Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association


Jun Wu, East China Normal University
David Danko, Weill Cornell Medicine
Ebrahim Afshinnekoo, Weill Cornell Medicine
Daniela Bezdan, Weill Cornell Medicine
Malay Bhattacharyya, Indian Statistical Institute, Kolkata
Eduardo Castro-Nallar, Universidad Andrés Bello
Agnieszka Chmielarczyk, Uniwersytet Jagielloński
Nur Hazlin Hazrin-Chong, Universiti Kebangsaan Malaysia
Youping Deng, John A. Burns School of Medicine
Emmanuel Dias-Neto, A.C.Camargo Cancer Center
Alina Frolova, Institute of Molecular Biology and Genetics National Academy of Sciences of Ukraine
Gabriella Mason-Buck, King's College London
Gregorio Iraola, Institut Pasteur de Montevideo
Soojin Jang, Institut Pasteur Korea
Paweł Łabaj, Uniwersytet Jagielloński
Patrick K.H. Lee, City University of Hong Kong
Marina Nieto-Caballero, College of Engineering and Applied Science
Olayinka O. Osuolale, Elizade University
Christos A. Ouzounis, Centre for Research and Technology-Hellas
Michael H. Perlin, University of Louisville
Bharath Prithiviraj, Reckitt Health US LLC
Nicolás Rascovan, Aix Marseille Université
Anna Różańska, Uniwersytet Jagielloński
Lynn M. Schriml, University of Maryland School of Medicine
Torsten Semmler, Robert Koch Institute
Haruo Suzuki, Keio University
Juan A. Ugalde, Millennium Initiative for Collaborative Research on Bacterial Resistance
Ben Young, Weill Cornell Medicine
Johannes Werner, Eberhard Karls Universität Tübingen
Maria Mercedes Zambrano, CorpoGen
Yongxiang Zhao, Guangxi Medical University
Christopher Mason, Weill Cornell Medicine
Tieliu Shi, East China Normal University

Article Type

Research Article

Publication Title

Environmental Research


In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.



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