Home chemical and microbial transitions across urbanization

Laura-Isobel McCall; Chris Callewaert; Qiyun Zhu; Se Jin Song; Amina Bouslimani; Jeremiah J Minich; Madeleine Ernst; Jean F Ruiz-Calderon; Humberto Cavallin; Henrique S Pereira; Atila Novoselac; Jean Hernandez; Rafael Rios; OraLee H Branch; Martin J Blaser; Luciana C Paulino; Pieter C Dorrestein; Rob Knight; Maria G Dominguez-Bello

doi:10.1038/s41564-019-0593-4

Home chemical and microbial transitions across urbanization

Nat Microbiol. 2020 Jan;5(1):108-115. doi: 10.1038/s41564-019-0593-4. Epub 2019 Nov 4.

Authors

Laura-Isobel McCall^#^{1

2}, Chris Callewaert^#^{3

4}, Qiyun Zhu^#³, Se Jin Song^{3

5}, Amina Bouslimani^{6

7}, Jeremiah J Minich⁸, Madeleine Ernst^{6

7}, Jean F Ruiz-Calderon⁹, Humberto Cavallin¹⁰, Henrique S Pereira¹¹, Atila Novoselac¹², Jean Hernandez¹³, Rafael Rios¹⁴, OraLee H Branch^{15

16}, Martin J Blaser¹⁷, Luciana C Paulino¹⁸, Pieter C Dorrestein^{19

20

21

22}, Rob Knight^{23

24

25

26}, Maria G Dominguez-Bello^{27

28}

Affiliations

¹ Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, USA.
² Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.
³ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
⁴ Center for Microbial Ecology and Technology, Ghent University, Gent, Belgium.
⁵ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
⁶ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
⁷ Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA.
⁸ Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
⁹ Biochemistry Department, University of Puerto Rico, San Juan, Puerto Rico, USA.
¹⁰ School of Architecture, University of Puerto Rico, San Juan, Puerto Rico, USA.
¹¹ Center for Environmental Sciences, Federal University of Amazonas, Manaus, Brazil.
¹² Department of Civil, Architectural and Environmental Engineering, University of Texas at Austin, Austin, TX, USA.
¹³ Department of Biology, University of Puerto Rico, San Juan, Puerto Rico, USA.
¹⁴ Department of Environmental Sciences, University of Puerto Rico, San Juan, Puerto Rico, USA.
¹⁵ College of Health and Human Services, Office of Research Integrity, Concordia University, Portland, OR, USA.
¹⁶ Universidad Nacional de la Amazonia Peruana, Iquitos, Peru.
¹⁷ Center for Advanced Biotechnology and Medicine, Rutgers University, Piskataway, NJ, USA.
¹⁸ Center for Natural Sciences and Humanities, Federal University of ABC, Santo André, Brazil.
¹⁹ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²⁰ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²² Collaborative Mass Spectrometry Innovation Center, University of California San Diego, La Jolla, CA, USA. pdorrestein@ucsd.edu.
²³ Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
²⁴ Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
²⁵ Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
²⁶ Department of Bioengineering, University of California San Diego, La Jolla, CA, USA. robknight@ucsd.edu.
²⁷ Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA. mg.dominguez-bello@rutgers.edu.
²⁸ Department of Anthropology, Rutgers University, New Brunswick, NJ, USA. mg.dominguez-bello@rutgers.edu.

^# Contributed equally.

Abstract

Urbanization represents a profound shift in human behaviour, and has considerable cultural and health-associated consequences^1,2. Here, we investigate chemical and microbial characteristics of houses and their human occupants across an urbanization gradient in the Amazon rainforest, from a remote Peruvian Amerindian village to the Brazilian city of Manaus. Urbanization was found to be associated with reduced microbial outdoor exposure, increased contact with housing materials, antimicrobials and cleaning products, and increased exposure to chemical diversity. The degree of urbanization correlated with changes in the composition of house bacterial and microeukaryotic communities, increased house and skin fungal diversity, and an increase in the relative abundance of human skin-associated fungi and bacteria in houses. Overall, our results indicate that urbanization has large-scale effects on chemical and microbial exposures and on the human microbiota.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Bacteria / classification
Bacteria / genetics
Bacteria / isolation & purification
Biodiversity*
Environmental Exposure / analysis*
Environmental Microbiology
Fungi / classification
Fungi / genetics
Fungi / isolation & purification
Household Products / analysis*
Housing
Humans
Microbiota
Rainforest
South America
Urbanization*

Abstract

Publication types

MeSH terms

Grants and funding