Dataset Information

A global metagenomic map of urban microbiomes and antimicrobial resistance.

ABSTRACT: We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.

SUBMITTER: Danko D

PROVIDER: S-EPMC8238498 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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A global metagenomic map of urban microbiomes and antimicrobial resistance.

Danko David D Bezdan Daniela D Afshin Evan E EE Ahsanuddin Sofia S Bhattacharya Chandrima C Butler Daniel J DJ Chng Kern Rei KR Donnellan Daisy D Hecht Jochen J Jackson Katelyn K Kuchin Katerina K Karasikov Mikhail M Lyons Abigail A Mak Lauren L Meleshko Dmitry D Mustafa Harun H Mutai Beth B Neches Russell Y RY Ng Amanda A Nikolayeva Olga O Nikolayeva Tatyana T Png Eileen E Ryon Krista A KA Sanchez Jorge L JL Shaaban Heba H Sierra Maria A MA Thomas Dominique D Young Ben B Abudayyeh Omar O OO Alicea Josue J Bhattacharyya Malay M Blekhman Ran R Castro-Nallar Eduardo E Cañas Ana M AM Chatziefthimiou Aspassia D AD Crawford Robert W RW De Filippis Francesca F Deng Youping Y Desnues Christelle C Dias-Neto Emmanuel E Dybwad Marius M Elhaik Eran E Ercolini Danilo D Frolova Alina A Gankin Dennis D Gootenberg Jonathan S JS Graf Alexandra B AB Green David C DC Hajirasouliha Iman I Hastings Jaden J A JJA Hernandez Mark M Iraola Gregorio G Jang Soojin S Kahles Andre A Kelly Frank J FJ Knights Kaymisha K Kyrpides Nikos C NC Łabaj Paweł P PP Lee Patrick K H PKH Leung Marcus H Y MHY Ljungdahl Per O PO Mason-Buck Gabriella G McGrath Ken K Meydan Cem C Mongodin Emmanuel F EF Moraes Milton Ozorio MO Nagarajan Niranjan N Nieto-Caballero Marina M Noushmehr Houtan H Oliveira Manuela M Ossowski Stephan S Osuolale Olayinka O OO Özcan Orhan O Paez-Espino David D Rascovan Nicolás N Richard Hugues H Rätsch Gunnar G Schriml Lynn M LM Semmler Torsten T Sezerman Osman U OU Shi Leming L Shi Tieliu T Siam Rania R Song Le Huu LH Suzuki Haruo H Court Denise Syndercombe DS Tighe Scott W SW Tong Xinzhao X Udekwu Klas I KI Ugalde Juan A JA Valentine Brandon B Vassilev Dimitar I DI Vayndorf Elena M EM Velavan Thirumalaisamy P TP Wu Jun J Zambrano María M MM Zhu Jifeng J Zhu Sibo S Mason Christopher E CE

Cell 20210526 13

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known s ...[more]

PMID: 34043940

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Project description:Urban microbiome plays crucial roles in human health and are related to various diseases. The MetaSUB Consortium has conducted the most comprehensive global survey of urban microbiomes to date, profiling microbial taxa/functional genes across 60 cities worldwide. However, the influence of environmental/demographic factors on urban microbiome remains to be elucidated. We collected 35 environmental and demographic characteristics to examine their effects on global urban microbiome diversity/composition by PERMANOVA and regression models. PM10 concentration was the primary determinant factor positively associated with microbial α-diversity (observed species: p = 0.004, β = 1.66, R2 = 0.46; Fisher's alpha: p = 0.005, β = 0.68, R2 = 0.43), whereas GDP per capita was negatively associated (observed species: p = 0.046, β = -0.70, R2 = 0.10; Fisher's alpha: p = 0.004, β = -0.34, R2 = 0.22). The β-diversity of urban microbiome was shaped by seven environmental characteristics, including Köppen climate type, vegetation type, greenness fraction, soil type, PM2.5 concentration, annual average precipitation and temperature (PERMANOVA, p < 0.001, R2 = 0.01-0.06), cumulatively accounted for 20.3% of the microbial community variance. Canonical correspondence analysis (CCA) identified microbial species most strongly associated with environmental characteristic variation. Cities in East Asia with higher precipitation showed an increased abundance of Corynebacterium metruchotii, and cities in America with a higher greenness fraction exhibited a higher abundance of Corynebacterium casei. The prevalence of antimicrobial resistance (AMR) genes were negatively associated with GDP per capita and positively associated with solar radiation (p < 0.005). Total pathogens prevalence was positively associated with urban population and negatively associated with average temperature in June (p < 0.05). Our study presents the first comprehensive analysis of the influence of environmental/demographic characteristics on global urban microbiome. Our findings indicate that managing air quality and urban greenness is essential for regulating urban microbial diversity and composition. Meanwhile, socio-economic considerations, particularly reducing antibiotic usage in regions with lower GDP, are paramount in curbing the spread of antimicrobial resistance in urban environments.

Dataset Information

A global metagenomic map of urban microbiomes and antimicrobial resistance.

Publications

A global metagenomic map of urban microbiomes and antimicrobial resistance.

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