But like all allies, we and our crops can count on microbial partners only as long as interests align. When we scramble microbiomes through indiscriminately using microbial toxins like broad-spectrum antibiotics and agrochemicals, they can turn on us. Troublesome microbes – pests and pathogens previously held in check by their benign brethren – can proliferate and wreak havoc. In the long run, this undermines both the microbial foundation of the natural defenses of our crops and our own immune system.
Indeed, our century-long war on microbes has delivered both major victories and unforeseen consequences. While we’ve tamed many infectious diseases, we now face superbugs, disease-causing microbes that we can no longer kill using antibiotics. Loss or alteration of the human microbiome is also implicated in some common chronic diseases that plague our modern lives, including both type 1 and type 2 diabetes, inflammatory bowel disease, certain cancers, multiple sclerosis, asthma and allergies.
And in agriculture, although we may have high crop yields most years, farmers also face fields more vulnerable to pest outbreaks and resurgence, and global losses in soil fertility. Over the past several decades, we’ve been learning that in many cases these problems, and their solutions, are rooted in how we treat the microbial communities living in the soil.
We need a different front-line strategy if we are to preserve our dwindling choices of effective antibiotics and pesticides for when we truly need them. What might work better? Promoting the interests of our microbial allies, the ones that benefit us when we partner with them. Conserving and protecting microbiomes is the direction in which new practices in medicine and agriculture should aim.