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Decoding personal biotic and abiotic airborne exposome

Nature Protocols volume 16, pages 1129–1151 (2021)Cite this article

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Abstract

The complexity and dynamics of human diseases are driven by the interactions between internal molecular activities and external environmental exposures. Although advances in omics technology have dramatically broadened the understanding of internal molecular and cellular mechanisms, understanding of the external environmental exposures, especially at the personal level, is still rudimentary in comparison. This is largely owing to our limited ability to efficiently collect the personal environmental exposome (PEE) and extract the nucleic acids and chemicals from PEE. Here we describe a protocol that integrates hardware and experimental pipelines to collect and decode biotic and abiotic external exposome at the individual level. The described protocol has several advantages over conventional approaches, such as exposome monitoring at the personal level, decontamination steps to increase sensitivity and simultaneous capture and high-throughput profiling of biotic and abiotic exposures. The protocol takes ~18 h of bench time over 2–3 d to prepare samples for high-throughput profiling and up to a couple of weeks of instrumental time to analyze, depending on the number of samples. Hundreds to thousands of species and organic compounds could be detected in the airborne particulate samples using this protocol. The composition and complexity of the biotic and abiotic substances are heavily influenced by the sampling spatiotemporal factors. Basic skillsets in molecular biology and analytical chemistry are required to carry out this protocol. This protocol could be modified to decode biotic and abiotic substances in other types of low or ultra-low input samples.

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Fig. 1: An overview of the personal exposome collection, extraction and processing pipeline.
Fig. 2: Overview of the modified MicroPEM exposometer to include sampling devices for biologicals and chemicals.
Fig. 3: The design of the chemical cartridge and a 3D-printed product.
Fig. 4: The personal exposome collection, extraction and processing pipeline are highly sensitive.

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Data availability

The biotic exposome data generated using the protocol in the relevant study1 were deposited to the National Center of Biotechnology Information under bioproject ID PRJNA421162.

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Acknowledgements

We thank X. Wang and X. Li for their contributions to the development of the methods. This work was supported by Zhejiang University Life Sciences Institute start-up funds and the Leona M. and Harry B. Helmsley Charitable Trust (grant G-2004-03820).

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Author notes

  1. These authors contributed equally: Chao Jiang, Xinyue Zhang, Peng Gao.

Authors and Affiliations

  1. Life Sciences Institute, Zhejiang University, Hangzhou, China

    Chao Jiang & Qiong Chen

  2. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA

    Xinyue Zhang, Peng Gao & Michael Snyder

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  1. Chao Jiang
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  2. Xinyue Zhang
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  3. Peng Gao
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  4. Qiong Chen
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  5. Michael Snyder
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Contributions

C.J. conceived the study. M.S. supervised the study. C.J., X.Z. and P.G. drafted and revised the protocol with input from Q.C. and M.S.

Corresponding authors

Correspondence to Chao Jiang or Michael Snyder.

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Competing interests

Two provisional patents were filed (pending application numbers 62/488119 and 62/488256).

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Peer review information Nature Protocols thanks Lea Maitre and Simone Morais for their contribution to the peer review of this work.

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Related links

Key references using this protocol

Jiang C. et al. Cell 175, 277–291 (2018): https://doi.org/10.1016/j.cell.2018.08.060

Cissé O. et al. mBio 11, e03138-19 (2020): https://doi.org/10.1128/mBio.03138-19

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Jiang, C., Zhang, X., Gao, P. et al. Decoding personal biotic and abiotic airborne exposome. Nat Protoc 16, 1129–1151 (2021). https://doi.org/10.1038/s41596-020-00451-8

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