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

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

1 Scopus Citations
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Author(s)

  • Jun Wu
  • David Danko
  • Ebrahim Afshinnekoo
  • Daniela Bezdan
  • Malay Bhattacharyya
  • Eduardo Castro-Nallar
  • Agnieszka Chmielarczyk
  • Nur Hazlin Hazrin-Chong
  • Youping Deng
  • Emmanuel Dias-Neto
  • Alina Frolova
  • Gabriella Mason-Buck
  • Gregorio Iraola
  • Soojin Jang
  • Paweł Łabaj
  • Patrick K.H. Lee
  • Marina Nieto-Caballero
  • Olayinka O. Osuolale
  • Christos A. Ouzounis
  • Michael H. Perlin
  • Bharath Prithiviraj
  • Nicolás Rascovan
  • Anna Różańska
  • Lynn M. Schriml
  • Torsten Semmler
  • Haruo Suzuki
  • Juan A. Ugalde
  • Ben Young
  • Johannes Werner
  • Maria Mercedes Zambrano
  • Yongxiang Zhao
  • Christopher Mason
  • Tieliu Shi
  • MetaSUB Consortium, including

Related Research Unit(s)

Detail(s)

Original languageEnglish
Article number112183
Journal / PublicationEnvironmental Research
Volume207
Online published9 Oct 2021
Publication statusPublished - 1 May 2022

Abstract

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.

Research Area(s)

  • Biosynthetic gene clusters, Functional diversity, Metagenomic analysis, Novel species uncovering, Urban environmental microbiome

Citation Format(s)

Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. / Wu, Jun; Danko, David; Afshinnekoo, Ebrahim; Bezdan, Daniela; Bhattacharyya, Malay; Castro-Nallar, Eduardo; Chmielarczyk, Agnieszka; Hazrin-Chong, Nur Hazlin; Deng, Youping; Dias-Neto, Emmanuel; Frolova, Alina; Mason-Buck, Gabriella; Iraola, Gregorio; Jang, Soojin; Łabaj, Paweł; Lee, Patrick K.H.; Nieto-Caballero, Marina; Osuolale, Olayinka O.; Ouzounis, Christos A.; Perlin, Michael H.; Prithiviraj, Bharath; Rascovan, Nicolás; Różańska, Anna; Schriml, Lynn M.; Semmler, Torsten; Suzuki, Haruo; Ugalde, Juan A.; Young, Ben; Werner, Johannes; Zambrano, Maria Mercedes; Zhao, Yongxiang; Mason, Christopher; Shi, Tieliu; MetaSUB Consortium, including.

In: Environmental Research, Vol. 207, 112183, 01.05.2022.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review