Deciphering One Health microbiomes using field-deployable biosensors

Microbiomes play a vital role in the health of plants, animals, humans, and the environment (One Health). Characterizing microbiomes typically requires lab-based techniques such as polymerase chain reaction (PCR) or next-generation sequencing (NGS), which are slow, labor-intensive, and expensive. Developing biosensors that can characterize microbiomes in the field can enable rapid turnaround and allow stakeholders to make quick decisions. We present a novel biosensor platform for field-deployable microbiome characterization. Our biosensors are based on loop-mediated isothermal amplification (LAMP) on microfluidic paper-based analytical devices (μPADs). LAMP is a rapid and sensitive nucleic acid amplification technique that does not require specialized equipment, making it ideal for field use. μPADs are portable, low-cost, and easy-to-use devices that can be used to perform complex assays without the need for electricity or specialized training. We demonstrate the use of our biosensors to detect bacteria and viruses with high analytical sensitivity and specificity (>~90%). We also show that our biosensors can be used to characterize microbiomes in animal and plant farms. For example, we have used our biosensors to detect bacteria associated with bovine respiratory disease in cattle feedlot and to quantify the levels of Bacteroidales as fecal indicators around fresh produce operations. Our biosensors have the potential to transform how microbiomes are characterized in the field. They can be used to monitor animal and plant health, ensure food safety, and diagnose human diseases. Our biosensors are also affordable and easy-to-use, making them accessible to a wide range of users.