The longest U.S. federal shutdown concluded late last Wednesday, reopening government agencies after 43 days. However, experts warn of lasting fractures in the nation's food supply chain due to halted operations at USDA and FDA. These disruptions, combined with prior policy changes, threaten farmers, food safety, and access for vulnerable communities.
The federal government shutdown, the longest in U.S. history at 43 days, ended late on Wednesday, November 13, 2025, when Congress passed a stopgap funding bill extending operations through January 30, 2026. This deal includes a one-year extension of the 2018 farm bill and annual USDA funding, but it cuts over $75 million from conservation technical assistance programs and removes payment limits for cost-sharing conservation efforts, according to Mike Lavender, policy director at the National Sustainable Agriculture Coalition.
Impacts on agricultural research emerged quickly. At the USDA's Agricultural Research Service lab in Peoria, Illinois, technician Ethan Roberts reported that projects on fungal diseases like fumonisin toxin and wheat scab blight, plus new crop uses, were mothballed for six weeks. "Basically, we just lost, like, a month and a half worth of progress and work, and a lot of those things will have to be restarted," Roberts said. The lab preserved critical microorganism collections during the shutdown, but overall, the USDA has lost about 20,000 staff this year, eroding U.S. leadership in agricultural research. Roberts noted, "The United States was definitely the leader in agricultural research in the entire world, and that’s slipping out of our grasp."
Food safety suffered too, with the FDA losing around 4,000 staff between January and April 2025, and shutdown slowdowns limiting inspections and investigations. Data scientist Ginni Braich from the University of Colorado, Boulder, explained, "When agencies like the USDA or FDA halt or scale back operations, there are ripple effects through the supply chain because of the effect on crop payments, insurance, inspections, and nutrition programs."
Farmers face mounting pressures: soaring bankruptcies, record-high debt, low commodity prices, tariffs, high energy and fertilizer costs, droughts, and climate change. Agricultural economist Alla Semenova at St. Mary’s College of Maryland warned that the shutdown could lead to crop deficits and rising food prices, with risks to the supply chain in 2026 and 2027. USDA Deputy Secretary Stephen Vaden announced on Monday another tranche of $16 billion in weather-related emergency aid.
Nutrition programs like SNAP, serving 42 million Americans, were delayed, exacerbating food insecurity. Senior policy analyst Parker Gilkesson at the Center for Law and Social Policy said, "When SNAP shrinks, the whole food economy shrinks. And it doesn’t just affect households who receive SNAP. It affects every household." New work requirements and funding changes compound the issues. Economist Jared Grant at Ohio State University highlighted dropping consumer confidence, potentially slowing spending and economic growth. Rodger Cooley of the Chicago Food Policy Action Council pointed to immigration enforcement policies causing labor shortages in farming as a key ongoing threat.