The video clips are upsetting.

There’s a big bin full of dead lambs, a piglet slipping across a filth-strewn floor in search of its mother and a calf lying dead in a shed with blood seeping from its nose and mouth.

The latest compilation of factory farming horrors assembled by the campaign group, Animal Aid, packs an emotional punch. But it also underlines the serious message that the anti-meat activists want to get across: that industrial farms can hurt humans as well.

At least 12 major diseases, which between them cause millions of people to suffer and tens of thousands to die around the world, can be blamed on factory farming, they claim. These include swine flu, bird flu, salmonella, e-coli and mad cow disease.

But the campaign has provoked a vitriolic response from the National Farmers Union (NFU) in Scotland, who condemned it as “poisonous”. Others, however, argue that the campaigners have a point, but just take it too far.

The arguments, though sometimes bitter, are important because they are about how we look after the animals on which we rely for food. And they raise the question of what we can eat without being cruel – and without putting our own health at risk.

The video clips that Animal Aid has posted online come from uninvited visits their activists made to more than 40 farms in the UK over the last three years. They included 15 pig farms and 12 chicken farms, as well as dairy and goat enterprises.

“We found some disgusting, appalling and depressing scenes,” Animal Aid’s director, Andrew Tyler, told the Sunday Herald. “We have exposed filth, overcrowding, suffering, disease and death.”

The group has also released a new report summarising the dozen deadly diseases which they claim can be linked to intensive, factory farming (see below). “If you farm animals intensively, they get diseases,” argued Mr Tyler.

“And if people come into contact with them, they run the risk of getting sick. That is the pay-off you get from cruelty and exploitation.”

Swine flu, the report pointed out, came from pigs and had killed more than 18,000 people around the world. In the UK, there are 450,000 cases of sickness a year caused by the animal bacteria, salmonella and campylobacter.

Scotland suffered Britain’s deadliest e-coli outbreak in 1996 when the 0157:H7 strain killed 21 people and infected 400 more in Lanarkshire, the report said. They had eaten contaminated meat from a local butcher.

According to Animal Aid, approximately two-thirds of the 1,400 known human pathogens may have originated in animals. Tuberculosis is thought to have been acquired from the domestication of goats, measles and smallpox from farming cows, whooping cough from pigs, typhoid fever from chickens, and influenza from ducks.