Barcoded microbial system for high-resolution object provenance

Jason Qian; Zhi-Xiang Lu; Christopher P Mancuso; Han-Ying Jhuang; Rocío Del Carmen Barajas-Ornelas; Sarah A Boswell; Fernando H Ramírez-Guadiana; Victoria Jones; Akhila Sonti; Kole Sedlack; Lior Artzi; Giyoung Jung; Mohammad Arammash; Mary E Pettit; Michael Melfi; Lorena Lyon; Siân V Owen; Michael Baym; Ahmad S Khalil; Pamela A Silver; David Z Rudner; Michael Springer

doi:10.1126/science.aba5584

Barcoded microbial system for high-resolution object provenance

Science. 2020 Jun 5;368(6495):1135-1140. doi: 10.1126/science.aba5584.

Authors

Jason Qian^#^{1

2

3}, Zhi-Xiang Lu^#^{1

2}, Christopher P Mancuso^#⁴, Han-Ying Jhuang^#¹, Rocío Del Carmen Barajas-Ornelas^#⁵, Sarah A Boswell^#^{1

2}, Fernando H Ramírez-Guadiana⁵, Victoria Jones^{1

6}, Akhila Sonti⁴, Kole Sedlack⁴, Lior Artzi⁵, Giyoung Jung⁷, Mohammad Arammash¹, Mary E Pettit¹, Michael Melfi¹, Lorena Lyon¹, Siân V Owen⁶, Michael Baym^{2

6}, Ahmad S Khalil^{4

8}, Pamela A Silver^{1

8}, David Z Rudner⁵, Michael Springer^{9

2}

Affiliations

¹ Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
² Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
³ Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA.
⁴ Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA.
⁵ Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
⁶ Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
⁷ Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁸ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
⁹ Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA. michael_springer@hms.harvard.edu.

^# Contributed equally.

PMID: 32499444
DOI: 10.1126/science.aba5584

Abstract

Determining where an object has been is a fundamental challenge for human health, commerce, and food safety. Location-specific microbes in principle offer a cheap and sensitive way to determine object provenance. We created a synthetic, scalable microbial spore system that identifies object provenance in under 1 hour at meter-scale resolution and near single-spore sensitivity and can be safely introduced into and recovered from the environment. This system solves the key challenges in object provenance: persistence in the environment, scalability, rapid and facile decoding, and biocontainment. Our system is compatible with SHERLOCK, a Cas13a RNA-guided nucleic acid detection assay, facilitating its implementation in a wide range of applications.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

CRISPR-Cas Systems
DNA Barcoding, Taxonomic / methods*
DNA, Bacterial / genetics
DNA, Bacterial / isolation & purification*
DNA, Fungal / genetics
DNA, Fungal / isolation & purification*
Environmental Microbiology*
Microbiota / genetics*
RNA, Guide, CRISPR-Cas Systems
Spores / genetics*

Substances

DNA, Bacterial
DNA, Fungal