BANGOR — America’s booming brewing industry and farmers alike are bothered and befuddled by a proposed U.S. Food and Drug Administration rule change that could alter a partnership that dates back to Neolithic times.

In Maine and across the country, brewers and farmers have formed handshake agreements: Brewers brew beer, producing barrels or truckloads full of heavy, wet spent grains. These grains have been heated up to extract sugars, proteins and other nutrients that go on to make beer. The process is called mashing. The spent grains are a byproduct — with no real usefulness purpose left for the brewer.

To the farmer, spent grains are a valuable dietary supplement for their livestock. It’s common for breweries to reach out to local farms to offer up their spent grains as animal feed. Most often, farmers are happy to oblige, picking up the spent grains themselves a few times per week. Little or no money exchanges hands during these deals. Brewers are glad to get rid of the grain, and farmers are glad to take it off their hands.

Andrew Geaghan of Geaghan Brothers Brewing Co. in Bangor, a company that brewed more than 15,000 gallons of beer in 2013, said each batch of beer uses about 350-500 pounds of grain per batch. At the end of the mashing process, it comes out even heavier because it’s saturated with water.

Geaghan’s formed a partnership with Fair View Farm in Hampden.

“It’s a really favorable relationship for both of us,” Geaghan said. “It’s a product that we extract what we can from it, and it leaves a nice feed for his cattle that is locally sourced and a high-protein, good fiber source, [and] a nice hydration source as well. It’s really a win-win for everybody.”

Those sorts of partnerships have existed for as long as agriculture has existed, but the FDA’s rule proposal could change that.

The proposed rule is aimed at “ensuring the safety of animal food for animals consuming the food and ensuring the safety of animal food for humans handling the food, particularly pet food,” according to the FDA.

It requires facilities producing animal food to have written plans that identify hazards, specify steps to minimize those hazards, and monitor and record the safety of the feed.

“FDA understands that many breweries and distilleries sell spent grains … as animal food. Because those spent grains are not alcoholic beverages themselves, and they are not in a prepackaged form that prevents any direct human contact with the food, the Agency tentatively concludes that subpart C of this proposed rule would apply to them,” according to the FDA rule.

Most small and medium-sized brewers wouldn’t be able to follow these rules without significant investment. Breweries that want to send their spent grains to farmers would have to dry, package and analyze the grains, all without it touching human hands. These efforts would cost brewers money, time and resources, making it too much of a hassle for some to continue partnerships with farmers, according to critics.

Geaghan said that one of the few alternatives would be to take the grain to a landfill, which carries costs of its own.

John “Jack” Perry, 81, runs Fair View Farm, which has a herd of 50 beef cattle. He has been taking Geaghan’s spent grains since the company started brewing in 2011. Before that, he used spent grains from Sea Dog Brewing Co.

“This is real good stuff,” Perry said. “It keeps [the cattle] in good shape, and they really seem to like it.”

Perry said running a farm in recent years has been a challenge. Getting the free spent grains helps keep his cattle heavy through winter and reduces their hay consumption. He said he wouldn’t be able to afford to stay in business if he had to buy fresh, commercial grain.

He said he has never had any concerns about contamination coming from Geaghan’s or any other brewer’s spent grain.

Brandon Mazer is legal counsel for Maine’s largest brewer, Shipyard, which produces 400-600 tons of spent grain per week during its peak production seasons. Those grains are dumped onto a truck trailer and go to farms as feed.

“It’s a very big umbrella, and we got sucked under it,” Mazer said of the proposed FDA rule change. He said that no brewers in Maine, and few in the country, are equipped with the machinery, personnel or money to meet the requirements outlined by the FDA.

The Brewers Association, Beer Institute, American Malting Barley Association and other brewing organizations have voiced strong opposition to the new restrictions, calling for an exemption for brewers.

The Beer Institute says that in 2012 alone, U.S. brewers produced about 2.7 million tons of spent grain.

The FDA has extended the public comment period on this set of rules until March 31, and brewers and farmers that work with them say they are watching closely.

“The goal of brewing is not to manufacture beer and animal feed simultaneously. The goal of brewing is to manufacture beer,” the institute wrote in a letter to the FDA, adding that regulating this long-used byproduct would impose unnecessary difficulties on businesses that just want to make beer.

To view the complete rule, visit http://www.fda.gov/Food/GuidanceRegulation/FSMA/ucm366510.htm. For the FDA fact sheet on the rule, visit http://www.fda.gov/Food/GuidanceRegulation/FSMA/ucm366510.htm#facsheet.