Follow the barcoded microbes

doi:10.1126/science.abc4246

GSTDTAP > 气候变化

DOI	10.1126/science.abc4246
	Follow the barcoded microbes
	Jeff Nivala
	2020-06-05
发表期刊	Science
出版年	2020
英文摘要	Tracking where a physical object originated and where it has been, known as object provenance, is becoming increasingly important with the globalization of supply chains ([ 1 ][1]). Object-labeling technologies that are scalable, robust, and difficult to falsify would support, for example, the mitigation of foodborne illness outbreaks and the manufacture of counterfeit goods. However, there currently exists no single tagging method that satisfies all these requirements. On page 1135 of this issue, Qian et al. ([ 2 ][2]) describe a new tagging technique, called the barcoded microbial spores (BMS) system, that uses genetically engineered microbes as molecular tags to address the object provenance problem. The authors demonstrate that BMS can label a range of surfaces and persist for months in real-world conditions. Furthermore, they show how this technology can tag objects that come into only brief contact with BMS-labeled surfaces, suggesting the utility of BMS in forensic surveillance applications ([ 3 ][3]). Microbes are ubiquitous in our everyday environments, with different geographical locations having distinct microbial populations. Physical objects can even take on the microbial signature of their environments over time ([ 4 ][4], [ 5 ][5]), which has led to the suggestion that this naturally occurring signature could be used for object provenance ([ 6 ][6]). Although it would be convenient to have environmental microbes acting as automatic label-makers, actually implementing such an approach would pose a number of challenges. For instance, extensive environmental mapping of microbes would have to be done first. This would be expensive and time-consuming. Furthermore, environmental microbial abundances can be similar at disparate locales and also change over time, making the use of natural microbe labels a nonstarter for many applications. Instead, Qian et al. take this concept into the realm of synthetic biology by engineering synthetic strains of microbes to function as molecular labels. To do this, they inserted short, specific DNA sequences (barcodes) into the genomes of the bacterium Bacillus subtilis and the yeast Saccharomyces cerevisiae . They designed and experimentally validated dozens of barcode sequences that could be used in combinations to generate an essentially infinite number of potential tag sets. To tag an object, a set of barcoded strains were mixed together in spore form and sprayed on the surface of an object. A spore is a physically tough, inactive cell state that can persist in harsh environmental conditions without growth ([ 7 ][7]). This resilience allows the barcoded microbial spores to endure in diverse ecosystems without rupturing and exposing their DNA barcodes to the elements, risking tag loss. To identify the barcodes, the surface of the object is swabbed to collect a sample, which is prepared for input to one of a number of different decoding devices, including a DNA sequencer or a quantitative polymerase chain reaction machine. In addition to these readout options, Qian et al. also focused on using a nascent DNA detection technology called SHERLOCK ([ 8 ][8]), which is more amenable to deployment in field settings. This feature is critical to many potential provenance applications. BMS decoding should also be compatible with other field-deployable DNA-sensing technologies, such as commercial nanopore devices ([ 9 ][9]), although the authors did not explore this compatibility. The release of genetically modified organisms into uncontrolled environments may come with risks. So, Qian et al. built clever safeguards into the BMS system to prevent the unintended spread and proliferation of their microbial tags in the environment, beginning with careful selection of the microbial species themselves. Both B. subtilis and S. cerevisiae are commonly found in the environment and in food samples, and products derived from them have already been granted “generally recognized as safe” (GRAS) status by the U.S. Food and Drug Administration. To prevent their proliferation in native environments, Qian et al. used auxotrophic B. subtilis and S. cerevisiae strains that require supplementation of key amino acids for growth. The authors took additional steps to prevent the microbial spores from returning to an active cellular state by either removing genes essential to this process (for B. subtilis ) or by boiling the spores to permanently heat-inactivate them ( S. cerevisiae ). These measures were adequate to ensure that the spores did not replicate even in the most favorable laboratory conditions. As there is still the potential for auxotrophs to grow by scavenging for metabolites in the environment, these additional safeguards are prudent. An alternative strategy to biocontainment would be the use of so-called “recoded” cell strains that have been engineered to be dependent on completely synthetic amino acids that are not found in natural ecosystems ([ 10 ][10], [ 11 ][11]). ![Figure][12] Produce provenance data encoded in the DNA of a synthetic microbe Genetically barcoded spores could be used for a new generation of object (e.g., food) provenance applications. GRAPHIC: V. ALTOUNIAN/ SCIENCE The value of a provenance system depends on its lifetime and applicability to different objects. The BMS system was prototyped on an impressive number of surfaces and simulated environments, including sand, soil, carpet, and wood, in addition to an outdoor grass area. Notably, the barcoded microbes persisted and remained detectable on these surfaces for months, even after real or simulated weather conditions and physical perturbations such as vacuuming and sweeping. Beyond typical object provenance, in which the labels are applied directly to the object being tracked, Qian et al. also demonstrated that BMS tags could be transferred to other objects that come in transient contact with a labeled surface. The authors found that they could even trace the path of shoes that had walked on a BMS-tagged floor. The potential use for such a technology by, for example, law enforcement is compelling, although additional work is needed to determine how the BMS system withstands more rigorous real-world stresses, such as the application of cleaning agents to the surface. Perhaps the most powerful use of microbial tags will come from their application to agricultural and other food supply chains. For example, the tags could safely be sprayed directly on food products, as Qian et al. showed with leafy plants (see the figure). Bacillus thuringiensis , which is closely related to B. subtilis , is already in common use as an insecticide for agricultural products that are commercially available today ([ 12 ][13]). The authors found that B. thuringiensis genomic DNA can be detected on store-bought produce even after washing, boiling, frying, and microwaving, thus highlighting the hardiness of DNA-based tags. As would be expected, other microbe and DNA-based provenance systems are also being developed, in both academia ([ 13 ][14]) and industry. We may well be on a path to a brave new world in which food provenance tracking goes not just from the farm to the table, but all the way to the sewer ([ 14 ][15]). 1. [↵][16]1. P. M. Wognum et al ., Adv. Eng. Inform. 25, 65 (2011). [OpenUrl][17][CrossRef][18] 2. [↵][19]1. J. Qian et al ., Science 368, 1135 (2020). 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领域	气候变化 ; 资源环境
URL	查看原文
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.173/C666/handle/2XK7JSWQ/273433
专题	气候变化资源环境科学
推荐引用方式 GB/T 7714	Jeff Nivala. Follow the barcoded microbes[J]. Science,2020.
APA	Jeff Nivala.(2020).Follow the barcoded microbes.Science.
MLA	Jeff Nivala."Follow the barcoded microbes".Science (2020).