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A joint microbiome study by the Institute for Medical Genetics and Applied Genomics at the University Hospital Tübingen and the Weill Cornell Graduate School in New York discovered thousands of new bacteria and viruses worldwide. By studying these samples, the researchers, who are members of the international MetaSUB consortium, can identify antibiotic-resistant strains and develop new drugs. The results of the study are currently published in the journal Cell.
During a three-year study, researchers from the international consortium Metagonomics and Metadesign of Subways and Urban Biomes (MetaSUB) discovered 10,928 strains of viruses and 748 strains of bacteria that are not yet listed in any reference database. In 60 cities in 32 different countries, the research team led by Daniela Bezdan (University Hospital Tübingen), David Denko and Chris Mason (Weill Cornell Graduate School New York) collected more than 5,000 samples from densely populated subway stations, train stations and hospitals to analyze them using next-generation sequencing, a method for sequencing DNA. With the help of the researched microbial samples, known as microbiomes, the researchers hope to learn more about bacteria, viruses and other microorganisms that live among humans. "While further research is needed, this data demonstrates the value and potential for microbiome mapping and monitoring, and the insights it can provide physicians, scientists and public health officials," says Daniela Bezdan.
The widespread sampling yielded a city-specific mix of rare bacterial species that form a unique microbiome that allowed researchers to predict with about 90 percent accuracy where a person lives - just by sequencing the DNA on their shoes. Many factors were found to influence a city's microbiome, including overall population and population density, elevation, proximity to the ocean and climate. Insights into these different signatures could enable future forensic studies.
"A microbiome contains molecular echoes of the place where it was collected. A coastal sample may contain salt-loving microbes while a sample from a densely populated city may show striking biodiversity," Dr. Danko explains.
These new findings may help identify antibiotic-resistant strains. Predicting antibiotic resistance from genetic sequences alone is challenging, but the research team was able to map some resistance-related genes, determine their abundance and confirm their ability to transmit resistance. This revealed that some cities have more resistance genes than others, and thus there are city-specific signatures for some of these genes. Since many of the antibiotics and drugs currently in use are derived from microbial sources, studying the molecules and proteins produced by microbes should help discover additional molecules and new antibiotics. These have the potential to contribute to the development of new drugs as well as laboratory tools and approaches.
Viral species such as SARS-CoV-2 could not be detected by the DNA analysis methods used in this study. “In future studies we will look at RNA in addition to DNA, allowing detection of RNA viruses such as SARS-CoV-2, in urban environments of more than 50 countries worldwide,” says Daniela Bezdan.
University Hospital Tübingen
Institute for Medical Genetics and Applied Genomics
Daniela Bezdan
Calwerstraße 7, 72076 Tübingen
Mobile: +49 170 111 77 17
daniela.bezdan@med.uni-tuebingen.de
David Danko, Daniela Bezdan et. al. A global metagenomic map of urban microbiomes and antimicrobial resistance; https://doi.org/10.1016/j.cell.2021.05.002
Complementary publication
M. H. Y. Leung, X. Tong, K. O. Bøifot, D. Bezdan, et.al. Characterization of the public transit air microbiome and resistome reveals geographical specificity;
https://doi.org/10.1186/s40168-021-01044-7
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