Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association
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Date
2021-09
Journal Title
Journal ISSN
Volume Title
Publisher
Elsevier: Environmental Research
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 cooccurrence
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.
Description
Staff Publication
Keywords
Urban environmental microbiome, Metagenomic analysis, Novel species uncovering, Functional diversity, Biosynthetic gene clusters