I'm looking forward to what this worldwide exploration will find. In particular, King's Forensics are interested in the potential of this research to be applied to Forensic Science as an intelligence tool to aid in criminal investigations - where someone might have been and what they might have touched before, during and after a crime event.”

The London MetaSUB project would not be possible without the volunteers from AEFS and the citizen scientists that give up their time to help with the sampling. In addition, the MetaSUB project, especially gCSD enables public engagement and an opportunity to involve members of the public in the research being carried out at King’s.

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Professor of Forensic Genetics